format-version: 1.2 data-version: 2024-04-10 date: 10:04:2024 18:16 saved-by: Evan Christensen subsetdef: Alliance_of_Genome_Resources "Alliance of Genome Resources Gene Biotype Slim" subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: DBVAR "database of genomic structural variation" subsetdef: SOFA "SO feature annotation" synonymtypedef: aa1 "amino acid 1 letter code" synonymtypedef: aa3 "amino acid 3 letter code" synonymtypedef: AAMOD "amino acid modification" synonymtypedef: AGR "Alliance of Genome Resources" synonymtypedef: BS "biosapiens" synonymtypedef: dbsnp "dbsnp variant terms" synonymtypedef: dbvar "DBVAR" synonymtypedef: ebi_variants "ensembl variant terms" synonymtypedef: RNAMOD "RNA modification" EXACT synonymtypedef: VAR "variant annotation term" default-namespace: sequence ontology: so property_value: IAO:0000700 SO:0000110 property_value: IAO:0000700 SO:0000400 property_value: IAO:0000700 SO:0001060 property_value: IAO:0000700 SO:0001260 [Term] id: SO:0000000 name: Sequence_Ontology subset: SOFA is_obsolete: true [Term] id: SO:00000000002382 name: 5_prime_UTR_uORF_variant def: "A 5' UTR variant within an upstream open reading frame." [PMID:32461616, PMID:32926138] comment: Added 10 Apr 2024 at the request of Sarah Hunt (EBI). See GitHub Issue #647. is_a: SO:0001623 ! 5_prime_UTR_variant created_by: evan creation_date: 2024-04-10T17:49:03Z [Term] id: SO:0000001 name: region def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] subset: SOFA synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:00000010002382 name: 5_prime_UTR_uORF_stop_codon_variant def: "A 5' UTR variant where a stop codon in an upstream open reading frame is introduced, moved or lost." [PMID:32461616, PMID:32926138] comment: Added 10 Apr 2024 at the request of Sarah Hunt (EBI). See GitHub Issue #622. is_a: SO:00000000002382 ! 5_prime_UTR_uORF_variant created_by: evan creation_date: 2024-04-10T17:56:17Z [Term] id: SO:0000002 name: sequence_secondary_structure def: "A folded sequence." [SO:ke] synonym: "INSDC_feature:misc_structure" EXACT [] synonym: "sequence secondary structure" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:00000020002382 name: 5_prime_UTR_uORF_frameshift_variant def: "A 5' UTR variant which disrupts the translation of an upstream open reading frame because the number of nucleotides inserted or deleted is not a multiple of three." [PMID:32461616, PMID:32926138] comment: Added 10 Apr 2024 at the request of Sarah Hunt (EBI). See GitHub Issue #621. synonym: "uFrameshift (UTRannotator)" EXACT [] is_a: SO:00000000002382 ! 5_prime_UTR_uORF_variant created_by: evan creation_date: 2024-04-10T17:58:40Z [Term] id: SO:0000003 name: G_quartet def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract] synonym: "G quartet" EXACT [] synonym: "G tetrad" EXACT [] synonym: "G-quadruplex" EXACT [] synonym: "G-quartet" EXACT [] synonym: "G-tetrad" EXACT [] synonym: "G_quadruplex" EXACT [] synonym: "guanine tetrad" EXACT [] xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:00000030002382 name: 5_prime_UTR_uORF_stop_codon_gain_variant def: "A 5' UTR variant where a premature stop codon is gained in an upstream open reading frame." [PMID:32461616, PMID:32926138] comment: Added 10 Apr 2024 at the request of Sarah Hunt (EBI). See GitHub Issue #624. synonym: "uSTOP_gained" EXACT [] {comment="UTRannotator"} is_a: SO:00000010002382 ! 5_prime_UTR_uORF_stop_codon_variant created_by: evan creation_date: 2024-04-10T18:01:42Z [Term] id: SO:0000004 name: interior_coding_exon def: "A coding exon that is not the most 3-prime or the most 5-prime in a given transcript." [] subset: SOFA synonym: "interior coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:00000040002382 name: 5_prime_UTR_uORF_stop_codon_loss_variant def: "A 5' UTR variant where the stop codon of an upstream open reading frame is lost." [PMID:32461616, PMID:32926138] comment: Added 10 Apr 2024 at the request of Sarah Hunt (EBI). See GitHub Issue #623. synonym: "uSTOP_lost" EXACT [] {comment="UTRannotator"} is_a: SO:00000010002382 ! 5_prime_UTR_uORF_stop_codon_variant created_by: evan creation_date: 2024-04-10T18:05:50Z [Term] id: SO:0000005 name: satellite_DNA def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.insdc.org/files/feature_table.html] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:satellite" EXACT [] synonym: "satellite DNA" EXACT [] xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" is_a: SO:0000705 ! tandem_repeat [Term] id: SO:0000006 name: PCR_product def: "A region amplified by a PCR reaction." [SO:ke] comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. subset: SOFA synonym: "amplicon" RELATED [] synonym: "PCR product" EXACT [] xref: http://en.wikipedia.org/wiki/RAPD "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000007 name: read_pair def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls] subset: SOFA synonym: "mate pair" EXACT [] synonym: "read-pair" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000149 ! contig relationship: part_of SO:0001790 ! paired_end_fragment [Term] id: SO:0000008 name: gene_sensu_your_favorite_organism is_obsolete: true [Term] id: SO:0000009 name: gene_class is_obsolete: true [Term] id: SO:0000010 name: protein_coding def: "A gene which, when transcribed, can be translated into a protein." [] synonym: "protein-coding" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000011 name: non_protein_coding def: "A gene which can be transcribed, but will not be translated into a protein." [] synonym: "non protein-coding" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000012 name: scRNA_primary_transcript def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] synonym: "scRNA primary transcript" EXACT [] synonym: "scRNA transcript" EXACT [] synonym: "small cytoplasmic RNA" RELATED [] synonym: "small cytoplasmic RNA transcript" EXACT [] synonym: "small_cytoplasmic_RNA" RELATED [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000013 name: scRNA def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:scRNA" EXACT [] synonym: "small cytoplasmic RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000012 ! scRNA_primary_transcript [Term] id: SO:0000014 name: INR_motif def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867] comment: Binds TAF1, TAF2. synonym: "DMp2" RELATED [] synonym: "initiator" EXACT [] synonym: "initiator motif" EXACT [] synonym: "INR motif" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000015 name: DPE_motif def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12515390, PMID:12537576, PMID:12651739, PMID:16858867] comment: Binds TAF6, TAF9. synonym: "CRWMGCGWKCGCTTS" NARROW [] synonym: "downstream core promoter element" EXACT [] synonym: "DPE motif" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000016 name: BREu_motif def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867] comment: Binds TFIIB. synonym: "B-recognition element" EXACT [] synonym: "BRE motif" EXACT [] synonym: "BREu" RELATED [] synonym: "BREu motif" EXACT [] synonym: "TFIIB recognition element" RELATED [] synonym: "transcription factor B-recognition element" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000017 name: PSE_motif def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes." [PMID:11390411, PMID:12621023, PMID:12651739, PMID:23166507, PMID:8339931] synonym: "proximal sequence element" EXACT [] synonym: "PSE motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000167 ! promoter [Term] id: SO:0000018 name: linkage_group def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] synonym: "linkage group" EXACT [] xref: http://en.wikipedia.org/wiki/Linkage_group "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000020 name: RNA_internal_loop def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke] synonym: "RNA internal loop" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000021 name: asymmetric_RNA_internal_loop def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke] synonym: "asymmetric RNA internal loop" EXACT [] is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000022 name: A_minor_RNA_motif def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke] synonym: "A minor RNA motif" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000023 name: K_turn_RNA_motif def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke] synonym: "K turn RNA motif" EXACT [] synonym: "K-turn" EXACT [] synonym: "kink turn" EXACT [] synonym: "kink-turn motif" EXACT [] xref: http://en.wikipedia.org/wiki/K-turn "wiki" is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000024 name: sarcin_like_RNA_motif def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662] synonym: "sarcin like RNA motif" EXACT [] synonym: "sarcin/ricin domain" EXACT [] synonym: "sarcin/ricin loop" EXACT [] synonym: "sarcin/ricin RNA domain" EXACT [] is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000025 name: symmetric_RNA_internal_loop def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke] synonym: "A-minor RNA motif" EXACT [] is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000026 name: RNA_junction_loop synonym: "RNA junction loop" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000027 name: RNA_hook_turn synonym: "hook turn" RELATED [] synonym: "hook-turn motif" EXACT [] synonym: "RNA hook turn" EXACT [] is_a: SO:0000026 ! RNA_junction_loop [Term] id: SO:0000028 name: base_pair def: "Two bases paired opposite each other by hydrogen bonds creating a secondary structure." [] synonym: "base pair" EXACT [] xref: http://en.wikipedia.org/wiki/Base_pair "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000029 name: WC_base_pair def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293] synonym: "canonical base pair" EXACT [] synonym: "Watson Crick base pair" EXACT [] synonym: "Watson-Crick base pair" RELATED [] synonym: "Watson-Crick pair" EXACT [] synonym: "WC base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000030 name: sugar_edge_base_pair def: "A type of non-canonical base-pairing." [PMID:12177293] synonym: "sugar edge base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000031 name: aptamer def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] xref: http://en.wikipedia.org/wiki/Aptamer "wiki" is_a: SO:0000696 ! oligo [Term] id: SO:0000032 name: DNA_aptamer def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu] synonym: "DNA aptamer" EXACT [] is_a: SO:0000031 ! aptamer [Term] id: SO:0000033 name: RNA_aptamer def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] synonym: "RNA aptamer" EXACT [] is_a: SO:0000031 ! aptamer [Term] id: SO:0000034 name: morpholino_oligo def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/] synonym: "morphant" BROAD [] synonym: "morpholino" EXACT [] synonym: "morpholino oligo" EXACT [] is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001183 ! morpholino_backbone relationship: has_quality SO:0001183 ! morpholino_backbone [Term] id: SO:0000035 name: riboswitch def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:riboswitch" EXACT [] synonym: "riboswitch RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Riboswitch "wiki" is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000036 name: matrix_attachment_site def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:matrix_attachment_region" EXACT [] synonym: "MAR" EXACT [] synonym: "matrix association region" EXACT [] synonym: "matrix attachment region" EXACT [] synonym: "matrix attachment site" EXACT [] synonym: "nuclear matrix association region" EXACT [] synonym: "nuclear matrix attachment site" EXACT [] synonym: "S/MAR" EXACT [] synonym: "S/MAR element" RELATED [] synonym: "scaffold attachment site" EXACT [] synonym: "scaffold matrix attachment region" EXACT [] synonym: "SMAR" EXACT [] xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki" is_a: SO:0000626 ! chromosomal_regulatory_element [Term] id: SO:0000037 name: locus_control_region def: "A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma] comment: Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene. synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:locus_control_region" EXACT [] synonym: "LCR" EXACT [] synonym: "locus control element" RELATED [] synonym: "locus control region" EXACT [] xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000038 name: match_set def: "A collection of match parts." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000039 name: match_part def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke] subset: SOFA synonym: "match part" EXACT [] is_a: SO:0001410 ! experimental_feature relationship: part_of SO:0000343 ! match [Term] id: SO:0000040 name: genomic_clone def: "A clone of a DNA region of a genome." [SO:ma] synonym: "genomic clone" EXACT [] is_a: SO:0000151 ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! genomic_DNA [Term] id: SO:0000041 name: sequence_operation def: "An operation that can be applied to a sequence, that results in a change." [SO:ke] synonym: "sequence operation" EXACT [] is_obsolete: true [Term] id: SO:0000042 name: pseudogene_attribute def: "An attribute of a pseudogene (SO:0000336)." [SO:ma] synonym: "pseudogene attribute" EXACT [] is_obsolete: true [Term] id: SO:0000043 name: processed_pseudogene def: "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Please not the synonym R psi M uses the spelled out form of the greek letter. synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:processed" EXACT [] synonym: "processed pseudogene" EXACT [] synonym: "pseudogene by reverse transcription" RELATED [] synonym: "R psi G" RELATED [] synonym: "retropseudogene" EXACT [] is_a: SO:0000336 ! pseudogene [Term] id: SO:0000044 name: pseudogene_by_unequal_crossing_over def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke] synonym: "pseudogene by unequal crossing over" EXACT [] is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0000045 name: delete def: "To remove a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000046 name: insert def: "To insert a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000047 name: invert def: "To invert a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000048 name: substitute def: "To substitute a subsection of sequence for another." [SO:ke] is_obsolete: true [Term] id: SO:0000049 name: translocate def: "To translocate a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000050 name: gene_part def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000051 name: probe def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma] xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki" is_a: SO:0000696 ! oligo [Term] id: SO:0000052 name: assortment_derived_deficiency synonym: "assortment-derived_deficiency" RELATED [] is_obsolete: true [Term] id: SO:0000053 name: sequence_variant_affecting_regulatory_region def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting regulatory region" RELATED [] synonym: "sequence variant affecting regulatory region" EXACT [] is_obsolete: true replaced_by: SO:0001556 [Term] id: SO:0000054 name: aneuploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] xref: http://en.wikipedia.org/wiki/Aneuploid "wiki" is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0000055 name: hyperploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke] xref: http://en.wikipedia.org/wiki/Hyperploid "wiki" is_a: SO:0000054 ! aneuploid [Term] id: SO:0000056 name: hypoploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke] xref: http://en.wikipedia.org/wiki/Hypoploid "wiki" is_a: SO:0000054 ! aneuploid [Term] id: SO:0000057 name: operator def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] comment: Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529. subset: SOFA synonym: "operator segment" EXACT [] xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000058 name: assortment_derived_aneuploid synonym: "assortment-derived_aneuploid" RELATED [] is_obsolete: true [Term] id: SO:0000059 name: nuclease_binding_site def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb] subset: SOFA synonym: "nuclease binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0000060 name: compound_chromosome_arm def: "One arm of a compound chromosome." [] comment: FLAG - this term is should probably be a part of rather than an is_a. synonym: "compound chromosome arm" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:0000061 name: restriction_enzyme_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb] comment: A region of a molecule that binds to a restriction enzyme. synonym: "restriction endonuclease binding site" EXACT [] synonym: "restriction enzyme binding site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000062 name: deficient_intrachromosomal_transposition def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] synonym: "deficient intrachromosomal transposition" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000041 ! intrachromosomal_transposition relationship: has_part SO:0000159 ! deletion [Term] id: SO:0000063 name: deficient_interchromosomal_transposition def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke] synonym: "deficient interchromosomal transposition" EXACT [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:0000064 name: gene_by_transcript_attribute comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. is_obsolete: true [Term] id: SO:0000065 name: free_chromosome_arm def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke] synonym: "free chromosome arm" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000066 name: gene_by_polyadenylation_attribute is_obsolete: true [Term] id: SO:0000067 name: gene_to_gene_feature synonym: "gene to gene feature" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000068 name: overlapping def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke] is_a: SO:0000067 ! gene_to_gene_feature [Term] id: SO:0000069 name: inside_intron def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke] synonym: "inside intron" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000070 name: inside_intron_antiparallel def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke] synonym: "inside intron antiparallel" EXACT [] is_a: SO:0000069 ! inside_intron [Term] id: SO:0000071 name: inside_intron_parallel def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke] synonym: "inside intron parallel" EXACT [] is_a: SO:0000069 ! inside_intron [Term] id: SO:0000072 name: end_overlapping_gene is_obsolete: true [Term] id: SO:0000073 name: five_prime_three_prime_overlap def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke] synonym: "five prime-three prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000074 name: five_prime_five_prime_overlap def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke] synonym: "five prime-five prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000075 name: three_prime_three_prime_overlap def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke] synonym: "three prime-three prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000076 name: three_prime_five_prime_overlap def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke] synonym: "5' 3' overlap" EXACT [] synonym: "three prime five prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000077 name: antisense def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke] xref: http://en.wikipedia.org/wiki/Antisense "wiki" is_a: SO:0000068 ! overlapping [Term] id: SO:0000078 name: polycistronic_transcript def: "A transcript that is polycistronic." [SO:xp] synonym: "polycistronic transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000079 name: dicistronic_transcript def: "A transcript that is dicistronic." [SO:ke] synonym: "dicistronic transcript" EXACT [] is_a: SO:0000078 ! polycistronic_transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:0000080 name: operon_member def: "A gene that is a member of an operon, which is a set of genes transcribed together as a unit." [] synonym: "operon member" EXACT [] is_a: SO:0000081 ! gene_array_member [Term] id: SO:0000081 name: gene_array_member synonym: "gene array member" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000082 name: processed_transcript_attribute is_obsolete: true [Term] id: SO:0000083 name: macronuclear_sequence def: "DNA belonging to the macronuclei of ciliates." [] synonym: "macronuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000084 name: micronuclear_sequence def: "DNA belonging to the micronuclei of a cell." [] synonym: "micronuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000085 name: gene_by_genome_location is_obsolete: true [Term] id: SO:0000086 name: gene_by_organelle_of_genome is_obsolete: true [Term] id: SO:0000087 name: nuclear_gene def: "A gene from nuclear sequence." [SO:xp] synonym: "nuclear gene" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! nuclear_sequence [Term] id: SO:0000088 name: mt_gene def: "A gene located in mitochondrial sequence." [SO:xp] synonym: "mitochondrial gene" EXACT [] synonym: "mt gene" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000089 name: kinetoplast_gene def: "A gene located in kinetoplast sequence." [SO:xp] synonym: "kinetoplast gene" EXACT [] is_a: SO:0000088 ! mt_gene intersection_of: SO:0000088 ! mt_gene intersection_of: has_origin SO:0000741 ! kinetoplast relationship: has_origin SO:0000741 ! kinetoplast [Term] id: SO:0000090 name: plastid_gene def: "A gene from plastid sequence." [SO:xp] synonym: "plastid gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000740 ! plastid_sequence relationship: has_origin SO:0000740 ! plastid_sequence [Term] id: SO:0000091 name: apicoplast_gene def: "A gene from apicoplast sequence." [SO:xp] synonym: "apicoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000743 ! apicoplast_sequence relationship: has_origin SO:0000743 ! apicoplast_sequence [Term] id: SO:0000092 name: ct_gene def: "A gene from chloroplast sequence." [SO:xp] synonym: "chloroplast gene" EXACT [] synonym: "ct gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! chloroplast_sequence [Term] id: SO:0000093 name: chromoplast_gene def: "A gene from chromoplast_sequence." [SO:xp] synonym: "chromoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! chromoplast_sequence [Term] id: SO:0000094 name: cyanelle_gene def: "A gene from cyanelle sequence." [SO:xp] synonym: "cyanelle gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! cyanelle_sequence [Term] id: SO:0000095 name: leucoplast_gene def: "A plastid gene from leucoplast sequence." [SO:xp] synonym: "leucoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! leucoplast_sequence [Term] id: SO:0000096 name: proplastid_gene def: "A gene from proplastid sequence." [SO:ke] synonym: "proplastid gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000748 ! proplastid_sequence relationship: has_origin SO:0000748 ! proplastid_sequence [Term] id: SO:0000097 name: nucleomorph_gene def: "A gene from nucleomorph sequence." [SO:xp] synonym: "nucleomorph gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! nucleomorphic_sequence [Term] id: SO:0000098 name: plasmid_gene def: "A gene from plasmid sequence." [SO:xp] synonym: "plasmid gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000749 ! plasmid_location relationship: has_origin SO:0000749 ! plasmid_location [Term] id: SO:0000099 name: proviral_gene def: "A gene from proviral sequence." [SO:xp] synonym: "proviral gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000751 ! proviral_location relationship: has_origin SO:0000751 ! proviral_location [Term] id: SO:0000100 name: endogenous_retroviral_gene def: "A proviral gene with origin endogenous retrovirus." [SO:xp] synonym: "endogenous retroviral gene" EXACT [] is_a: SO:0000099 ! proviral_gene intersection_of: SO:0000099 ! proviral_gene intersection_of: has_origin SO:0000903 ! endogenous_retroviral_sequence relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence [Term] id: SO:0000101 name: transposable_element def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] subset: SOFA synonym: "transposable element" EXACT [] synonym: "transposon" EXACT [] xref: http://en.wikipedia.org/wiki/Transposable_element "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000102 name: expressed_sequence_match def: "A match to an EST or cDNA sequence." [SO:ke] subset: SOFA synonym: "expressed sequence match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000103 name: clone_insert_end def: "The end of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert end" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000104 name: polypeptide alt_id: SO:0000358 def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. subset: SOFA synonym: "protein" EXACT [] xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" is_a: SO:0001411 ! biological_region relationship: derives_from SO:0000316 ! CDS [Term] id: SO:0000105 name: chromosome_arm def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] synonym: "chromosome arm" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000106 name: non_capped_primary_transcript is_obsolete: true [Term] id: SO:0000107 name: sequencing_primer def: "A single stranded oligo used for polymerase chain reaction." [] synonym: "sequencing primer" EXACT [] is_a: SO:0000112 ! primer [Term] id: SO:0000108 name: mRNA_with_frameshift def: "An mRNA with a frameshift." [SO:xp] synonym: "frameshifted mRNA" EXACT [] synonym: "mRNA with frameshift" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000865 ! frameshift relationship: has_quality SO:0000865 ! frameshift [Term] id: SO:0000109 name: sequence_variant_obs def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] subset: SOFA synonym: "mutation" RELATED [] is_obsolete: true [Term] id: SO:0000110 name: sequence_feature def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] subset: SOFA synonym: "INSDC_feature:misc_feature" EXACT [] synonym: "INSDC_note:other" EXACT [] synonym: "INSDC_note:sequence_feature" EXACT [] synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] disjoint_from: SO:0000400 ! sequence_attribute [Term] id: SO:0000111 name: transposable_element_gene def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke] synonym: "transposable element gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: part_of SO:0000101 ! transposable_element relationship: part_of SO:0000101 ! transposable_element [Term] id: SO:0000112 name: primer def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke] subset: SOFA synonym: "DNA primer" EXACT [] synonym: "primer oligonucleotide" EXACT [] synonym: "primer polynucleotide" EXACT [] synonym: "primer sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki" is_a: SO:0000441 ! ss_oligo [Term] id: SO:0000113 name: proviral_region def: "A viral sequence which has integrated into a host genome." [SO:ke] subset: SOFA synonym: "proviral region" EXACT [] synonym: "proviral sequence" RELATED [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000114 name: methylated_cytosine def: "A methylated deoxy-cytosine." [SO:ke] subset: SOFA synonym: "methylated C" EXACT [] synonym: "methylated cytosine" EXACT [] synonym: "methylated cytosine base" EXACT [] synonym: "methylated cytosine residue" EXACT [] synonym: "methylated_C" EXACT [] is_a: SO:0000306 ! methylated_DNA_base_feature is_a: SO:0001963 ! modified_cytosine [Term] id: SO:0000115 name: transcript_feature is_obsolete: true [Term] id: SO:0000116 name: edited def: "An attribute describing a sequence that is modified by editing." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000117 name: transcript_with_readthrough_stop_codon is_obsolete: true [Term] id: SO:0000118 name: transcript_with_translational_frameshift def: "A transcript with a translational frameshift." [SO:xp] synonym: "transcript with translational frameshift" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000887 ! translationally_frameshifted relationship: has_quality SO:0000887 ! translationally_frameshifted [Term] id: SO:0000119 name: regulated def: "An attribute to describe a sequence that is regulated." [SO:ke] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000120 name: protein_coding_primary_transcript def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] comment: May contain introns. subset: SOFA synonym: "pre mRNA" RELATED [] synonym: "protein coding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000121 name: forward_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "DNA forward primer" EXACT [] synonym: "forward DNA primer" EXACT [] synonym: "forward primer" EXACT [] synonym: "forward primer oligo" EXACT [] synonym: "forward primer oligonucleotide" EXACT [] synonym: "forward primer polynucleotide" EXACT [] synonym: "forward primer sequence" EXACT [] is_a: SO:0000112 ! primer intersection_of: SO:0000112 ! primer intersection_of: has_quality SO:0001030 ! forward relationship: has_quality SO:0001030 ! forward [Term] id: SO:0000122 name: RNA_sequence_secondary_structure def: "A folded RNA sequence." [SO:ke] synonym: "RNA sequence secondary structure" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000123 name: transcriptionally_regulated def: "An attribute describing a gene that is regulated at transcription." [SO:ma] comment: By:. synonym: "transcriptionally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000124 name: transcriptionally_constitutive def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke] synonym: "transcriptionally constitutive" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000125 name: transcriptionally_induced def: "An inducer molecule is required for transcription to occur." [SO:ke] synonym: "transcriptionally induced" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000126 name: transcriptionally_repressed def: "A repressor molecule is required for transcription to stop." [SO:ke] synonym: "transcriptionally repressed" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000127 name: silenced_gene def: "A gene that is silenced." [SO:xp] synonym: "silenced gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000893 ! silenced relationship: has_quality SO:0000893 ! silenced [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification def: "A gene that is silenced by DNA modification." [SO:xp] synonym: "gene silenced by DNA modification" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000894 ! silenced_by_DNA_modification relationship: has_quality SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000129 name: gene_silenced_by_DNA_methylation def: "A gene that is silenced by DNA methylation." [SO:xp] synonym: "gene silenced by DNA methylation" EXACT [] synonym: "methylation-silenced gene" EXACT [] is_a: SO:0000128 ! gene_silenced_by_DNA_modification intersection_of: SO:0000128 ! gene_silenced_by_DNA_modification intersection_of: has_quality SO:0000895 ! silenced_by_DNA_methylation relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation [Term] id: SO:0000130 name: post_translationally_regulated def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke] synonym: "post translationally regulated" EXACT [] synonym: "post-translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000131 name: translationally_regulated def: "An attribute describing a gene that is regulated as it is translated." [SO:ke] synonym: "translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000132 name: reverse_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "DNA reverse primer" EXACT [] synonym: "reverse DNA primer" EXACT [] synonym: "reverse primer" EXACT [] synonym: "reverse primer oligo" EXACT [] synonym: "reverse primer oligonucleotide" EXACT [] synonym: "reverse primer sequence" EXACT [] is_a: SO:0000112 ! primer intersection_of: SO:0000112 ! primer intersection_of: has_quality SO:0001031 ! reverse relationship: has_quality SO:0001031 ! reverse [Term] id: SO:0000133 name: epigenetically_modified def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke] synonym: "epigenetically modified" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000134 name: genomically_imprinted def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] synonym: "genomically imprinted" EXACT [] synonym: "imprinted" BROAD [] xref: http:http\://en.wikipedia.org/wiki/Genomic_imprinting "wiki" is_a: SO:0000119 ! regulated is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000135 name: maternally_imprinted def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "maternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000136 name: paternally_imprinted def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "paternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000137 name: allelically_excluded def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] comment: Examples are x-inactivation and immunoglobulin formation. synonym: "allelically excluded" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000138 name: gene_rearranged_at_DNA_level def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] synonym: "gene rearranged at DNA level" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000904 ! rearranged_at_DNA_level relationship: has_quality SO:0000904 ! rearranged_at_DNA_level [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:ribosome_binding_site" EXACT [] synonym: "ribosome entry site" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000140 name: attenuator def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] subset: SOFA synonym: "attenuator sequence" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:attenuator" EXACT [] xref: http://en.wikipedia.org/wiki/Attenuator "wiki" is_a: SO:0001680 ! translation_regulatory_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000141 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.insdc.org/files/feature_table.html] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:terminator" EXACT [] synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000142 name: DNA_sequence_secondary_structure def: "A folded DNA sequence." [SO:ke] synonym: "DNA sequence secondary structure" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000143 name: assembly_component def: "A region of known length which may be used to manufacture a longer region." [SO:ke] subset: SOFA synonym: "assembly component" EXACT [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000144 name: primary_transcript_attribute is_obsolete: true [Term] id: SO:0000145 name: recoded_codon def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp] synonym: "recoded codon" EXACT [] is_a: SO:0000360 ! codon [Term] id: SO:0000146 name: capped def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000147 name: exon def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:exon" EXACT [] xref: http://en.wikipedia.org/wiki/Exon "wiki" is_a: SO:0000833 ! transcript_region [Term] id: SO:0000148 name: supercontig def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] subset: SOFA synonym: "scaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly relationship: part_of SO:0000719 ! ultracontig [Term] id: SO:0000149 name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] subset: SOFA xref: http://en.wikipedia.org/wiki/Contig "wiki" is_a: SO:0000143 ! assembly_component is_a: SO:0000353 ! sequence_assembly relationship: part_of SO:0000148 ! supercontig [Term] id: SO:0000150 name: read def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [Term] id: SO:0000151 name: clone def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] subset: SOFA xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000152 name: YAC def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "yeast artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000153 name: BAC def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "bacterial artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000154 name: PAC def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. synonym: "P1" EXACT [] synonym: "P1 artificial chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000155 name: plasmid def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "plasmid sequence" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000156 name: cosmid def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cosmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Cosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000157 name: phagemid def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma] synonym: "phagemid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Phagemid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000158 name: fosmid def: "A cloning vector that utilizes the E. coli F factor." [SO:ma] comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. synonym: "fosmid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Fosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000159 name: deletion alt_id: SO:1000033 def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] subset: SOFA synonym: "deleted_sequence" EXACT [] synonym: "nucleotide deletion" EXACT [] synonym: "nucleotide_deletion" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" xref: loinc:LA6692-3 "Deletion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000160 name: lambda_clone def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] is_obsolete: true [Term] id: SO:0000161 name: methylated_adenine def: "A modified base in which adenine has been methylated." [SO:ke] subset: SOFA synonym: "methylated A" EXACT [] synonym: "methylated adenine" EXACT [] synonym: "methylated adenine base" EXACT [] synonym: "methylated adenine residue" EXACT [] synonym: "methylated_A" EXACT [] is_a: SO:0000306 ! methylated_DNA_base_feature is_a: SO:0001962 ! modified_adenine [Term] id: SO:0000162 name: splice_site def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. subset: SOFA synonym: "splice site" EXACT [] xref: http://en.wikipedia.org/wiki/Splice_site "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000163 name: five_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "5' splice site" EXACT [] synonym: "donor" RELATED [] synonym: "donor splice site" EXACT [] synonym: "five prime splice site" EXACT [] synonym: "splice donor site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000164 name: three_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "3' splice site" RELATED [] synonym: "acceptor" RELATED [] synonym: "acceptor splice site" EXACT [] synonym: "splice acceptor site" EXACT [] synonym: "three prime splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000165 name: enhancer def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.insdc.org/files/feature_table.html] comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:enhancer" EXACT [] xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000166 name: enhancer_bound_by_factor def: "An enhancer bound by a factor." [SO:xp] synonym: "enhancer bound by factor" EXACT [] is_a: SO:0000165 ! enhancer intersection_of: SO:0000165 ! enhancer intersection_of: has_quality SO:0000277 ! bound_by_factor relationship: has_quality SO:0000277 ! bound_by_factor [Term] id: SO:0000167 name: promoter def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:promoter" EXACT [] synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0000842 ! gene_component_region is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000168 name: restriction_enzyme_cut_site def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma] is_obsolete: true [Term] id: SO:0000169 name: RNApol_I_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221. synonym: "pol I promoter" EXACT [] synonym: "polymerase I promoter" EXACT [] synonym: "RNA polymerase A promoter" EXACT [] synonym: "RNApol I promoter" EXACT [] is_a: SO:0002221 ! eukaryotic_promoter [Term] id: SO:0000170 name: RNApol_II_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221. synonym: "pol II promoter" RELATED [] synonym: "polymerase II promoter" EXACT [] synonym: "RNA polymerase B promoter" EXACT [] synonym: "RNApol II promoter" EXACT [] is_a: SO:0002221 ! eukaryotic_promoter [Term] id: SO:0000171 name: RNApol_III_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221. synonym: "pol III promoter" EXACT [] synonym: "polymerase III promoter" EXACT [] synonym: "RNA polymerase C promoter" EXACT [] synonym: "RNApol III promoter" EXACT [] is_a: SO:0002221 ! eukaryotic_promoter [Term] id: SO:0000172 name: CAAT_signal def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.insdc.org/files/feature_table.html] synonym: "CAAT box" EXACT [] synonym: "CAAT signal" EXACT [] synonym: "CAAT-box" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:CAAT_signal" EXACT [] xref: http://en.wikipedia.org/wiki/CAAT_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000173 name: GC_rich_promoter_region def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.insdc.org/files/feature_table.html] synonym: "GC rich promoter region" EXACT [] synonym: "GC-rich region" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:GC_rich_promoter_region" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000174 name: TATA_box def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.insdc.org/files/feature_table.html, PMID:16858867] comment: Binds TBP. synonym: "Goldstein-Hogness box" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:TATA_box" EXACT [] synonym: "TATA box" EXACT [] xref: http://en.wikipedia.org/wiki/TATA_box "wiki" is_a: SO:0001660 ! core_eukaryotic_promoter_element [Term] id: SO:0000175 name: minus_10_signal def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.insdc.org/files/feature_table.html] comment: Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021. synonym: "-10 signal" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:minus_10_signal" EXACT [] synonym: "minus 10 signal" EXACT [] synonym: "Pribnow box" EXACT [] synonym: "Pribnow Schaller box" EXACT [] synonym: "Pribnow-Schaller box" EXACT [] xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70_element relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf_element [Term] id: SO:0000176 name: minus_35_signal def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.insdc.org/files/feature_table.html] comment: Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021. synonym: "-35 signal" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:minus_35_signal" EXACT [] synonym: "minus 35 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70_element relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf_element [Term] id: SO:0000177 name: cross_genome_match def: "A nucleotide match against a sequence from another organism." [SO:ma] subset: SOFA synonym: "cross genome match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000178 name: operon def: "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020. subset: SOFA synonym: "INSDC_feature:operon" EXACT [] xref: http://en.wikipedia.org/wiki/Operon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:0000179 name: clone_insert_start def: "The start of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert start" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000180 name: retrotransposon def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r] synonym: "class I" RELATED [] synonym: "class I transposon" EXACT [] synonym: "retrotransposon element" EXACT [] xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki" is_a: SO:0000101 ! transposable_element [Term] id: SO:0000181 name: translated_nucleotide_match def: "A match against a translated sequence." [SO:ke] subset: SOFA synonym: "translated nucleotide match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000182 name: DNA_transposon def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke] synonym: "class II" RELATED [] synonym: "class II transposon" EXACT [] synonym: "DNA transposon" EXACT [] is_a: SO:0000101 ! transposable_element [Term] id: SO:0000183 name: non_transcribed_region def: "A region of the gene which is not transcribed." [SO:ke] subset: SOFA synonym: "non transcribed region" EXACT [] synonym: "non-transcribed sequence" EXACT [] synonym: "nontranscribed region" EXACT [] synonym: "nontranscribed sequence" EXACT [] is_a: SO:0000842 ! gene_component_region [Term] id: SO:0000184 name: U2_intron def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511] comment: May have either GT-AG or AT-AG 5' and 3' boundaries. synonym: "U2 intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000185 name: primary_transcript def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "INSDC_feature:precursor_RNA" EXACT [] synonym: "INSDC_feature:prim_transcript" EXACT [] synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000186 name: LTR_retrotransposon def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] synonym: "long terminal repeat retrotransposon" EXACT [] synonym: "LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000187 name: repeat_family def: "A group of characterized repeat sequences." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000188 name: intron def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.insdc.org/files/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:intron" EXACT [] xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000189 name: non_LTR_retrotransposon def: "A retrotransposon without long terminal repeat sequences." [SO:ke] synonym: "non LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000190 name: five_prime_intron def: "An intron that is the most 5-prime in a given transcript." [] synonym: "5' intron" EXACT [] synonym: "5' intron sequence" EXACT [] synonym: "five prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000191 name: interior_intron def: "An intron that is not the most 3-prime or the most 5-prime in a given transcript." [] synonym: "interior intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000192 name: three_prime_intron def: "An intron that is the most 3-prime in a given transcript." [] synonym: "3' intron" EXACT [] synonym: "3' intron sequence" RELATED [] synonym: "three prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000193 name: RFLP_fragment def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] subset: SOFA synonym: "restriction fragment length polymorphism" EXACT [] synonym: "RFLP" EXACT [] synonym: "RFLP fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" is_a: SO:0000412 ! restriction_fragment [Term] id: SO:0000194 name: LINE_element def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] synonym: "LINE" EXACT [] synonym: "LINE element" EXACT [] synonym: "Long interspersed element" EXACT [] synonym: "Long interspersed nuclear element" EXACT [] is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000195 name: coding_exon def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] subset: SOFA synonym: "coding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000196 name: five_prime_coding_exon_coding_region def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "five prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000197 name: three_prime_coding_exon_coding_region def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "three prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000198 name: noncoding_exon def: "An exon that does not contain any codons." [SO:ke] subset: SOFA synonym: "noncoding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000199 name: translocation def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke] subset: DBVAR synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "translocated sequence" EXACT [] is_a: SO:0001785 ! structural_alteration [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] subset: SOFA synonym: "5' coding exon" EXACT [] synonym: "five prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000201 name: interior_exon def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] synonym: "interior exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000202 name: three_prime_coding_exon def: "The coding exon that is most 3-prime on a given transcript." [SO:ma] synonym: "3' coding exon" RELATED [] synonym: "three prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000203 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] subset: SOFA synonym: "untranslated region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000204 name: five_prime_UTR def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.insdc.org/files/feature_table.html] subset: SOFA synonym: "5' UTR" EXACT [] synonym: "five prime UTR" EXACT [] synonym: "five_prime_untranslated_region" EXACT [] synonym: "INSDC_feature:5'UTR" EXACT [] xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000205 name: three_prime_UTR def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.insdc.org/files/feature_table.html] subset: SOFA synonym: "INSDC_feature:3'UTR" EXACT [] synonym: "three prime untranslated region" EXACT [] synonym: "three prime UTR" EXACT [] xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000206 name: SINE_element def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke] synonym: "Short interspersed element" EXACT [] synonym: "Short interspersed nuclear element" EXACT [] synonym: "SINE element" EXACT [] xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki" is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000207 name: simple_sequence_length_variation def: "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke] synonym: "simple sequence length polymorphism" RELATED [] synonym: "simple sequence length variation" EXACT [] synonym: "SSLP" RELATED [] xref: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism "WIKI" is_a: SO:0000248 ! sequence_length_alteration [Term] id: SO:0000208 name: terminal_inverted_repeat_element def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "terminal inverted repeat element" EXACT [] synonym: "TIR element" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000209 name: rRNA_primary_transcript def: "A primary transcript encoding a ribosomal RNA." [SO:ke] subset: SOFA synonym: "ribosomal RNA primary transcript" EXACT [] synonym: "rRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000210 name: tRNA_primary_transcript def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke] synonym: "tRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000211 name: alanine_tRNA_primary_transcript def: "A primary transcript encoding alanyl tRNA." [SO:ke] synonym: "alanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000212 name: arginine_tRNA_primary_transcript def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke] synonym: "arginine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000213 name: asparagine_tRNA_primary_transcript def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke] synonym: "asparagine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000214 name: aspartic_acid_tRNA_primary_transcript def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke] synonym: "aspartic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000215 name: cysteine_tRNA_primary_transcript def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke] synonym: "cysteine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000216 name: glutamic_acid_tRNA_primary_transcript def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000217 name: glutamine_tRNA_primary_transcript def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000218 name: glycine_tRNA_primary_transcript def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke] synonym: "glycine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000219 name: histidine_tRNA_primary_transcript def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke] synonym: "histidine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000220 name: isoleucine_tRNA_primary_transcript def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke] synonym: "isoleucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000221 name: leucine_tRNA_primary_transcript def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke] synonym: "leucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000222 name: lysine_tRNA_primary_transcript def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke] synonym: "lysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000223 name: methionine_tRNA_primary_transcript def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke] synonym: "methionine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000224 name: phenylalanine_tRNA_primary_transcript def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke] synonym: "phenylalanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000225 name: proline_tRNA_primary_transcript def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke] synonym: "proline tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000226 name: serine_tRNA_primary_transcript def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] synonym: "serine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000227 name: threonine_tRNA_primary_transcript def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke] synonym: "threonine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000228 name: tryptophan_tRNA_primary_transcript def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke] synonym: "tryptophan tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000229 name: tyrosine_tRNA_primary_transcript def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke] synonym: "tyrosine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000230 name: valine_tRNA_primary_transcript def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke] synonym: "valine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000231 name: snRNA_primary_transcript def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] synonym: "snRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000232 name: snoRNA_primary_transcript def: "A primary transcript encoding one or more small nucleolar RNAs (SO:0000275)." [SO:ke] comment: This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520). synonym: "snoRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: mature_transcript def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript relationship: derives_from SO:0000185 ! primary_transcript [Term] id: SO:0000234 name: mRNA def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:mRNA" EXACT [] synonym: "messenger RNA" EXACT [] synonym: "protein_coding_transcript" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A DNA site where a transcription factor binds." [SO:ke] comment: Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "TF binding site" EXACT [] synonym: "transcription factor binding site" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000727 ! cis_regulatory_module [Term] id: SO:0000236 name: ORF def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "open reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000237 name: transcript_attribute def: "An attribute describing a transcript." [] synonym: "transcript attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000238 name: foldback_element def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "foldback element" EXACT [] synonym: "long inverted repeat element" RELATED [] synonym: "LVR element" RELATED [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000239 name: flanking_region def: "The sequences extending on either side of a specific region." [SO:ke] subset: SOFA synonym: "flanking region" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000240 name: chromosome_variation def: "A deviation in chromosome structure or number." [] synonym: "chromosome variation" EXACT [] is_a: SO:0001507 ! variant_collection relationship: part_of SO:0001524 ! chromosomally_aberrant_genome [Term] id: SO:0000241 name: internal_UTR def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm] synonym: "internal UTR" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000242 name: untranslated_region_polycistronic_mRNA def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke] synonym: "untranslated region polycistronic mRNA" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000243 name: internal_ribosome_entry_site def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] synonym: "internal ribosomal entry sequence" EXACT [] synonym: "internal ribosomal entry site" EXACT [] synonym: "internal ribosome entry sequence" RELATED [] synonym: "internal ribosome entry site" EXACT [] synonym: "IRES" EXACT [] xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000244 name: four_cutter_restriction_site synonym: "4-cutter_restriction_site" RELATED [] synonym: "four-cutter_restriction_sit" RELATED [] is_obsolete: true [Term] id: SO:0000245 name: mRNA_by_polyadenylation_status is_obsolete: true [Term] id: SO:0000246 name: polyadenylated def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000247 name: mRNA_not_polyadenylated is_obsolete: true [Term] id: SO:0000248 name: sequence_length_alteration def: "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke] synonym: "sequence length alteration" EXACT [] is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0000249 name: six_cutter_restriction_site synonym: "6-cutter_restriction_site" RELATED [] synonym: "six-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000250 name: modified_RNA_base_feature def: "A post_transcriptionally modified base." [SO:ke] synonym: "modified RNA base feature" EXACT [] is_a: SO:0001236 ! base [Term] id: SO:0000251 name: eight_cutter_restriction_site synonym: "8-cutter_restriction_site" RELATED [] synonym: "eight-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000252 name: rRNA def: "rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity." [http://www.insdc.org/files/feature_table.html, ISBN:0198506732] comment: Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493 subset: SOFA synonym: "INSDC_feature:rRNA" EXACT [] synonym: "INSDC_qualifier:unknown" BROAD [] synonym: "ribosomal ribonucleic acid" EXACT [] synonym: "ribosomal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000253 name: tRNA def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:tRNA" EXACT [] synonym: "INSDC_qualifier:unknown" BROAD [] synonym: "transfer ribonucleic acid" RELATED [] synonym: "transfer RNA" RELATED [] xref: http://en.wikipedia.org/wiki/TRNA "wiki" is_a: SO:0002247 ! sncRNA relationship: derives_from SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000254 name: alanyl_tRNA def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke] synonym: "alanyl tRNA" EXACT [] synonym: "alanyl-transfer ribonucleic acid" EXACT [] synonym: "alanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript [Term] id: SO:0000255 name: rRNA_small_subunit_primary_transcript def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke] synonym: "rRNA small subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000256 name: asparaginyl_tRNA def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke] synonym: "asparaginyl tRNA" EXACT [] synonym: "asparaginyl-transfer ribonucleic acid" EXACT [] synonym: "asparaginyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript [Term] id: SO:0000257 name: aspartyl_tRNA def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke] synonym: "aspartyl tRNA" EXACT [] synonym: "aspartyl-transfer ribonucleic acid" EXACT [] synonym: "aspartyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript [Term] id: SO:0000258 name: cysteinyl_tRNA def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke] synonym: "cysteinyl tRNA" EXACT [] synonym: "cysteinyl-transfer ribonucleic acid" EXACT [] synonym: "cysteinyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript [Term] id: SO:0000259 name: glutaminyl_tRNA def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke] synonym: "glutaminyl tRNA" EXACT [] synonym: "glutaminyl-transfer ribonucleic acid" EXACT [] synonym: "glutaminyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript [Term] id: SO:0000260 name: glutamyl_tRNA def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke] synonym: "glutamyl tRNA" EXACT [] synonym: "glutamyl-transfer ribonucleic acid" EXACT [] synonym: "glutamyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript [Term] id: SO:0000261 name: glycyl_tRNA def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke] synonym: "glycyl tRNA" EXACT [] synonym: "glycyl-transfer ribonucleic acid" RELATED [] synonym: "glycyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript [Term] id: SO:0000262 name: histidyl_tRNA def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke] synonym: "histidyl tRNA" EXACT [] synonym: "histidyl-transfer ribonucleic acid" EXACT [] synonym: "histidyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript [Term] id: SO:0000263 name: isoleucyl_tRNA def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke] synonym: "isoleucyl tRNA" EXACT [] synonym: "isoleucyl-transfer ribonucleic acid" EXACT [] synonym: "isoleucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript [Term] id: SO:0000264 name: leucyl_tRNA def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke] synonym: "leucyl tRNA" EXACT [] synonym: "leucyl-transfer ribonucleic acid" EXACT [] synonym: "leucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript [Term] id: SO:0000265 name: lysyl_tRNA def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke] synonym: "lysyl tRNA" EXACT [] synonym: "lysyl-transfer ribonucleic acid" EXACT [] synonym: "lysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript [Term] id: SO:0000266 name: methionyl_tRNA def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke] synonym: "methionyl tRNA" EXACT [] synonym: "methionyl-transfer ribonucleic acid" EXACT [] synonym: "methionyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript [Term] id: SO:0000267 name: phenylalanyl_tRNA def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke] synonym: "phenylalanyl tRNA" EXACT [] synonym: "phenylalanyl-transfer ribonucleic acid" EXACT [] synonym: "phenylalanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript [Term] id: SO:0000268 name: prolyl_tRNA def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke] synonym: "prolyl tRNA" EXACT [] synonym: "prolyl-transfer ribonucleic acid" EXACT [] synonym: "prolyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript [Term] id: SO:0000269 name: seryl_tRNA def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke] synonym: "seryl tRNA" EXACT [] synonym: "seryl-transfer ribonucleic acid" RELATED [] synonym: "seryl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript [Term] id: SO:0000270 name: threonyl_tRNA def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke] synonym: "threonyl tRNA" EXACT [] synonym: "threonyl-transfer ribonucleic acid" EXACT [] synonym: "threonyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript [Term] id: SO:0000271 name: tryptophanyl_tRNA def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke] synonym: "tryptophanyl tRNA" EXACT [] synonym: "tryptophanyl-transfer ribonucleic acid" EXACT [] synonym: "tryptophanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript [Term] id: SO:0000272 name: tyrosyl_tRNA def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke] synonym: "tyrosyl tRNA" EXACT [] synonym: "tyrosyl-transfer ribonucleic acid" EXACT [] synonym: "tyrosyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript [Term] id: SO:0000273 name: valyl_tRNA def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke] synonym: "valyl tRNA" EXACT [] synonym: "valyl-transfer ribonucleic acid" EXACT [] synonym: "valyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript [Term] id: SO:0000274 name: snRNA def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.insdc.org/files/feature_table.html, PMID:11733745, WB:ems] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:snRNA" EXACT [] synonym: "small nuclear RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnRNA "wiki" is_a: SO:0002247 ! sncRNA relationship: derives_from SO:0000231 ! snRNA_primary_transcript [Term] id: SO:0000275 name: snoRNA def: "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." [GOC:kgc, PMID:31828325] comment: Updated the definition of snoRNA (SO:0000275) from "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:snoRNA" EXACT [] synonym: "small nucleolar RNA" EXACT [] is_a: SO:0002247 ! sncRNA relationship: derives_from SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000276 name: miRNA alt_id: SO:0000649 def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:miRNA" EXACT [] synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] synonym: "small temporal RNA" EXACT [] synonym: "stRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA relationship: derives_from SO:0001244 ! pre_miRNA [Term] id: SO:0000277 name: bound_by_factor def: "An attribute describing a sequence that is bound by another molecule." [SO:ke] comment: Formerly called transcript_by_bound_factor. synonym: "bound by factor" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000278 name: transcript_bound_by_nucleic_acid def: "A transcript that is bound by a nucleic acid." [SO:xp] comment: Formerly called transcript_by_bound_nucleic_acid. synonym: "transcript bound by nucleic acid" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000876 ! bound_by_nucleic_acid relationship: has_quality SO:0000876 ! bound_by_nucleic_acid [Term] id: SO:0000279 name: transcript_bound_by_protein def: "A transcript that is bound by a protein." [SO:xp] comment: Formerly called transcript_by_bound_protein. synonym: "transcript bound by protein" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000875 ! bound_by_protein relationship: has_quality SO:0000875 ! bound_by_protein [Term] id: SO:0000280 name: engineered_gene def: "A gene that is engineered." [SO:xp] synonym: "engineered gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0000804 ! engineered_region intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000281 name: engineered_foreign_gene def: "A gene that is engineered and foreign." [SO:xp] synonym: "engineered foreign gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000285 ! foreign_gene is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000280 ! engineered_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000282 name: mRNA_with_minus_1_frameshift def: "An mRNA with a minus 1 frameshift." [SO:xp] synonym: "mRNA with minus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000866 ! minus_1_frameshift relationship: has_quality SO:0000866 ! minus_1_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene def: "A transposable_element that is engineered and foreign." [SO:xp] synonym: "engineered foreign transposable element gene" EXACT [] is_a: SO:0000111 ! transposable_element_gene is_a: SO:0000281 ! engineered_foreign_gene intersection_of: SO:0000111 ! transposable_element_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000284 name: type_I_enzyme_restriction_site def: "The recognition site is bipartite and interrupted." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000285 name: foreign_gene def: "A gene that is foreign." [SO:xp] synonym: "foreign gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000286 name: long_terminal_repeat def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.insdc.org/files/feature_table.html] synonym: "direct terminal repeat" RELATED [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:long_terminal_repeat" EXACT [] synonym: "long terminal repeat" EXACT [] synonym: "LTR" EXACT [] xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki" is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000287 name: fusion_gene def: "A gene that is a fusion." [SO:xp] synonym: "fusion gene" EXACT [] xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000806 ! fusion relationship: has_quality SO:0000806 ! fusion [Term] id: SO:0000288 name: engineered_fusion_gene def: "A fusion gene that is engineered." [SO:xp] synonym: "engineered fusion gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000287 ! fusion_gene intersection_of: SO:0000287 ! fusion_gene intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000289 name: microsatellite def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:microsatellite" EXACT [] synonym: "microsatellite locus" EXACT [] synonym: "microsatellite marker" EXACT [] synonym: "short tandem repeat" EXACT [] synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/] xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000290 name: dinucleotide_repeat_microsatellite_feature def: "A region of a repeating dinucleotide sequence (two bases)." [] synonym: "dinucleotide repeat microsatellite" EXACT [] synonym: "dinucleotide repeat microsatellite feature" EXACT [] synonym: "dinucleotide repeat microsatellite locus" EXACT [] synonym: "dinucleotide repeat microsatellite marker" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000291 name: trinucleotide_repeat_microsatellite_feature def: "A region of a repeating trinucleotide sequence (three bases)." [] synonym: "dinucleotide repeat microsatellite marker" RELATED [] synonym: "rinucleotide repeat microsatellite" EXACT [] synonym: "trinucleotide repeat microsatellite feature" EXACT [] synonym: "trinucleotide repeat microsatellite locus" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000292 name: repetitive_element is_obsolete: true [Term] id: SO:0000293 name: engineered_foreign_repetitive_element def: "A repetitive element that is engineered and foreign." [SO:xp] synonym: "engineered foreign repetitive element" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000657 ! repeat_region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000294 name: inverted_repeat def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:inverted" EXACT [] synonym: "inverted repeat" EXACT [] synonym: "inverted repeat sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000295 name: U12_intron def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511] comment: May have either GT-AC or AT-AC 5' and 3' boundaries. synonym: "U12 intron" EXACT [] synonym: "U12-dependent intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000296 name: origin_of_replication def: "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites." [http://www.insdc.org/files/feature_table.html, NCBI:cf] subset: SOFA synonym: "INSDC_feature:rep_origin" EXACT [] synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0001235 ! replicon [Term] id: SO:0000297 name: D_loop def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.insdc.org/files/feature_table.html] comment: Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) synonym: "D-loop" EXACT [] synonym: "displacement loop" RELATED [] synonym: "INSDC_feature:D-loop" EXACT [] xref: http://en.wikipedia.org/wiki/D_loop "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000298 name: recombination_feature def: "A feature where there has been exchange of genetic material in the event of mitosis or meiosis" [] synonym: "INSDC_feature:misc_recomb" BROAD [] synonym: "INSDC_qualifier:other" EXACT [] synonym: "recombination feature" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000299 name: specific_recombination_site def: "A location where recombination or occurs during mitosis or meiosis." [] synonym: "specific recombination site" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000300 name: recombination_feature_of_rearranged_gene def: "A location where a gene is rearranged due to recombination during mitosis or meiosis." [] synonym: "recombination feature of rearranged gene" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000301 name: vertebrate_immune_system_gene_recombination_feature def: "A feature where recombination has occurred for the purpose of generating a diversity in the immune system." [] synonym: "vertebrate immune system gene recombination feature" EXACT [] is_a: SO:0000300 ! recombination_feature_of_rearranged_gene [Term] id: SO:0000302 name: J_gene_recombination_feature def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J gene recombination feature" EXACT [] synonym: "J-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000303 name: clip def: "Part of the primary transcript that is clipped off during processing." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000304 name: type_II_enzyme_restriction_site def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000305 name: modified_DNA_base def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.insdc.org/files/feature_table.html] comment: Modified base:. subset: SOFA synonym: "INSDC_feature:modified_base" EXACT [] synonym: "modified base site" EXACT [] is_a: SO:0001236 ! base is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_DNA_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_DNA_base [Term] id: SO:0000307 name: CpG_island def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] subset: SOFA synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000308 name: sequence_feature_locating_method is_obsolete: true [Term] id: SO:0000309 name: computed_feature is_obsolete: true [Term] id: SO:0000310 name: predicted_ab_initio_computation is_obsolete: true [Term] id: SO:0000311 name: computed_feature_by_similarity def: "." [SO:ma] comment: similar to: is_obsolete: true [Term] id: SO:0000312 name: experimentally_determined def: "Attribute to describe a feature that has been experimentally verified." [SO:ke] synonym: "experimentally determined" EXACT [] is_a: SO:0000789 ! validated [Term] id: SO:0000313 name: stem_loop alt_id: SO:0000019 def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.insdc.org/files/feature_table.html] synonym: "INSDC_feature:stem_loop" EXACT [] synonym: "RNA_hairpin_loop" EXACT [] synonym: "stem loop" EXACT [] synonym: "stem-loop" EXACT [] xref: http://en.wikipedia.org/wiki/Stem_loop "wiki" is_a: SO:0000122 ! RNA_sequence_secondary_structure [Term] id: SO:0000314 name: direct_repeat def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke] subset: SOFA synonym: "direct repeat" EXACT [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:direct" EXACT [] xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: TSS def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] comment: Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant. subset: SOFA synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:transcription_start_site" EXACT [] synonym: "transcription start site" EXACT [] synonym: "transcription_start_site" EXACT [] is_a: SO:0000835 ! primary_transcript_region is_a: SO:0002309 ! core_promoter_element [Term] id: SO:0000316 name: CDS def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SOFA synonym: "coding sequence" EXACT [] synonym: "coding_sequence" EXACT [] synonym: "INSDC_feature:CDS" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000317 name: cDNA_clone def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cDNA clone" EXACT [] is_a: SO:0000151 ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000318 name: start_codon def: "First codon to be translated by a ribosome." [SO:ke] subset: SOFA synonym: "initiation codon" EXACT [] synonym: "start codon" EXACT [] xref: http://en.wikipedia.org/wiki/Start_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000319 name: stop_codon def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] subset: SOFA synonym: "stop codon" EXACT [] xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000320 name: intronic_splice_enhancer def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke] synonym: "intronic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer relationship: part_of SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000321 name: mRNA_with_plus_1_frameshift def: "An mRNA with a plus 1 frameshift." [SO:ke] synonym: "mRNA with plus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000868 ! plus_1_frameshift relationship: has_quality SO:0000868 ! plus_1_frameshift [Term] id: SO:0000322 name: nuclease_hypersensitive_site def: "A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance." [] comment: Relationship to accessible_DNA_region added 11 Feb 2021. GREEKC pointed out that this is an assay based term, but we need a biological term for the accessible DNA. See GitHub Issue #531. synonym: "nuclease hypersensitive site" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site is_a: SO:0002331 ! accessible_DNA_region [Term] id: SO:0000323 name: coding_start def: "The first base to be translated into protein." [SO:ke] synonym: "coding start" EXACT [] synonym: "translation initiation site" EXACT [] synonym: "translation start" RELATED [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000324 name: tag def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] subset: SOFA is_a: SO:0000696 ! oligo [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] subset: SOFA synonym: "35S rRNA primary transcript" EXACT [] synonym: "rRNA large subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000326 name: SAGE_tag def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] subset: SOFA synonym: "SAGE tag" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000327 name: coding_end def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke] synonym: "coding end" EXACT [] synonym: "translation termination site" EXACT [] synonym: "translation_end" EXACT [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000328 name: microarray_oligo def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [] synonym: "microarray oligo" EXACT [] synonym: "microarray oligonucleotide" EXACT [] is_a: SO:0000051 ! probe [Term] id: SO:0000329 name: mRNA_with_plus_2_frameshift def: "An mRNA with a plus 2 frameshift." [SO:xp] synonym: "mRNA with plus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000869 ! plus_2_framshift relationship: has_quality SO:0000869 ! plus_2_framshift [Term] id: SO:0000330 name: conserved_region def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:conserved_region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000331 name: STS def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] subset: SOFA synonym: "INSDC_feature:STS" EXACT [] synonym: "sequence tag site" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000332 name: coding_conserved_region def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "coding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000333 name: exon_junction def: "The boundary between two exons in a processed transcript." [SO:ke] subset: SOFA synonym: "exon junction" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000334 name: nc_conserved_region def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved non-coding element" EXACT [] synonym: "conserved non-coding sequence" EXACT [] synonym: "nc conserved region" EXACT [] synonym: "noncoding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000335 name: mRNA_with_minus_2_frameshift def: "A mRNA with a minus 2 frameshift." [SO:ke] synonym: "mRNA with minus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000867 ! minus_2_frameshift relationship: has_quality SO:0000867 ! minus_2_frameshift [Term] id: SO:0000336 name: pseudogene def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: Alliance_of_Genome_Resources subset: SOFA synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "INSDC_qualifier:unknown" EXACT [] xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region relationship: non_functional_homolog_of SO:0000704 ! gene [Term] id: SO:0000337 name: RNAi_reagent def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] subset: SOFA synonym: "RNAi reagent" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0000338 name: MITE def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083] synonym: "miniature inverted repeat transposable element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000339 name: recombination_hotspot def: "A region in a genome which promotes recombination." [SO:rd] synonym: "recombination hotspot" EXACT [] xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki" is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000340 name: chromosome def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Chromosome "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000341 name: chromosome_band def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] subset: SOFA synonym: "chromosome band" EXACT [] synonym: "cytoband" EXACT [] synonym: "cytological band" EXACT [] xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000342 name: site_specific_recombination_target_region def: "A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis." [] synonym: "site specific recombination target region" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000343 name: match def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000344 name: splice_enhancer def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA synonym: "splice enhancer" EXACT [] is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000324 ! tag relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000346 name: loxP_site def: "Cre-Recombination target sequence." [] synonym: "Cre-recombination target region" RELATED [] synonym: "loxP site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000347 name: nucleotide_match def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA synonym: "nucleotide match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000348 name: nucleic_acid def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] synonym: "nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki" is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000349 name: protein_match def: "A match against a protein sequence." [SO:ke] subset: SOFA synonym: "protein match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000350 name: FRT_site def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] synonym: "FLP recombination target region" EXACT [] synonym: "FRT site" EXACT [] is_a: SO:0000948 ! inversion_site [Term] id: SO:0000351 name: synthetic_sequence def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] synonym: "synthetic sequence" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000352 name: DNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000353 name: sequence_assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA synonym: "sequence assembly" EXACT [] xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" is_a: SO:0001248 ! assembly [Term] id: SO:0000354 name: group_1_intron_homing_endonuclease_target_region def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke] synonym: "group 1 intron homing endonuclease target region" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site [Term] id: SO:0000355 name: haplotype_block def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma] synonym: "haplotype block" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000356 name: RNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000357 name: flanked def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000359 name: floxed def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] xref: http://en.wikipedia.org/wiki/Floxed "wiki" is_a: SO:0000357 ! flanked [Term] id: SO:0000360 name: codon def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Codon "wiki" is_a: SO:0000851 ! CDS_region [Term] id: SO:0000361 name: FRT_flanked def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] synonym: "FRT flanked" EXACT [] is_a: SO:0000357 ! flanked [Term] id: SO:0000362 name: invalidated_by_chimeric_cDNA def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] synonym: "invalidated by chimeric cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000363 name: floxed_gene def: "A transgene that is floxed." [SO:xp] synonym: "floxed gene" EXACT [] is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene intersection_of: has_quality SO:0000359 ! floxed relationship: has_quality SO:0000359 ! floxed [Term] id: SO:0000364 name: transposable_element_flanking_region def: "The region of sequence surrounding a transposable element." [SO:ke] synonym: "transposable element flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0000365 name: integron def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as] xref: http://en.wikipedia.org/wiki/Integron "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000366 name: insertion_site def: "The junction where an insertion occurred." [SO:ke] subset: SOFA synonym: "insertion site" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000367 name: attI_site def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as] synonym: "attI site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000368 name: transposable_element_insertion_site def: "The junction in a genome where a transposable_element has inserted." [SO:ke] subset: SOFA synonym: "transposable element insertion site" EXACT [] is_a: SO:0000366 ! insertion_site [Term] id: SO:0000369 name: integrase_coding_region is_obsolete: true [Term] id: SO:0000370 name: small_regulatory_ncRNA def: "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others)." [PMID:28541282, PomBase:al, SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0002247 ! sncRNA [Term] id: SO:0000371 name: conjugative_transposon def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html] synonym: "conjugative transposon" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000372 name: enzymatic_RNA def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533. subset: SOFA synonym: "enzymatic RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0000373 name: recombinationally_inverted_gene def: "A recombinationally rearranged gene by inversion." [SO:xp] synonym: "recombinationally inverted gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene intersection_of: SO:0000456 ! recombinationally_rearranged_gene intersection_of: has_quality SO:1000036 ! inversion relationship: has_quality SO:1000036 ! inversion [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" is_a: SO:0000372 ! enzymatic_RNA intersection_of: SO:0000372 ! enzymatic_RNA intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000375 name: cytosolic_5_8S_rRNA def: "Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes." [https://rfam.xfam.org/family/RF00002] comment: Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 5.8S LSU rRNA" EXACT [] synonym: "cytosolic 5.8S ribosomal RNA" EXACT [] synonym: "cytosolic 5.8S rRNA" EXACT [] synonym: "cytosolic rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002240 ! cytosolic_rRNA_5_8S_gene [Term] id: SO:0000376 name: RNA_6S def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] synonym: "6S RNA" EXACT [] synonym: "RNA 6S" EXACT [] xref: http://en.wikipedia.org/wiki/6S_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000377 name: CsrB_RsmB_RNA def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] synonym: "CsrB RsmB RNA" EXACT [] synonym: "CsrB-RsmB RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000378 name: DsrA_RNA def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] synonym: "DsrA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000379 name: GcvB_RNA def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022] synonym: "GcvB RNA" EXACT [] xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki" is_a: SO:0000378 ! DsrA_RNA [Term] id: SO:0000380 name: hammerhead_ribozyme def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] subset: SOFA synonym: "hammerhead ribozyme" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:hammerhead_ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" is_a: SO:0000715 ! RNA_motif intersection_of: SO:0000715 ! RNA_motif intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000381 name: group_IIA_intron def: "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon." [PMID:20463000] synonym: "group IIA intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000382 name: group_IIB_intron def: "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon." [PMID:20463000] synonym: "group IIB intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000383 name: MicF_RNA def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033] synonym: "MicF RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki" is_a: SO:0000644 ! antisense_RNA [Term] id: SO:0000384 name: OxyS_RNA def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] synonym: "OxyS RNA" EXACT [] xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000385 name: RNase_MRP_RNA def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:RNase_MRP_RNA" EXACT [] synonym: "RNase MRP RNA" EXACT [] is_a: SO:0000372 ! enzymatic_RNA [Term] id: SO:0000386 name: RNase_P_RNA def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] comment: Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:RNase_P_RNA" EXACT [] synonym: "RNase P RNA" EXACT [] is_a: SO:0000372 ! enzymatic_RNA [Term] id: SO:0000387 name: RprA_RNA def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] synonym: "RprA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000388 name: RRE_RNA def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] synonym: "RRE RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000389 name: spot_42_RNA def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] synonym: "spot-42 RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000390 name: telomerase_RNA def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:telomerase_RNA" EXACT [] synonym: "telomerase RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000391 name: U1_snRNA def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] subset: SOFA synonym: "small nuclear RNA U1" EXACT [RSC:cb] synonym: "snRNA U1" EXACT [RSC:cb] synonym: "U1 small nuclear RNA" EXACT [RSC:cb] synonym: "U1 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000392 name: U2_snRNA def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] subset: SOFA synonym: "small nuclear RNA U2" EXACT [RSC:CB] synonym: "snRNA U2" EXACT [RSC:CB] synonym: "U2 small nuclear RNA" EXACT [RSC:CB] synonym: "U2 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000393 name: U4_snRNA def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U4" EXACT [RSC:cb] synonym: "snRNA U4" EXACT [RSC:cb] synonym: "U4 small nuclear RNA" EXACT [RSC:cb] synonym: "U4 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000394 name: U4atac_snRNA def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:12409455] subset: SOFA synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] synonym: "snRNA U4atac" EXACT [RSC:cb] synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] synonym: "U4atac snRNA" EXACT [] is_a: SO:0000274 ! snRNA [Term] id: SO:0000395 name: U5_snRNA def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] subset: SOFA synonym: "small nuclear RNA U5" EXACT [RSC:cb] synonym: "snRNA U5" EXACT [RSC:cb] synonym: "U5 small nuclear RNA" EXACT [RSC:cb] synonym: "U5 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000396 name: U6_snRNA def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U6" EXACT [RSC:cb] synonym: "snRNA U6" EXACT [RSC:cb] synonym: "U6 small nuclear RNA" EXACT [RSC:cb] synonym: "U6 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] subset: SOFA synonym: "snRNA U6atac" EXACT [RSC:cb] synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] synonym: "U6atac snRNA" EXACT [RSC:cb] is_a: SO:0000274 ! snRNA [Term] id: SO:0000398 name: U11_snRNA def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] subset: SOFA synonym: "small nuclear RNA U11" EXACT [RSC:cb] synonym: "snRNA U11" EXACT [RSC:cb] synonym: "U11 small nuclear RNA" EXACT [RSC:cb] synonym: "U11 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000399 name: U12_snRNA def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] subset: SOFA synonym: "small nuclear RNA U12" EXACT [RSC:cb] synonym: "snRNA U12" EXACT [RSC:cb] synonym: "U12 small nuclear RNA" EXACT [RSC:cb] synonym: "U12 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000400 name: sequence_attribute def: "An attribute describes a quality of sequence." [SO:ke] synonym: "sequence attribute" EXACT [] [Term] id: SO:0000401 name: gene_attribute def: "An attribute describing a gene." [] synonym: "gene attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000402 name: enhancer_attribute is_obsolete: true [Term] id: SO:0000403 name: U14_snoRNA alt_id: SO:0005839 def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. subset: SOFA synonym: "small nucleolar RNA U14" EXACT [] synonym: "snoRNA U14" EXACT [] synonym: "U14 small nucleolar RNA" EXACT [] synonym: "U14 snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript [Term] id: SO:0000404 name: vault_RNA def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:vault_RNA" EXACT [] synonym: "vault RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000405 name: Y_RNA def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:Y_RNA" EXACT [] synonym: "Y RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000406 name: twintron def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908] xref: http://en.wikipedia.org/wiki/Twintron "wiki" is_a: SO:0000188 ! intron [Term] id: SO:0000407 name: cytosolic_18S_rRNA def: "Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes." [SO:ke] comment: Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 18S ribosomal RNA" EXACT [] synonym: "cytosolic 18S rRNA" EXACT [] synonym: "cytosolic rRNA 18S" EXACT [] xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" is_a: SO:0000650 ! cytosolic_SSU_rRNA relationship: derives_from SO:0002236 ! cytosolic_rRNA_18S_gene [Term] id: SO:0000408 name: site def: "The interbase position where something (eg an aberration) occurred." [SO:ke] is_obsolete: true [Term] id: SO:0000409 name: binding_site alt_id: BS:00033 def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. subset: biosapiens subset: SOFA synonym: "binding site" EXACT [] synonym: "binding_or_interaction_site" EXACT [] synonym: "INSDC_feature:misc_binding" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] comment: See GO:0042277 : peptide binding. subset: SOFA synonym: "INSDC_feature:protein_bind" EXACT [] synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000411 name: rescue_region def: "A region that rescues." [SO:xp] synonym: "rescue fragment" EXACT [] synonym: "rescue region" EXACT [] synonym: "rescue segment" RELATED [] is_a: SO:0000695 ! reagent intersection_of: SO:0000695 ! reagent intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000412 name: restriction_fragment def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] subset: SOFA synonym: "restriction fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" is_a: SO:0000143 ! assembly_component [Term] id: SO:0000413 name: sequence_difference def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA synonym: "INSDC_feature:misc_difference" EXACT [] synonym: "sequence difference" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000414 name: invalidated_by_genomic_contamination def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke] synonym: "invalidated by genomic contamination" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000415 name: invalidated_by_genomic_polyA_primed_cDNA def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke] synonym: "invalidated by genomic polyA primed cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000416 name: invalidated_by_partial_processing def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke] synonym: "invalidated by partial processing" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000417 name: polypeptide_domain alt_id: BS:00012 alt_id: BS:00134 alt_id: SO:0001069 def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. subset: biosapiens synonym: "domain" BROAD BS [uniprot:feature_type] synonym: "polypeptide domain" EXACT [] synonym: "polypeptide_structural_domain" EXACT BS [] synonym: "structural domain" BROAD BS [] is_a: SO:0001070 ! polypeptide_structural_region is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0000418 name: signal_peptide alt_id: BS:00159 def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.insdc.org/files/feature_table.html] comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. subset: biosapiens subset: SOFA synonym: "INSDC_feature:sig_peptide" EXACT [] synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] synonym: "signal peptide coding sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" is_a: SO:0001527 ! peptide_localization_signal relationship: derives_from SO:0002251 ! signal_peptide_region_of_CDS relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0000419 name: mature_protein_region alt_id: BS:00149 def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.insdc.org/files/feature_table.html, SO:cb] comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. subset: biosapiens subset: SOFA synonym: "chain" RELATED [uniprot:feature_type] synonym: "INSDC_feature:mat_peptide" EXACT [] synonym: "mature peptide" RELATED [] synonym: "mature protein region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: derives_from SO:0002249 ! mature_protein_region_of_CDS relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0000420 name: five_prime_terminal_inverted_repeat def: "An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon." [] synonym: "5' TIR" EXACT [] synonym: "five prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000421 name: three_prime_terminal_inverted_repeat def: "An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon." [] synonym: "3' TIR" EXACT [] synonym: "three prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000422 name: U5_LTR_region def: "The U5 segment of the long terminal repeats." [] synonym: "U5 long terminal repeat region" EXACT [] synonym: "U5 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000423 name: R_LTR_region def: "The R segment of the long terminal repeats." [] synonym: "R long terminal repeat region" EXACT [] synonym: "R LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000424 name: U3_LTR_region def: "The U3 segment of the long terminal repeats." [] synonym: "U3 long terminal repeat region" EXACT [] synonym: "U3 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000425 name: five_prime_LTR def: "The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome." [] synonym: "5' long terminal repeat" EXACT [] synonym: "5' LTR" EXACT [] synonym: "five prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000426 name: three_prime_LTR def: "The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome." [] synonym: "3' long terminal repeat" EXACT [] synonym: "3' LTR" EXACT [] synonym: "three prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000427 name: R_five_prime_LTR_region def: "The R segment of the three-prime long terminal repeat." [] synonym: "R 5' long term repeat region" EXACT [] synonym: "R five prime LTR region" EXACT [] is_a: SO:0000423 ! R_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000428 name: U5_five_prime_LTR_region def: "The U5 segment of the three-prime long terminal repeat." [] synonym: "U5 5' long terminal repeat region" EXACT [] synonym: "U5 five prime LTR region" EXACT [] is_a: SO:0000422 ! U5_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000429 name: U3_five_prime_LTR_region def: "The U3 segment of the three-prime long terminal repeat." [] synonym: "U3 5' long term repeat region" EXACT [] synonym: "U3 five prime LTR region" EXACT [] is_a: SO:0000424 ! U3_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000430 name: R_three_prime_LTR_region def: "The R segment of the three-prime long terminal repeat." [] synonym: "R 3' long terminal repeat region" EXACT [] synonym: "R three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000431 name: U3_three_prime_LTR_region def: "The U3 segment of the three-prime long terminal repeat." [] synonym: "U3 3' long terminal repeat region" EXACT [] synonym: "U3 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000432 name: U5_three_prime_LTR_region def: "The U5 segment of the three-prime long terminal repeat." [] synonym: "U5 3' long terminal repeat region" EXACT [] synonym: "U5 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000433 name: non_LTR_retrotransposon_polymeric_tract def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:non_ltr_retrotransposon_polymeric_tract" EXACT [] synonym: "non LTR retrotransposon polymeric tract" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000434 name: target_site_duplication def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html] synonym: "target site duplication" EXACT [] is_a: SO:0000314 ! direct_repeat intersection_of: SO:0000314 ! direct_repeat intersection_of: derives_from SO:0000101 ! transposable_element relationship: derives_from SO:0000101 ! transposable_element [Term] id: SO:0000435 name: RR_tract def: "A polypurine tract within an LTR_retrotransposon." [SO:ke] synonym: "LTR retrotransposon poly purine tract" RELATED [] synonym: "RR tract" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000436 name: ARS def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] subset: SOFA synonym: "autonomously replicating sequence" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000437 name: assortment_derived_duplication is_obsolete: true [Term] id: SO:0000438 name: gene_not_polyadenylated is_obsolete: true [Term] id: SO:0000439 name: inverted_ring_chromosome def: "A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome." [] synonym: "inverted ring chromosome" EXACT [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000045 ! ring_chromosome [Term] id: SO:0000440 name: vector_replicon def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "vector" EXACT [] synonym: "vector replicon" EXACT [] xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki" is_a: SO:0001235 ! replicon relationship: part_of SO:0000151 ! clone [Term] id: SO:0000441 name: ss_oligo def: "A single stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" EXACT [] synonym: "ss oligo" EXACT [] synonym: "ss oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo def: "A double stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "double stranded oligonucleotide" EXACT [] synonym: "ds oligo" EXACT [] synonym: "ds-oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000443 name: polymer_attribute def: "An attribute to describe the kind of biological sequence." [SO:ke] synonym: "polymer attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000444 name: three_prime_noncoding_exon def: "Non-coding exon in the 3' UTR." [SO:ke] synonym: "three prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000445 name: five_prime_noncoding_exon def: "Non-coding exon in the 5' UTR." [SO:ke] synonym: "5' nc exon" EXACT [] synonym: "5' non coding exon" EXACT [] synonym: "five prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000446 name: UTR_intron def: "Intron located in the untranslated region." [SO:ke] synonym: "UTR intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000447 name: five_prime_UTR_intron def: "An intron located in the 5' UTR." [SO:ke] synonym: "five prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000448 name: three_prime_UTR_intron def: "An intron located in the 3' UTR." [SO:ke] synonym: "three prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000449 name: random_sequence def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma] synonym: "random sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000450 name: interband def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma] synonym: "chromosome interband" RELATED [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000451 name: gene_with_polyadenylated_mRNA def: "A gene that encodes a polyadenylated mRNA." [SO:xp] synonym: "gene with polyadenylated mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: transcribed_to SO:0000871 ! polyadenylated_mRNA relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA [Term] id: SO:0000452 name: transgene_attribute is_obsolete: true [Term] id: SO:0000453 name: chromosomal_transposition def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke] synonym: "chromosomal transposition" EXACT [] synonym: "transposition" NARROW [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000454 name: rasiRNA def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284, PMID:18032451] comment: Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:rasiRNA" EXACT [] synonym: "repeat associated small interfering RNA" EXACT [] is_a: SO:0001035 ! piRNA [Term] id: SO:0000455 name: gene_with_mRNA_with_frameshift def: "A gene that encodes an mRNA with a frameshift." [SO:xp] synonym: "gene with mRNA with frameshift" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000865 ! frameshift relationship: has_quality SO:0000865 ! frameshift [Term] id: SO:0000456 name: recombinationally_rearranged_gene def: "A gene that is recombinationally rearranged." [SO:ke] synonym: "recombinationally rearranged gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000940 ! recombinationally_rearranged relationship: has_quality SO:0000940 ! recombinationally_rearranged [Term] id: SO:0000457 name: interchromosomal_duplication def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke] synonym: "interchromosomal duplication" EXACT [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:0000458 name: D_gene_segment def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D gene" EXACT [] synonym: "D-GENE" EXACT [] synonym: "INSDC_feature:D_segment" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000459 name: gene_with_trans_spliced_transcript def: "A gene with a transcript that is trans-spliced." [SO:xp] synonym: "gene with trans spliced transcript" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: transcribed_to SO:0000479 ! trans_spliced_transcript relationship: transcribed_to SO:0000479 ! trans_spliced_transcript [Term] id: SO:0000460 name: vertebrate_immunoglobulin_T_cell_receptor_segment def: "Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor." [] comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'. synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000461 name: inversion_derived_bipartite_deficiency def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] synonym: "inversion derived bipartite deficiency" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000462 name: pseudogenic_region def: "A non-functional descendant of a functional entity." [SO:cjm] subset: SOFA synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000463 name: encodes_alternately_spliced_transcripts def: "A gene that encodes more than one transcript." [SO:ke] synonym: "encodes alternately spliced transcripts" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000464 name: decayed_exon def: "A non-functional descendant of an exon." [SO:ke] comment: Does not have to be part of a pseudogene. subset: SOFA synonym: "decayed exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon [Term] id: SO:0000465 name: inversion_derived_deficiency_plus_duplication def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus duplication" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000466 name: V_gene_segment def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "INSDC_feature:V_segment" EXACT [] synonym: "V gene" EXACT [] synonym: "V gene segment" EXACT [] synonym: "V-GENE" EXACT [] synonym: "variable_gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000467 name: post_translationally_regulated_by_protein_stability def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke] synonym: "post translationally regulated by protein stability" EXACT [] synonym: "post-translationally regulated by protein stability" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000468 name: golden_path_fragment def: "One of the pieces of sequence that make up a golden path." [SO:rd] subset: SOFA synonym: "golden path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000688 ! golden_path [Term] id: SO:0000469 name: post_translationally_regulated_by_protein_modification def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke] synonym: "post translationally regulated by protein modification" EXACT [] synonym: "post-translationally regulated by protein modification" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000470 name: J_gene_segment def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "INSDC_feature:J_segment" EXACT [] synonym: "J gene" EXACT [] synonym: "J-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000471 name: autoregulated def: "The gene product is involved in its own transcriptional regulation." [SO:ke] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000472 name: tiling_path def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] subset: SOFA synonym: "tiling path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000473 name: negatively_autoregulated def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke] synonym: "negatively autoregulated" EXACT [] is_a: SO:0000126 ! transcriptionally_repressed is_a: SO:0000471 ! autoregulated [Term] id: SO:0000474 name: tiling_path_fragment def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] subset: SOFA synonym: "tiling path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000472 ! tiling_path [Term] id: SO:0000475 name: positively_autoregulated def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke] synonym: "positively autoregulated" EXACT [] is_a: SO:0000125 ! transcriptionally_induced is_a: SO:0000471 ! autoregulated [Term] id: SO:0000476 name: contig_read def: "A DNA sequencer read which is part of a contig." [SO:ke] synonym: "contig read" EXACT [] is_a: SO:0000150 ! read [Term] id: SO:0000477 name: polycistronic_gene def: "A gene that is polycistronic." [SO:ke] is_obsolete: true [Term] id: SO:0000478 name: C_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C gene" EXACT [] synonym: "C_GENE" EXACT [] synonym: "constant gene" EXACT [] synonym: "INSDC_feature:C_region" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000479 name: trans_spliced_transcript def: "A transcript that is trans-spliced." [SO:xp] synonym: "INSDC_feature:tRNA" BROAD [] synonym: "INSDC_qualifier:trans_splicing" EXACT [] synonym: "trans spliced transcript" EXACT [] synonym: "trans-spliced transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000870 ! trans_spliced relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000480 name: tiling_path_clone def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke] synonym: "tiling path clone" EXACT [] is_a: SO:0000151 ! clone is_a: SO:0000474 ! tiling_path_fragment [Term] id: SO:0000481 name: terminal_inverted_repeat def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke] synonym: "terminal inverted repeat" EXACT [] synonym: "TIR" EXACT [] is_a: SO:0000294 ! inverted_repeat relationship: part_of SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000482 name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration." [] synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000483 name: nc_primary_transcript def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_coding_exon_noncoding_region def: "The sequence of the 3' exon that is not coding." [SO:ke] subset: SOFA synonym: "three prime coding exon noncoding region" EXACT [] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000485 name: DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-CLUSTER" EXACT [] synonym: "DJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region def: "The sequence of the 5' exon preceding the start codon." [SO:ke] subset: SOFA synonym: "five prime coding exon noncoding region" EXACT [] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000487 name: VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-C-CLUSTER" EXACT [] synonym: "VDJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000488 name: VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-CLUSTER" EXACT [] synonym: "VDJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000489 name: VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-C-CLUSTER" RELATED [] synonym: "VJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000490 name: VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-C-CLUSTER" EXACT [] synonym: "VJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000491 name: VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-CLUSTER" EXACT [] synonym: "VJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000492 name: D_gene_recombination_feature def: "Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence." [] synonym: "D gene recombination feature" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000493 name: three_prime_D_heptamer def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-HEPTAMER" EXACT [] synonym: "three prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000494 name: three_prime_D_nonamer def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-NOMAMER" EXACT [] synonym: "three prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000495 name: three_prime_D_spacer def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-SPACER" EXACT [] synonym: "three prime D spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000496 name: five_prime_D_heptamer def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-HEPTAMER" EXACT [] synonym: "five prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000497 name: five_prime_D_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-NONAMER" EXACT [] synonym: "five prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000498 name: five_prime_D_spacer def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'-SPACER" EXACT [] synonym: "five prime D spacer" EXACT [] synonym: "five prime D-spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000499 name: virtual_sequence def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] subset: SOFA synonym: "virtual sequence" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000500 name: Hoogsteen_base_pair def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293] synonym: "Hoogsteen base pair" EXACT [] xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0000501 name: reverse_Hoogsteen_base_pair def: "A type of non-canonical base-pairing." [SO:ke] synonym: "reverse Hoogsteen base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000502 name: transcribed_region def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. subset: SOFA is_obsolete: true [Term] id: SO:0000503 name: alternately_spliced_gene_encodeing_one_transcript is_obsolete: true [Term] id: SO:0000504 name: D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ C cluster" EXACT [] synonym: "D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000505 name: D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ cluster" EXACT [] synonym: "D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000506 name: D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J C cluster" EXACT [] synonym: "D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000507 name: pseudogenic_exon def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke] comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "pseudogenic exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon relationship: part_of SO:0000516 ! pseudogenic_transcript [Term] id: SO:0000508 name: D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J cluster" EXACT [] synonym: "D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000509 name: D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J C cluster" EXACT [] synonym: "D-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000510 name: VD_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V_D_GENE" EXACT [] synonym: "VD gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000511 name: J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J C cluster" EXACT [] synonym: "J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000512 name: inversion_derived_deficiency_plus_aneuploid def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus aneuploid" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000513 name: J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J cluster" EXACT [] synonym: "J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000514 name: J_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J nonamer" EXACT [] synonym: "J-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000515 name: J_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J heptamer" EXACT [] synonym: "J-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000516 name: pseudogenic_transcript def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke] comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "INSDC_feature:misc_RNA" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "pseudogenic transcript" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000673 ! transcript relationship: part_of SO:0000336 ! pseudogene [Term] id: SO:0000517 name: J_spacer def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J spacer" EXACT [] synonym: "J-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000518 name: V_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ cluster" EXACT [] synonym: "V-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000519 name: V_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J cluster" EXACT [] synonym: "V-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000520 name: V_VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ C cluster" EXACT [] synonym: "V-(VDJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000521 name: V_VDJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ cluster" EXACT [] synonym: "V-(VDJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000522 name: V_VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J cluster" EXACT [] synonym: "V-(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000523 name: V_VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ C cluster" EXACT [] synonym: "V-(VJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000524 name: V_VJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ cluster" EXACT [] synonym: "V-(VJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000525 name: V_VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J cluster" EXACT [] synonym: "V-(VJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000526 name: V_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V cluster" EXACT [] synonym: "V-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment [Term] id: SO:0000527 name: V_D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ C cluster" EXACT [] synonym: "V-D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000528 name: V_D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ cluster" EXACT [] synonym: "V-D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000529 name: V_D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J C cluster" EXACT [] synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000530 name: V_D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J cluster" EXACT [] synonym: "V-D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000531 name: V_D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J C cluster" EXACT [] synonym: "V-D-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000532 name: V_D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J cluster" EXACT [] synonym: "V-D-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000533 name: V_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V heptamer" EXACT [] synonym: "V-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000534 name: V_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J cluster" EXACT [] synonym: "V-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000535 name: V_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J C cluster" EXACT [] synonym: "V-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000536 name: V_nonamer def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V nonamer" EXACT [] synonym: "V-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000537 name: V_spacer def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V spacer" EXACT [] synonym: "V-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000538 name: V_gene_recombination_feature def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V gene recombination feature" EXACT [] synonym: "V-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000539 name: DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-C-CLUSTER" EXACT [] synonym: "DJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000540 name: DJ_J_C_cluster def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-C-CLUSTER" EXACT [] synonym: "DJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000541 name: VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-C-CLUSTER" EXACT [] synonym: "VDJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000542 name: V_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ C cluster" EXACT [] synonym: "V-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000543 name: alternately_spliced_gene_encoding_greater_than_one_transcript is_obsolete: true [Term] id: SO:0000544 name: helitron def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569] synonym: "ISCR" RELATED [] xref: http://en.wikipedia.org/wiki/Helitron "wiki" is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000545 name: recoding_pseudoknot def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937] synonym: "recoding pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot relationship: part_of SO:1001268 ! recoding_stimulatory_region [Term] id: SO:0000546 name: designed_sequence def: "An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence." [] synonym: "designed sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000547 name: inversion_derived_bipartite_duplication def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km] synonym: "inversion derived bipartite duplication" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000548 name: gene_with_edited_transcript def: "A gene that encodes a transcript that is edited." [SO:xp] synonym: "gene with edited transcript" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: transcribed_to SO:0000873 ! edited_transcript relationship: transcribed_to SO:0000873 ! edited_transcript [Term] id: SO:0000549 name: inversion_derived_duplication_plus_aneuploid def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived duplication plus aneuploid" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000550 name: aneuploid_chromosome def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke] comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. synonym: "aneuploid chromosome" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000551 name: polyA_signal_sequence def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.insdc.org/files/feature_table.html] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:polyA_signal_sequence" EXACT [] synonym: "poly(A) signal" EXACT [] synonym: "polyA signal sequence" EXACT [] synonym: "polyadenylation termination signal" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000552 name: Shine_Dalgarno_sequence def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] comment: Not found in Eukaryotic sequence. synonym: "five prime ribosome binding site" EXACT [] synonym: "RBS" RELATED [] synonym: "Shine Dalgarno sequence" EXACT [] synonym: "Shine-Dalgarno sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000553 name: polyA_site alt_id: SO:0001430 def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.insdc.org/files/feature_table.html] subset: SOFA synonym: "INSDC_feature:polyA_site" EXACT [] synonym: "polyA cleavage site" EXACT [] synonym: "polyA junction" EXACT [] synonym: "polyA site" EXACT [] synonym: "polyA_junction" EXACT [] synonym: "polyadenylation site" RELATED [] is_a: SO:0000699 ! junction relationship: part_of SO:0000205 ! three_prime_UTR relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000554 name: assortment_derived_deficiency_plus_duplication is_obsolete: true [Term] id: SO:0000555 name: five_prime_clip def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.insdc.org/files/feature_table.html] synonym: "5' clip" RELATED [] synonym: "five prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000556 name: five_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'RS" EXACT [] synonym: "five prime D recombination signal sequence" EXACT [] synonym: "five prime D-recombination signal sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000557 name: three_prime_clip def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.insdc.org/files/feature_table.html] synonym: "3'-clip" EXACT [] synonym: "three prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000558 name: C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C cluster" EXACT [] synonym: "C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000559 name: D_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D cluster" EXACT [] synonym: "D-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment [Term] id: SO:0000560 name: D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J cluster" EXACT [] synonym: "D-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000561 name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "HEPTAMER" RELATED [] synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000562 name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene def: "Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [] synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000563 name: vertebrate_immune_system_gene_recombination_spacer def: "A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase." [] synonym: "vertebrate immune system gene recombination spacer" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000564 name: V_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J C cluster" EXACT [] synonym: "V-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000565 name: V_VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J C cluster" EXACT [] synonym: "V-(VDJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000566 name: V_VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J C cluster" EXACT [] synonym: "V-(VJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000567 name: inversion_derived_aneuploid_chromosome def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] synonym: "inversion derived aneuploid chromosome" EXACT [] is_a: SO:0000550 ! aneuploid_chromosome [Term] id: SO:0000568 name: bidirectional_promoter def: "A promoter that can allow for transcription in both directions." [PMID:21601935, SO:ke] comment: Definition updated in Aug 2020 by Dave Sant. synonym: "bidirectional promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0000569 name: retrotransposed alt_id: SO:0100042 def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke] comment: GO:0003964 RNA-directed DNA polymerase activity. xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000570 name: three_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-RS" EXACT [] synonym: "three prime D recombination signal sequence" EXACT [] synonym: "three_prime_D-recombination_signal_sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000571 name: miRNA_encoding def: "A region that can be transcribed into a microRNA (miRNA)." [] synonym: "miRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000572 name: DJ_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D-J-GENE" EXACT [] synonym: "DJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000573 name: rRNA_encoding def: "A region that can be transcribed into a ribosomal RNA (rRNA)." [] synonym: "rRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000574 name: VDJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-D-J-GENE" EXACT [] synonym: "VDJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000575 name: scRNA_encoding def: "A region that can be transcribed into a small cytoplasmic RNA (scRNA)." [] synonym: "scRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000576 name: VJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-J-GENE" EXACT [] synonym: "VJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000577 name: centromere def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA synonym: "INSDC_feature:centromere" EXACT [] xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000578 name: snoRNA_encoding def: "A region that can be transcribed into a small nucleolar RNA (snoRNA)." [] synonym: "snoRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000579 name: edited_transcript_feature def: "A locatable feature on a transcript that is edited." [SO:ma] synonym: "edited transcript feature" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000580 name: methylation_guide_snoRNA_primary_transcript def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke] synonym: "methylation guide snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000581 name: cap def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] subset: SOFA xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000582 name: rRNA_cleavage_snoRNA_primary_transcript def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] synonym: "rRNA cleavage snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000583 name: pre_edited_region def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "pre edited region" EXACT [] synonym: "pre-edited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000584 name: tmRNA def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] synonym: "10Sa RNA" RELATED [] synonym: "INSDC_feature:tmRNA" EXACT [] synonym: "ssrA" RELATED [] xref: http://en.wikipedia.org/wiki/TmRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000585 name: C_D_box_snoRNA_encoding def: "snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end." [] synonym: "C/D box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000586 name: tmRNA_primary_transcript def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke] synonym: "10Sa RNA primary transcript" RELATED [] synonym: "ssrA RNA primary transcript" RELATED [] synonym: "tmRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000587 name: group_I_intron def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:autocatalytically_spliced_intron" EXACT [] is_a: SO:0000188 ! intron intersection_of: SO:0000188 ! intron intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000589 name: SRP_RNA_primary_transcript def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke] synonym: "SRP RNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000590 name: SRP_RNA def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] subset: SOFA synonym: "7S RNA" RELATED [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:SRP_RNA" EXACT [] synonym: "signal recognition particle RNA" RELATED [] synonym: "SRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript [Term] id: SO:0000591 name: pseudoknot def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb] xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000592 name: H_pseudoknot def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract] synonym: "classical pseudoknot" EXACT [] synonym: "H pseudoknot" EXACT [] synonym: "H-pseudoknot" EXACT [] synonym: "H-type pseudoknot" EXACT [] synonym: "hairpin-type pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot [Term] id: SO:0000593 name: C_D_box_snoRNA def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577. subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] synonym: "SNORD" EXACT [PMID:31828325] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript [Term] id: SO:0000594 name: H_ACA_box_snoRNA def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577. synonym: "box H/ACA snoRNA" EXACT [] synonym: "H ACA box snoRNA" EXACT [] synonym: "H/ACA box snoRNA" EXACT [] synonym: "SNORA" EXACT [PMID:31828325] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript [Term] id: SO:0000595 name: C_D_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke] synonym: "C/D box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000596 name: H_ACA_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke] synonym: "H ACA box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000597 name: transcript_edited_by_U_insertion/deletion def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html] is_obsolete: true [Term] id: SO:0000598 name: edited_by_C_insertion_and_dinucleotide_insertion synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED [] is_obsolete: true [Term] id: SO:0000599 name: edited_by_C_to_U_substitution is_obsolete: true [Term] id: SO:0000600 name: edited_by_A_to_I_substitution is_obsolete: true [Term] id: SO:0000601 name: edited_by_G_addition is_obsolete: true [Term] id: SO:0000602 name: guide_RNA def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" EXACT [] synonym: "guide RNA" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:guide_RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000603 name: group_II_intron def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] comment: GO:0000373. subset: SOFA synonym: "group II intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000604 name: editing_block def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing block" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000605 name: intergenic_region def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000606 name: editing_domain def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing domain" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000607 name: unedited_region def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "unedited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000608 name: H_ACA_box_snoRNA_encoding def: "snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA)." [] synonym: "H ACA box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000609 name: oligo_U_tail def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] synonym: "oligo U tail" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000602 ! guide_RNA [Term] id: SO:0000610 name: polyA_sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] subset: SOFA synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch point" EXACT [] synonym: "branch site" EXACT [] synonym: "branch_point" EXACT [] is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000612 name: polypyrimidine_tract def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] subset: SOFA synonym: "polypyrimidine tract" EXACT [] xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000613 name: bacterial_RNApol_promoter def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC. synonym: "bacterial RNApol promoter" EXACT [] is_a: SO:0002222 ! prokaryotic_promoter [Term] id: SO:0000614 name: bacterial_terminator def: "A terminator signal for bacterial transcription." [SO:ke] comment: Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529. synonym: "bacterial terminator" EXACT [] is_a: SO:0000141 ! terminator [Term] id: SO:0000615 name: terminator_of_type_2_RNApol_III_promoter def: "A terminator signal for RNA polymerase III transcription." [SO:ke] synonym: "terminator of type 2 RNApol III promoter" EXACT [] is_a: SO:0000951 ! eukaryotic_terminator [Term] id: SO:0000616 name: transcription_end_site def: "The base where transcription ends." [SO:ke] subset: SOFA synonym: "transcription end site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000617 name: RNApol_III_promoter_type_1 def: "This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species." [PMID:12381659] synonym: "RNApol III promoter type 1" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000618 name: RNApol_III_promoter_type_2 def: "This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box." [PMID:12381659] synonym: "RNApol III promoter type 2" EXACT [] synonym: "tRNA promoter" RELATED [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000619 name: A_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] comment: Binds TFIIIC. synonym: "A-box" EXACT [] xref: http://en.wikipedia.org/wiki/A-box "wiki" is_a: SO:0001660 ! core_eukaryotic_promoter_element [Term] id: SO:0000620 name: B_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] comment: Binds TFIIIC. synonym: "B-box" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 def: "This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. " [PMID:12381659] synonym: "RNApol III promoter type 3" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000622 name: C_box def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke] synonym: "C-box" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 [Term] id: SO:0000623 name: snRNA_encoding def: "A region that can be transcribed into a small nuclear RNA (snRNA)." [] synonym: "snRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000624 name: telomere def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "INSDC_feature:telomere" EXACT [] synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:silencer" EXACT [] xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000626 name: chromosomal_regulatory_element def: "Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix." [] synonym: "chromosomal regulatory element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000627 name: insulator def: "A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region." [NCBI:cf, PMID:12154228, SO:regcreative] comment: moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:insulator" EXACT [] synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000628 name: chromosomal_structural_element def: "Regions of the chromosome that are important for structural elements." [] subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000629 name: five_prime_open_reading_frame def: "An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame." [PMID:12890013] synonym: "five prime open reading frame" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000630 name: upstream_AUG_codon def: "A start codon upstream of the ORF." [SO:ke] synonym: "upstream AUG codon" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000631 name: polycistronic_primary_transcript def: "A primary transcript encoding for more than one gene product." [SO:ke] synonym: "polycistronic primary transcript" EXACT [] is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000185 ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000632 name: monocistronic_primary_transcript def: "A primary transcript encoding for one gene product." [SO:ke] synonym: "monocistronic primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript is_a: SO:0000665 ! monocistronic_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000633 name: monocistronic_mRNA def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] synonym: "monocistronic mRNA" EXACT [] synonym: "monocistronic processed transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki" is_a: SO:0000234 ! mRNA is_a: SO:0000665 ! monocistronic_transcript intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000634 name: polycistronic_mRNA def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] synonym: "polycistronic mRNA" EXACT [] synonym: "polycistronic processed transcript" RELATED [] xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki" is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000635 name: mini_exon_donor_RNA def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke] synonym: "mini exon donor RNA" EXACT [] synonym: "mini-exon donor RNA" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000636 name: spliced_leader_RNA def: "Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes." [PMID:24130571] synonym: "mini-exon" RELATED [] synonym: "spliced leader RNA" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000635 ! mini_exon_donor_RNA [Term] id: SO:0000637 name: engineered_plasmid def: "A plasmid that is engineered." [SO:xp] synonym: "engineered plasmid" EXACT [] synonym: "engineered plasmid gene" RELATED [] is_a: SO:0000155 ! plasmid is_a: SO:0000804 ! engineered_region intersection_of: SO:0000155 ! plasmid intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000638 name: transcribed_spacer_region def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html] synonym: "transcribed spacer region" EXACT [] is_a: SO:0000838 ! rRNA_primary_transcript_region [Term] id: SO:0000639 name: internal_transcribed_spacer_region def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke] synonym: "internal transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000640 name: external_transcribed_spacer_region def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke] synonym: "external transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000641 name: tetranucleotide_repeat_microsatellite_feature def: "A region of a repeating tetranucleotide sequence (four bases)." [] synonym: "tetranucleotide repeat microsatellite feature" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000642 name: SRP_RNA_encoding def: "A region that can be transcribed into a signal recognition particle RNA (SRP RNA)." [] synonym: "SRP RNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000643 name: minisatellite def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:minisatellite" EXACT [] synonym: "VNTR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/] xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000644 name: antisense_RNA def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:antisense_RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000645 ! antisense_primary_transcript [Term] id: SO:0000645 name: antisense_primary_transcript def: "The reverse complement of the primary transcript." [SO:ke] subset: SOFA synonym: "antisense primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000646 name: siRNA def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:siRNA" EXACT [] synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000647 name: miRNA_primary_transcript alt_id: SO:0000648 def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] synonym: "small temporal RNA primary transcript" EXACT [] synonym: "stRNA primary transcript" EXACT [] synonym: "stRNA_primary_transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA [Term] id: SO:0000650 name: cytosolic_SSU_rRNA def: "Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes." [SO:ke] comment: Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic small subunit rRNA" EXACT [] synonym: "cytosolic SSU ribosomal RNA" EXACT [] synonym: "cytosolic SSU rRNA" EXACT [] is_a: SO:0002343 ! cytosolic_rRNA relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript [Term] id: SO:0000651 name: cytosolic_LSU_rRNA def: "Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes." [SO:ke] comment: Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic large subunit rRNA" EXACT [] synonym: "cytosolic LSU RNA" EXACT [] synonym: "cytosolic LSU rRNA" EXACT [] is_a: SO:0002343 ! cytosolic_rRNA relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript [Term] id: SO:0000652 name: cytosolic_5S_rRNA def: "Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 5S LSU rRNA" EXACT [] synonym: "cytosolic 5S ribosomal RNA" EXACT [] synonym: "cytosolic 5S rRNA" EXACT [] synonym: "cytosolic rRNA 5S" EXACT [] xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002238 ! cytosolic_rRNA_5S_gene [Term] id: SO:0000653 name: cytosolic_28S_rRNA def: "Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes." [SO:ke] comment: Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 28S LSU rRNA" EXACT [] synonym: "cytosolic 28S ribosomal RNA" EXACT [] synonym: "cytosolic 28S rRNA" EXACT [] synonym: "cytosolic rRNA 28S" EXACT [] xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002239 ! cytosolic_rRNA_28S_gene [Term] id: SO:0000654 name: maxicircle_gene def: "A mitochondrial gene located in a maxicircle." [SO:xp] synonym: "maxi-circle gene" EXACT [] synonym: "maxicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: part_of SO:0000742 ! maxicircle relationship: part_of SO:0000742 ! maxicircle [Term] id: SO:0000655 name: ncRNA def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "INSDC_qualifier:other" BROAD [] synonym: "known_ncrna" EXACT [] synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000656 name: stRNA_encoding def: "A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development." [] synonym: "stRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000657 name: repeat_region def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:other" EXACT [] synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region relationship: has_part SO:0000726 ! repeat_unit [Term] id: SO:0000658 name: dispersed_repeat def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "dispersed repeat" EXACT [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:dispersed" EXACT [] synonym: "interspersed repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000659 name: tmRNA_encoding def: "A region that can be transcribed into a transfer-messenger RNA (tmRNA)." [] synonym: "tmRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000660 name: DNA_invertase_target_sequence is_obsolete: true [Term] id: SO:0000661 name: intron_attribute is_obsolete: true [Term] id: SO:0000662 name: spliceosomal_intron def: "An intron which is spliced by the spliceosome." [SO:ke] comment: GO:0000398. subset: SOFA synonym: "spliceosomal intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000663 name: tRNA_encoding def: "A region that can be transcribed into a transfer RNA (tRNA)." [] synonym: "tRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000664 name: introgressed_chromosome_region def: "A region of a chromosome that has been introduced by backcrossing with a separate species." [PMID:11454782] synonym: "introgressed chromosome region" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000665 name: monocistronic_transcript def: "A transcript that is monocistronic." [SO:xp] synonym: "monocistronic transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000666 name: mobile_intron def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke] synonym: "mobile intron" EXACT [] is_a: SO:0000188 ! intron is_a: SO:0001037 ! mobile_genetic_element intersection_of: SO:0000188 ! intron intersection_of: has_quality SO:0001234 ! mobile relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0000667 name: insertion alt_id: SO:1000034 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] subset: DBVAR subset: SOFA synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] xref: loinc:LA6687-3 "Insertion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000668 name: EST_match def: "A match against an EST sequence." [SO:ke] subset: SOFA synonym: "EST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000669 name: sequence_rearrangement_feature def: "A feature where a segment of DNA has been rearranged from what it was in the parent cell." [] synonym: "sequence rearrangement feature" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000670 name: chromosome_breakage_sequence def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma] synonym: "chromosome breakage sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000671 name: internal_eliminated_sequence def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma] synonym: "internal eliminated sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000672 name: macronucleus_destined_segment def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma] synonym: "macronucleus destined segment" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000673 name: transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] comment: Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020. subset: SOFA synonym: "INSDC_feature:misc_RNA" BROAD [] xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region relationship: overlaps SO:0002300 ! unit_of_gene_expression [Term] id: SO:0000674 name: non_canonical_splice_site def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke] synonym: "non canonical splice site" EXACT [] synonym: "non-canonical splice site" EXACT [] is_obsolete: true consider: SO:0000678 consider: SO:0000679 [Term] id: SO:0000675 name: canonical_splice_site def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke] synonym: "canonical splice site" EXACT [] is_obsolete: true consider: SO:0000676 consider: SO:0000677 [Term] id: SO:0000676 name: canonical_three_prime_splice_site def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke] synonym: "canonical 3' splice site" EXACT [] synonym: "canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000677 name: canonical_five_prime_splice_site def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke] synonym: "canonical 5' splice site" EXACT [] synonym: "canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000678 name: non_canonical_three_prime_splice_site def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke] synonym: "non canonical 3' splice site" RELATED [] synonym: "non canonical three prime splice site" EXACT [] synonym: "non-canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000679 name: non_canonical_five_prime_splice_site def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke] synonym: "non canonical 5' splice site" EXACT [] synonym: "non canonical five prime splice site" EXACT [] synonym: "non-canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000680 name: non_canonical_start_codon def: "A start codon that is not the usual AUG sequence." [SO:ke] synonym: "non ATG start codon" EXACT [] synonym: "non canonical start codon" EXACT [] synonym: "non-canonical start codon" EXACT [] is_a: SO:0000318 ! start_codon [Term] id: SO:0000681 name: aberrant_processed_transcript def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke] synonym: "aberrant processed transcript" EXACT [] is_a: SO:0000673 ! transcript [Term] id: SO:0000682 name: splicing_feature is_obsolete: true [Term] id: SO:0000683 name: exonic_splice_enhancer def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract] synonym: "exonic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer [Term] id: SO:0000684 name: nuclease_sensitive_site def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] subset: SOFA synonym: "nuclease sensitive site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000685 name: DNaseI_hypersensitive_site def: "DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I." [] synonym: "DHS" EXACT [] synonym: "DNaseI hypersensitive site" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:DNase_I_hypersensitive_site" EXACT [] is_a: SO:0000322 ! nuclease_hypersensitive_site [Term] id: SO:0000686 name: translocation_element def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma] synonym: "translocation element" EXACT [] is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:0000687 name: deletion_junction def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] subset: SOFA synonym: "deletion junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000688 name: golden_path def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] subset: SOFA synonym: "golden path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000689 name: cDNA_match def: "A match against cDNA sequence." [SO:ke] subset: SOFA synonym: "cDNA match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000690 name: gene_with_polycistronic_transcript def: "A gene that encodes a polycistronic transcript." [SO:xp] synonym: "gene with polycistronic transcript" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: transcribed_to SO:0000078 ! polycistronic_transcript relationship: transcribed_to SO:0000078 ! polycistronic_transcript [Term] id: SO:0000691 name: cleaved_initiator_methionine alt_id: BS:00067 def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR] subset: biosapiens synonym: "cleaved initiator methionine" EXACT [] synonym: "init_met" RELATED [uniprot:feature_type] synonym: "initiator methionine" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000692 name: gene_with_dicistronic_transcript def: "A gene that encodes a dicistronic transcript." [SO:xp] synonym: "gene with dicistronic transcript" EXACT [] is_a: SO:0000690 ! gene_with_polycistronic_transcript intersection_of: SO:0000690 ! gene_with_polycistronic_transcript intersection_of: transcribed_to SO:0000079 ! dicistronic_transcript relationship: transcribed_to SO:0000079 ! dicistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA def: "A gene that encodes an mRNA that is recoded." [SO:xp] synonym: "gene with recoded mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000881 ! recoded relationship: has_quality SO:0000881 ! recoded [Term] id: SO:0000694 name: SNP def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:0001483 ! SNV [Term] id: SO:0000695 name: reagent def: "A sequence used in experiment." [SO:ke] comment: Requested by Lynn Crosby, jan 2006. subset: SOFA is_a: SO:0001409 ! biomaterial_region [Term] id: SO:0000696 name: oligo def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] subset: SOFA synonym: "oligonucleotide" EXACT [] xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000697 name: gene_with_stop_codon_read_through def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp] synonym: "gene with stop codon read through" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_part SO:0000883 ! stop_codon_read_through relationship: has_part SO:0000883 ! stop_codon_read_through [Term] id: SO:0000698 name: gene_with_stop_codon_redefined_as_pyrrolysine def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] synonym: "gene with stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine [Term] id: SO:0000699 name: junction def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000700 name: remark def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000701 name: possible_base_call_error def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] subset: SOFA synonym: "possible base call error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000702 name: possible_assembly_error def: "A region of sequence where there may have been an error in the assembly." [SO:ke] subset: SOFA synonym: "possible assembly error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000703 name: experimental_result_region def: "A region of sequence implicated in an experimental result." [SO:ke] subset: SOFA synonym: "experimental result region" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000704 name: gene def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA synonym: "INSDC_feature:gene" EXACT [] xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:tandem" EXACT [] synonym: "tandem repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html is_a: SO:0000657 ! repeat_region [Term] id: SO:0000706 name: trans_splice_acceptor_site def: "The 3' splice site of the acceptor primary transcript." [SO:ke] comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. subset: SOFA synonym: "3' trans splice site" RELATED [] synonym: "trans splice acceptor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000707 name: trans_splice_donor_site def: "The 5' five prime splice site region of the donor RNA." [SO:ke] comment: SL RNA contains a donor site. synonym: "5 prime trans splice site" RELATED [] synonym: "trans splice donor site" EXACT [] synonym: "trans-splice donor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000708 name: SL1_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw] synonym: "SL1 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000709 name: SL2_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL2 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000710 name: gene_with_stop_codon_redefined_as_selenocysteine def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] synonym: "gene with stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine [Term] id: SO:0000711 name: gene_with_mRNA_recoded_by_translational_bypass def: "A gene with mRNA recoded by translational bypass." [SO:xp] synonym: "gene with mRNA recoded by translational bypass" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass relationship: has_quality SO:0000886 ! recoded_by_translational_bypass [Term] id: SO:0000712 name: gene_with_transcript_with_translational_frameshift def: "A gene encoding a transcript that has a translational frameshift." [SO:xp] synonym: "gene with transcript with translational frameshift" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_quality SO:0000887 ! translationally_frameshifted relationship: has_quality SO:0000887 ! translationally_frameshifted [Term] id: SO:0000713 name: DNA_motif def: "A motif that is active in the DNA form of the sequence." [SO:ke] synonym: "DNA motif" EXACT [] xref: http://en.wikipedia.org/wiki/DNA_motif "wiki" is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000714 name: nucleotide_motif def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:nucleotide_motif" EXACT [] synonym: "nucleotide motif" EXACT [] is_a: SO:0001683 ! sequence_motif [Term] id: SO:0000715 name: RNA_motif def: "A motif that is active in RNA sequence." [SO:ke] subset: SOFA synonym: "RNA motif" EXACT [] is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000716 name: dicistronic_mRNA def: "An mRNA that has the quality dicistronic." [SO:ke] synonym: "dicistronic mRNA" EXACT [] synonym: "dicistronic processed transcript" RELATED [] is_a: SO:0000079 ! dicistronic_transcript is_a: SO:0000634 ! polycistronic_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:0000717 name: reading_frame def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. subset: SOFA synonym: "reading frame" EXACT [] xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000718 name: blocked_reading_frame def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb] comment: Term requested by Rama from SGD. synonym: "blocked reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000719 name: ultracontig def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] subset: SOFA synonym: "pseudochromosome" EXACT [] synonym: "superscaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly [Term] id: SO:0000720 name: foreign_transposable_element def: "A transposable element that is foreign." [SO:ke] comment: requested by Michael on 19 Nov 2004. synonym: "foreign transposable element" EXACT [] is_a: SO:0000101 ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000721 name: gene_with_dicistronic_primary_transcript def: "A gene that encodes a dicistronic primary transcript." [SO:xp] comment: Requested by Michael, 19 nov 2004. synonym: "gene with dicistronic primary transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: transcribed_to SO:1001197 ! dicistronic_primary_transcript relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript [Term] id: SO:0000722 name: gene_with_dicistronic_mRNA def: "A gene that encodes a polycistronic mRNA." [SO:xp] comment: Requested by MA nov 19 2004. synonym: "gene with dicistronic mRNA" EXACT [] synonym: "gene with dicistronic processed transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: transcribed_to SO:0000716 ! dicistronic_mRNA relationship: transcribed_to SO:0000716 ! dicistronic_mRNA [Term] id: SO:0000723 name: iDNA def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma] synonym: "INSDC_feature:iDNA" EXACT [] synonym: "intervening DNA" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000724 name: oriT def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.insdc.org/files/feature_table.html] subset: SOFA synonym: "INSDC_feature:oriT" EXACT [] synonym: "origin of transfer" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000725 name: transit_peptide alt_id: BS:00055 def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.insdc.org/files/feature_table.html] comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. subset: biosapiens subset: SOFA synonym: "INSDC_feature:transit_peptide" EXACT [] synonym: "signal" RELATED [] synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: SO:0001527 ! peptide_localization_signal relationship: derives_from SO:0002252 ! transit_peptide_region_of_CDS [Term] id: SO:0000726 name: repeat_unit def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] comment: Added to comply with the feature table. A single repeat. synonym: "repeat unit" EXACT [] xref: http://www.insdc.org/files/feature_table.html is_a: SO:0001411 ! biological_region [Term] id: SO:0000727 name: cis_regulatory_module def: "A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs." [PMID:19660565, SO:SG] comment: Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "CRM" EXACT [] synonym: "TF module" EXACT [] synonym: "transcription factor module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000728 name: intein def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke] comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein. synonym: "protein intron" RELATED [] xref: http://en.wikipedia.org/wiki/Intein "wiki" is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000729 name: intein_containing def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke] synonym: "intein containing" EXACT [] is_a: SO:0000010 ! protein_coding [Term] id: SO:0000730 name: gap def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] subset: SOFA synonym: "INSDC_feature:assembly_gap" NARROW [] synonym: "INSDC_feature:gap" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000353 ! sequence_assembly [Term] id: SO:0000731 name: fragmentary def: "An attribute to describe a feature that is incomplete." [SO:ke] comment: Term added because of request by MO people. synonym: "fragment" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000732 name: predicted def: "An attribute describing an unverified region." [SO:ke] xref: http://en.wikipedia.org/wiki/Predicted "wiki" is_a: SO:0000905 ! status [Term] id: SO:0000733 name: feature_attribute def: "An attribute describing a located_sequence_feature." [SO:ke] synonym: "feature attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000734 name: exemplar_mRNA def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: Added for the MO people. synonym: "exemplar mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000864 ! exemplar relationship: has_quality SO:0000864 ! exemplar [Term] id: SO:0000735 name: sequence_location def: "The location of a sequence." [] synonym: "sequence location" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000736 name: organelle_sequence def: "A sequence of DNA that originates from a an organelle." [] synonym: "organelle sequence" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000737 name: mitochondrial_sequence def: "DNA belonging to the genome of a mitochondria." [] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "mitochondrial sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000738 name: nuclear_sequence def: "DNA belonging to the nuclear genome of cell." [] comment: Moved from is_a SO:0000736 (organelle_sequence) when brought to our attention by GitHub issue #489. synonym: "nuclear sequence" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000739 name: nucleomorphic_sequence def: "DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic." [] synonym: "nucleomorphic sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000740 name: plastid_sequence def: "DNA belonging to the genome of a plastid such as a chloroplast." [] synonym: "plastid sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000741 name: kinetoplast alt_id: SO:0000826 def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055] synonym: "kinetoplast_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki" is_a: SO:0001026 ! genome intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0000742 ! maxicircle intersection_of: has_part SO:0000980 ! minicircle relationship: has_part SO:0000742 ! maxicircle relationship: has_part SO:0000980 ! minicircle [Term] id: SO:0000742 name: maxicircle alt_id: SO:0000827 def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055] synonym: "maxicircle_chromosome" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000743 name: apicoplast_sequence def: "DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid." [] synonym: "apicoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000744 name: chromoplast_sequence def: "DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments." [] synonym: "chromoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000745 name: chloroplast_sequence def: "DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis." [] synonym: "chloroplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000746 name: cyanelle_sequence def: "DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae." [] synonym: "cyanelle sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000747 name: leucoplast_sequence def: "DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil." [] synonym: "leucoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000748 name: proplastid_sequence def: "DNA belonging to the genome of a proplastid such as an immature chloroplast." [] synonym: "proplastid sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000749 name: plasmid_location def: "The location of DNA that has come from a plasmid sequence." [] synonym: "plasmid location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000750 name: amplification_origin def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma] synonym: "amplification origin" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000751 name: proviral_location def: "The location of DNA that has come from a viral origin." [] synonym: "proviral location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000752 name: gene_group_regulatory_region def: "A region that is involved in the regulation of transcription of a group of regulated genes." [] comment: Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529. subset: SOFA synonym: "gene group regulatory region" EXACT [] is_obsolete: true replaced_by: SO:0001055 [Term] id: SO:0000753 name: clone_insert def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] subset: SOFA synonym: "clone insert" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000151 ! clone [Term] id: SO:0000754 name: lambda_vector def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] synonym: "lambda vector" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000755 name: plasmid_vector def: "A plasmid that has been generated to act as a vector for foreign sequence." [] synonym: "plasmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki" is_a: SO:0000440 ! vector_replicon intersection_of: SO:0001235 ! replicon intersection_of: derives_from SO:0000155 ! plasmid relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0000756 name: cDNA def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] synonym: "complementary DNA" EXACT [] xref: http://en.wikipedia.org/wiki/CDNA "wiki" is_a: SO:0000352 ! DNA [Term] id: SO:0000757 name: single_stranded_cDNA def: "DNA synthesized from RNA by reverse transcriptase, single stranded." [] synonym: "single strand cDNA" EXACT [] synonym: "single stranded cDNA" EXACT [] synonym: "single-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000758 name: double_stranded_cDNA def: "DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded." [] synonym: "double strand cDNA" RELATED [] synonym: "double stranded cDNA" EXACT [] synonym: "double-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000759 name: plasmid_clone is_obsolete: true [Term] id: SO:0000760 name: YAC_clone is_obsolete: true [Term] id: SO:0000761 name: phagemid_clone is_obsolete: true [Term] id: SO:0000762 name: PAC_clone synonym: "P1_clone" RELATED [] is_obsolete: true [Term] id: SO:0000763 name: fosmid_clone is_obsolete: true [Term] id: SO:0000764 name: BAC_clone is_obsolete: true [Term] id: SO:0000765 name: cosmid_clone is_obsolete: true [Term] id: SO:0000766 name: pyrrolysyl_tRNA def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke] synonym: "pyrrolysyl tRNA" EXACT [] synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT [] synonym: "pyrrolysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript [Term] id: SO:0000767 name: clone_insert_start is_obsolete: true [Term] id: SO:0000768 name: episome def: "A plasmid that may integrate with a chromosome." [SO:ma] is_a: SO:0000155 ! plasmid [Term] id: SO:0000769 name: tmRNA_coding_piece def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962] comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005. synonym: "tmRNA coding piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000770 name: tmRNA_acceptor_piece def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw] comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005. synonym: "tmRNA acceptor piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000771 name: QTL def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] comment: Added in respose to request by Simon Twigger November 14th 2005. synonym: "quantitative trait locus" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000772 name: genomic_island def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] comment: Genomic islands are transmissible elements characterized by large size (>10kb). synonym: "genomic island" EXACT [] xref: http://en.wikipedia.org/wiki/Genomic_island "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000773 name: pathogenic_island def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke] comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "pathogenic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000774 name: metabolic_island def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. synonym: "metabolic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000775 name: adaptive_island def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke] comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "adaptive island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000776 name: symbiosis_island def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. synonym: "symbiosis island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000777 name: pseudogenic_rRNA def: "A non functional descendant of an rRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "INSDC_feature:rRNA" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "pseudogenic rRNA" EXACT [] is_a: SO:0000516 ! pseudogenic_transcript [Term] id: SO:0000778 name: pseudogenic_tRNA def: "A non functional descendent of a tRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "INSDC_feature:tRNA" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "pseudogenic tRNA" EXACT [] is_a: SO:0000516 ! pseudogenic_transcript [Term] id: SO:0000779 name: engineered_episome def: "An episome that is engineered." [SO:xp] comment: Requested by Lynn Crosby Jan 2006. synonym: "engineered episome" EXACT [] is_a: SO:0000637 ! engineered_plasmid is_a: SO:0000768 ! episome intersection_of: SO:0000768 ! episome intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000780 name: transposable_element_attribute comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs is_obsolete: true [Term] id: SO:0000781 name: transgenic def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000782 name: natural def: "An attribute describing a feature that occurs in nature." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000783 name: engineered def: "An attribute to describe a region that was modified in vitro." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000784 name: foreign def: "An attribute to describe a region from another species." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000785 name: cloned_region def: "The region of sequence that has been inserted and is being propagated by the clone." [] comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. synonym: "cloned region" EXACT [] synonym: "cloned segment" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000786 name: reagent_attribute comment: Added jan 2006 by KE. synonym: "reagent attribute" EXACT [] is_obsolete: true [Term] id: SO:0000787 name: clone_attribute is_obsolete: true [Term] id: SO:0000788 name: cloned is_obsolete: true [Term] id: SO:0000789 name: validated def: "An attribute to describe a feature that has been proven." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000790 name: invalidated def: "An attribute describing a feature that is invalidated." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000791 name: cloned_genomic is_obsolete: true [Term] id: SO:0000792 name: cloned_cDNA is_obsolete: true [Term] id: SO:0000793 name: engineered_DNA is_obsolete: true [Term] id: SO:0000794 name: engineered_rescue_region def: "A rescue region that is engineered." [SO:xp] synonym: "engineered rescue fragment" EXACT [] synonym: "engineered rescue region" EXACT [] synonym: "engineered rescue segment" EXACT [] is_a: SO:0000411 ! rescue_region is_a: SO:0000804 ! engineered_region intersection_of: SO:0000411 ! rescue_region intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000795 name: rescue_mini_gene def: "A mini_gene that rescues." [SO:xp] synonym: "rescue mini gene" EXACT [] synonym: "rescue mini-gene" EXACT [] is_a: SO:0000815 ! mini_gene intersection_of: SO:0000815 ! mini_gene intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000796 name: transgenic_transposable_element def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc] comment: Modified as requested by Lynn - FB. May 2007. synonym: "transgenic transposable element" EXACT [] is_a: SO:0000101 ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: derives_from SO:0000151 ! clone intersection_of: has_quality SO:0000781 ! transgenic relationship: derives_from SO:0000151 ! clone relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000797 name: natural_transposable_element def: "TE that exists (or existed) in nature." [FB:mc] synonym: "natural transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000782 ! natural relationship: has_quality SO:0000782 ! natural [Term] id: SO:0000798 name: engineered_transposable_element def: "TE that has been modified by manipulations in vitro." [FB:mc] synonym: "engineered transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0000804 ! engineered_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000799 name: engineered_foreign_transposable_element def: "A transposable_element that is engineered and foreign." [FB:mc] synonym: "engineered foreign transposable element" EXACT [] is_a: SO:0000720 ! foreign_transposable_element is_a: SO:0000798 ! engineered_transposable_element is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000800 name: assortment_derived_duplication def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment derived duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000801 name: assortment_derived_deficiency_plus_duplication def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm] synonym: "assortment derived deficiency plus duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000802 name: assortment_derived_deficiency def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment-derived deficiency" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000803 name: assortment_derived_aneuploid def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm] synonym: "assortment derived aneuploid" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000804 name: engineered_region def: "A region that is engineered." [SO:xp] synonym: "construct" EXACT [] synonym: "engineered region" EXACT [] synonym: "engineered sequence" EXACT [] is_a: SO:0001409 ! biomaterial_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000805 name: engineered_foreign_region def: "A region that is engineered and foreign." [SO:xp] synonym: "engineered foreign region" EXACT [] is_a: SO:0000804 ! engineered_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000806 name: fusion def: "When two regions of DNA are joined together that are not normally together." [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000807 name: engineered_tag def: "A tag that is engineered." [SO:xp] synonym: "engineered tag" EXACT [] is_a: SO:0000324 ! tag is_a: SO:0000804 ! engineered_region intersection_of: SO:0000324 ! tag intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000808 name: validated_cDNA_clone def: "A cDNA clone that has been validated." [SO:xp] synonym: "validated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000789 ! validated relationship: has_quality SO:0000789 ! validated [Term] id: SO:0000809 name: invalidated_cDNA_clone def: "A cDNA clone that is invalid." [SO:xp] synonym: "invalidated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000790 ! invalidated relationship: has_quality SO:0000790 ! invalidated [Term] id: SO:0000810 name: chimeric_cDNA_clone def: "A cDNA clone invalidated because it is chimeric." [SO:xp] synonym: "chimeric cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA [Term] id: SO:0000811 name: genomically_contaminated_cDNA_clone def: "A cDNA clone invalidated by genomic contamination." [SO:xp] synonym: "genomically contaminated cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000414 ! invalidated_by_genomic_contamination relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination [Term] id: SO:0000812 name: polyA_primed_cDNA_clone def: "A cDNA clone invalidated by polyA priming." [SO:xp] synonym: "polyA primed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA [Term] id: SO:0000813 name: partially_processed_cDNA_clone def: "A cDNA invalidated clone by partial processing." [SO:xp] synonym: "partially processed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000416 ! invalidated_by_partial_processing relationship: has_quality SO:0000416 ! invalidated_by_partial_processing [Term] id: SO:0000814 name: rescue def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000815 name: mini_gene def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] synonym: "mini gene" EXACT [] is_a: SO:0000236 ! ORF [Term] id: SO:0000816 name: rescue_gene def: "A gene that rescues." [SO:xp] synonym: "rescue gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000817 name: wild_type def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke] synonym: "wild type" EXACT [] xref: http://en.wikipedia.org/wiki/Wild_type "wiki" xref: loinc:LA9658-1 "wild type" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000818 name: wild_type_rescue_gene def: "A gene that rescues." [SO:xp] synonym: "wild type rescue gene" EXACT [] is_a: SO:0000816 ! rescue_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000817 ! wild_type relationship: has_quality SO:0000817 ! wild_type [Term] id: SO:0000819 name: mitochondrial_chromosome def: "A chromosome originating in a mitochondria." [SO:xp] synonym: "mitochondrial chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000820 name: chloroplast_chromosome def: "A chromosome originating in a chloroplast." [SO:xp] synonym: "chloroplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! chloroplast_sequence [Term] id: SO:0000821 name: chromoplast_chromosome def: "A chromosome originating in a chromoplast." [SO:xp] synonym: "chromoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! chromoplast_sequence [Term] id: SO:0000822 name: cyanelle_chromosome def: "A chromosome originating in a cyanelle." [SO:xp] synonym: "cyanelle chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! cyanelle_sequence [Term] id: SO:0000823 name: leucoplast_chromosome def: "A chromosome with origin in a leucoplast." [SO:xp] synonym: "leucoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! leucoplast_sequence [Term] id: SO:0000824 name: macronuclear_chromosome def: "A chromosome originating in a macronucleus." [SO:xp] synonym: "macronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000083 ! macronuclear_sequence relationship: has_origin SO:0000083 ! macronuclear_sequence [Term] id: SO:0000825 name: micronuclear_chromosome def: "A chromosome originating in a micronucleus." [SO:xp] synonym: "micronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000084 ! micronuclear_sequence relationship: has_origin SO:0000084 ! micronuclear_sequence [Term] id: SO:0000828 name: nuclear_chromosome def: "A chromosome originating in a nucleus." [SO:xp] synonym: "nuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! nuclear_sequence [Term] id: SO:0000829 name: nucleomorphic_chromosome def: "A chromosome originating in a nucleomorph." [SO:xp] synonym: "nucleomorphic chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! nucleomorphic_sequence [Term] id: SO:0000830 name: chromosome_part def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosomal region" EXACT [] synonym: "chromosomal_region" EXACT [] synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000831 name: gene_member_region def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene [Term] id: SO:0000832 name: promoter_region def: "A region of sequence which is part of a promoter." [SO:ke] comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000833 name: transcript_region def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: mature_transcript_region def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000837 name: UTR_region def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000838 name: rRNA_primary_transcript_region def: "A region of an rRNA primary transcript." [SO:ke] comment: To allow transcribed_spacer_region to have a path to the root. synonym: "rRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000839 name: polypeptide_region alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000840 name: repeat_component def: "A region of a repeated sequence." [SO:ke] comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root. synonym: "repeat component" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000841 name: spliceosomal_intron_region def: "A region within an intron." [SO:ke] comment: A terms added to allow the parts of introns to have is_a paths to the root. subset: SOFA synonym: "spliceosomal intron region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region def: "A region of a gene that has a specific function." [] subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000704 ! gene [Term] id: SO:0000843 name: bacterial_RNApol_promoter_region def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke] comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000844 name: RNApol_II_promoter_region def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000845 name: RNApol_III_promoter_type_1_region def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000846 name: RNApol_III_promoter_type_2_region def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000847 name: tmRNA_region def: "A region of a tmRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root. synonym: "tmRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000584 ! tmRNA [Term] id: SO:0000848 name: LTR_component def: "The long terminal repeat found at the ends of the sequence to be inserted into the host genome." [] synonym: "long term repeat component" EXACT [] synonym: "LTR component" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000849 name: three_prime_LTR_component def: "A component of the three-prime long terminal repeat." [PMID:8649407] synonym: "3' long terminal repeat component" EXACT [] synonym: "three prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000426 ! three_prime_LTR [Term] id: SO:0000850 name: five_prime_LTR_component def: "A component of the five-prime long terminal repeat." [PMID:8649407] synonym: "5' long term repeat component" EXACT [] synonym: "five prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000851 name: CDS_region def: "A region of a CDS." [SO:cb] subset: SOFA synonym: "CDS region" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000852 name: exon_region def: "A region of an exon." [RSC:cb] subset: SOFA synonym: "exon region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000147 ! exon [Term] id: SO:0000853 name: homologous_region def: "A region that is homologous to another region." [SO:ke] synonym: "homolog" EXACT [] synonym: "homologous region" EXACT [] synonym: "homologue" EXACT [] xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki" is_a: SO:0000330 ! conserved_region intersection_of: SO:0000330 ! conserved_region intersection_of: has_quality SO:0000857 ! homologous relationship: has_quality SO:0000857 ! homologous [Term] id: SO:0000854 name: paralogous_region def: "A homologous_region that is paralogous to another region." [SO:ke] comment: A term to be used in conjunction with the paralogous_to relationship. synonym: "paralog" EXACT [] synonym: "paralogous region" EXACT [] synonym: "paralogue" EXACT [] xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki" is_a: SO:0000853 ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000859 ! paralogous relationship: has_quality SO:0000859 ! paralogous [Term] id: SO:0000855 name: orthologous_region def: "A homologous_region that is orthologous to another region." [SO:ke] comment: This term should be used in conjunction with the similarity relationships defined in SO. synonym: "ortholog" EXACT [] synonym: "orthologous region" EXACT [] synonym: "orthologue" EXACT [] xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki" is_a: SO:0000853 ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000858 ! orthologous relationship: has_quality SO:0000858 ! orthologous [Term] id: SO:0000856 name: conserved def: "A region that is similar or identical across more than one species." [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000857 name: homologous def: "Similarity due to common ancestry." [SO:ke] is_a: SO:0000856 ! conserved [Term] id: SO:0000858 name: orthologous def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000859 name: paralogous def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000860 name: syntenic def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] xref: http://en.wikipedia.org/wiki/Syntenic "wiki" is_a: SO:0000856 ! conserved [Term] id: SO:0000861 name: capped_primary_transcript def: "A primary transcript that is capped." [SO:xp] synonym: "capped primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000862 name: capped_mRNA def: "An mRNA that is capped." [SO:xp] synonym: "capped mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000863 name: mRNA_attribute def: "An attribute describing an mRNA feature." [SO:ke] synonym: "mRNA attribute" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000864 name: exemplar def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000865 name: frameshift def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke] xref: http://en.wikipedia.org/wiki/Frameshift "wiki" is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000866 name: minus_1_frameshift def: "A frameshift caused by deleting one base." [SO:ke] synonym: "minus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000867 name: minus_2_frameshift def: "A frameshift caused by deleting two bases." [SO:ke] synonym: "minus 2 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000868 name: plus_1_frameshift def: "A frameshift caused by inserting one base." [SO:ke] synonym: "plus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000869 name: plus_2_framshift def: "A frameshift caused by inserting two bases." [SO:ke] synonym: "plus 2 framshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000870 name: trans_spliced def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke] synonym: "trans-spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000871 name: polyadenylated_mRNA def: "An mRNA that is polyadenylated." [SO:xp] synonym: "polyadenylated mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000610 ! polyA_sequence intersection_of: has_quality SO:0000246 ! polyadenylated relationship: adjacent_to SO:0000610 ! polyA_sequence relationship: has_quality SO:0000246 ! polyadenylated [Term] id: SO:0000872 name: trans_spliced_mRNA def: "An mRNA that is trans-spliced." [SO:xp] synonym: "trans-spliced mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000479 ! trans_spliced_transcript intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000636 ! spliced_leader_RNA intersection_of: has_quality SO:0000870 ! trans_spliced relationship: adjacent_to SO:0000636 ! spliced_leader_RNA relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000873 name: edited_transcript def: "A transcript that is edited." [SO:ke] synonym: "edited transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000116 ! edited relationship: guided_by SO:0000602 ! guide_RNA relationship: has_part SO:0000977 ! anchor_binding_site relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000874 name: edited_transcript_by_A_to_I_substitution def: "A transcript that has been edited by A to I substitution." [SO:ke] synonym: "edited transcript by A to I substitution" EXACT [] is_a: SO:0000873 ! edited_transcript [Term] id: SO:0000875 name: bound_by_protein def: "An attribute describing a sequence that is bound by a protein." [SO:ke] synonym: "bound by protein" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000876 name: bound_by_nucleic_acid def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke] synonym: "bound by nucleic acid" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000877 name: alternatively_spliced def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke] synonym: "alternatively spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000878 name: monocistronic def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000879 name: dicistronic def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke] is_a: SO:0000880 ! polycistronic [Term] id: SO:0000880 name: polycistronic def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000881 name: recoded def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000882 name: codon_redefined def: "An attribute describing the alteration of codon meaning." [SO:ke] synonym: "codon redefined" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000883 name: stop_codon_read_through def: "A stop codon redefined to be a new amino acid." [SO:ke] synonym: "stop codon read through" EXACT [] synonym: "stop codon readthrough" RELATED [] is_a: SO:0000145 ! recoded_codon [Term] id: SO:0000884 name: stop_codon_redefined_as_pyrrolysine def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] synonym: "stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000885 name: stop_codon_redefined_as_selenocysteine def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke] synonym: "stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000886 name: recoded_by_translational_bypass def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke] synonym: "recoded by translational bypass" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000887 name: translationally_frameshifted def: "Recoding by frameshifting a particular site." [SO:ke] synonym: "translationally frameshifted" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000888 name: maternally_imprinted_gene def: "A gene that is maternally_imprinted." [SO:xp] synonym: "maternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000135 ! maternally_imprinted relationship: has_quality SO:0000135 ! maternally_imprinted [Term] id: SO:0000889 name: paternally_imprinted_gene def: "A gene that is paternally imprinted." [SO:xp] synonym: "paternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000136 ! paternally_imprinted relationship: has_quality SO:0000136 ! paternally_imprinted [Term] id: SO:0000890 name: post_translationally_regulated_gene def: "A gene that is post translationally regulated." [SO:xp] synonym: "post translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000130 ! post_translationally_regulated relationship: has_quality SO:0000130 ! post_translationally_regulated [Term] id: SO:0000891 name: negatively_autoregulated_gene def: "A gene that is negatively autoreguated." [SO:xp] synonym: "negatively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000473 ! negatively_autoregulated relationship: has_quality SO:0000473 ! negatively_autoregulated [Term] id: SO:0000892 name: positively_autoregulated_gene def: "A gene that is positively autoregulated." [SO:xp] synonym: "positively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000475 ! positively_autoregulated relationship: has_quality SO:0000475 ! positively_autoregulated [Term] id: SO:0000893 name: silenced def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke] xref: http://en.wikipedia.org/wiki/Silenced "wiki" is_a: SO:0000126 ! transcriptionally_repressed [Term] id: SO:0000894 name: silenced_by_DNA_modification def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0000895 name: silenced_by_DNA_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA methylation" EXACT [] is_a: SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000896 name: translationally_regulated_gene def: "A gene that is translationally regulated." [SO:xp] synonym: "translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000131 ! translationally_regulated relationship: has_quality SO:0000131 ! translationally_regulated [Term] id: SO:0000897 name: allelically_excluded_gene def: "A gene that is allelically_excluded." [SO:xp] synonym: "allelically excluded gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000137 ! allelically_excluded relationship: has_quality SO:0000137 ! allelically_excluded [Term] id: SO:0000898 name: epigenetically_modified_gene def: "A gene that is epigenetically modified." [SO:ke] synonym: "epigenetically modified gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0001720 ! epigenetically_modified_region intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified [Term] id: SO:0000899 name: nuclear_mitochondrial def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] synonym: "nuclear mitochondrial" EXACT [] is_obsolete: true [Term] id: SO:0000900 name: processed def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke] is_obsolete: true [Term] id: SO:0000901 name: unequally_crossed_over def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke] synonym: "unequally crossed over" EXACT [] is_obsolete: true [Term] id: SO:0000902 name: transgene def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] xref: http://en.wikipedia.org/wiki/Transgene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000781 ! transgenic relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000903 name: endogenous_retroviral_sequence def: "Endogenous DNA sequence that are likely to have arisen from retroviruses." [] synonym: "endogenous retroviral sequence" EXACT [] is_a: SO:0000751 ! proviral_location [Term] id: SO:0000904 name: rearranged_at_DNA_level def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke] synonym: "rearranged at DNA level" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000905 name: status def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke] comment: This term is the hypernym of attributes and should not be annotated to. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000906 name: independently_known def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke] synonym: "independently known" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000907 name: supported_by_sequence_similarity def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke] synonym: "supported by sequence similarity" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000908 name: supported_by_domain_match def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke] synonym: "supported by domain match" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000909 name: supported_by_EST_or_cDNA def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke] synonym: "supported by EST or cDNA" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000910 name: orphan def: "A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [] is_a: SO:0000732 ! predicted [Term] id: SO:0000911 name: predicted_by_ab_initio_computation def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke] synonym: "predicted by ab initio computation" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000912 name: asx_turn alt_id: BS:00203 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0000913 name: cloned_cDNA_insert def: "A clone insert made from cDNA." [SO:xp] synonym: "cloned cDNA insert" EXACT [] is_a: SO:0000753 ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000914 name: cloned_genomic_insert def: "A clone insert made from genomic DNA." [SO:xp] synonym: "cloned genomic insert" EXACT [] is_a: SO:0000753 ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! genomic_DNA [Term] id: SO:0000915 name: engineered_insert def: "A clone insert that is engineered." [SO:xp] synonym: "engineered insert" EXACT [] is_a: SO:0000753 ! clone_insert is_a: SO:0000804 ! engineered_region intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000916 name: edit_operation synonym: "edit operation" EXACT [] is_obsolete: true [Term] id: SO:0000917 name: insert_U def: "An edit to insert a U." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "insert U" EXACT [] is_obsolete: true [Term] id: SO:0000918 name: delete_U def: "An edit to delete a uridine." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "delete U" EXACT [] is_obsolete: true [Term] id: SO:0000919 name: substitute_A_to_I def: "An edit to substitute an I for an A." [SO:ke] synonym: "substitute A to I" EXACT [] is_obsolete: true [Term] id: SO:0000920 name: insert_C def: "An edit to insert a cytidine." [SO:ke] synonym: "insert C" EXACT [] is_obsolete: true [Term] id: SO:0000921 name: insert_dinucleotide def: "An edit to insert a dinucleotide." [SO:ke] synonym: "insert dinucleotide" EXACT [] is_obsolete: true [Term] id: SO:0000922 name: substitute_C_to_U def: "An edit to substitute an U for a C." [SO:ke] synonym: "substitute C to U" EXACT [] is_obsolete: true [Term] id: SO:0000923 name: insert_G def: "An edit to insert a G." [SO:ke] synonym: "insert G" EXACT [] is_obsolete: true [Term] id: SO:0000924 name: insert_GC def: "An edit to insert a GC dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GC" EXACT [] is_obsolete: true [Term] id: SO:0000925 name: insert_GU def: "An edit to insert a GU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GU" EXACT [] is_obsolete: true [Term] id: SO:0000926 name: insert_CU def: "An edit to insert a CU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert CU" EXACT [] is_obsolete: true [Term] id: SO:0000927 name: insert_AU def: "An edit to insert a AU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AU" EXACT [] is_obsolete: true [Term] id: SO:0000928 name: insert_AA def: "An edit to insert a AA dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AA" EXACT [] is_obsolete: true [Term] id: SO:0000929 name: edited_mRNA def: "An mRNA that is edited." [SO:xp] synonym: "edited mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000873 ! edited_transcript intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000116 ! edited relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000930 name: guide_RNA_region def: "A region of guide RNA." [SO:ma] synonym: "guide RNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000602 ! guide_RNA [Term] id: SO:0000931 name: anchor_region def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk] synonym: "anchor region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000932 name: pre_edited_mRNA def: "A primary transcript that, at least in part, encodes one or more proteins that has not been edited." [] synonym: "pre-edited mRNA" EXACT [] is_a: SO:0000120 ! protein_coding_primary_transcript [Term] id: SO:0000933 name: intermediate def: "An attribute to describe a feature between stages of processing." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000934 name: miRNA_target_site def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds] synonym: "miRNA target site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0000935 name: edited_CDS def: "A CDS that is edited." [SO:xp] synonym: "edited CDS" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000116 ! edited relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000936 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA." [] synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000937 name: vertebrate_immune_system_feature is_obsolete: true [Term] id: SO:0000938 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration." [] synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000939 name: vertebrate_immune_system_gene_recombination_signal_feature def: "Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system." [] synonym: "vertebrate immune system gene recombination signal feature" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000940 name: recombinationally_rearranged def: "A gene that is recombinationally rearranged." [] synonym: "recombinationally rearranged" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000941 name: recombinationally_rearranged_vertebrate_immune_system_gene def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] synonym: "recombinationally rearranged vertebrate immune system gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000942 name: attP_site def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as] synonym: "attP site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0001042 ! phage_sequence [Term] id: SO:0000943 name: attB_site def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as] synonym: "attB site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000944 name: attL_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as] synonym: "attBP'" RELATED [] synonym: "attL site" RELATED [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000945 name: attR_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as] synonym: "attPB'" RELATED [] synonym: "attR site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000946 name: integration_excision_site def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as] synonym: "attachment site" RELATED [] synonym: "integration excision site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000947 name: resolution_site def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] synonym: "res site" EXACT [] synonym: "resolution site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000948 name: inversion_site def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase. synonym: "inversion site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000949 name: dif_site def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as] synonym: "dif site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000950 name: attC_site def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as] synonym: "attC site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000951 name: eukaryotic_terminator def: "A signal for RNA polymerase to terminate transcription." [] synonym: "eukaryotic terminator" EXACT [] is_a: SO:0000141 ! terminator [Term] id: SO:0000952 name: oriV def: "An origin of vegetative replication in plasmids and phages." [SO:as] synonym: "origin of vegetative replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000953 name: oriC def: "An origin of bacterial chromosome replication." [SO:as] synonym: "origin of bacterial chromosome replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000954 name: DNA_chromosome def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] synonym: "DNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0000955 name: double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] synonym: "double stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! double [Term] id: SO:0000956 name: single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] synonym: "single stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! single [Term] id: SO:0000957 name: linear_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma] synonym: "linear double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000958 name: circular_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma] synonym: "circular double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000959 name: linear_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma] synonym: "linear single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000960 name: circular_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000961 name: RNA_chromosome def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] synonym: "RNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000356 ! RNA relationship: has_quality SO:0000356 ! RNA [Term] id: SO:0000962 name: single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] synonym: "single stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! single [Term] id: SO:0000963 name: linear_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma] synonym: "linear single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000964 name: linear_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma] synonym: "linear double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000965 name: double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] synonym: "double stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! double [Term] id: SO:0000966 name: circular_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000967 name: circular_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma] synonym: "circular double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000968 name: sequence_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "sequence replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000969 name: rolling_circle comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581. synonym: "rolling circle" EXACT [] xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki" is_obsolete: true [Term] id: SO:0000970 name: theta_replication comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582 synonym: "theta replication" EXACT [] is_obsolete: true [Term] id: SO:0000971 name: DNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260. synonym: "DNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000972 name: RNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "RNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000973 name: insertion_sequence def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as] synonym: "insertion sequence" EXACT [] synonym: "IS" RELATED [] xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki" is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000975 name: minicircle_gene def: "A gene found within a minicircle." [] synonym: "minicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: part_of SO:0000980 ! minicircle relationship: part_of SO:0000980 ! minicircle [Term] id: SO:0000976 name: cryptic def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000977 name: anchor_binding_site comment: Part of an edited transcript only. synonym: "anchor binding site" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000978 name: template_region def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk] synonym: "information region" EXACT [] synonym: "template region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000979 name: gRNA_encoding def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma] synonym: "gRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000980 name: minicircle alt_id: SO:0000974 def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055] synonym: "minicircle_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Minicircle "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000981 name: rho_dependent_bacterial_terminator def: "A transcription terminator that is dependent upon Rho." [] synonym: "rho dependent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000982 name: rho_independent_bacterial_terminator def: "A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure." [] synonym: "rho independent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000983 name: strand_attribute def: "The attribute of how many strands are present in a nucleotide polymer." [] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "strand attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000984 name: single def: "When a nucleotide polymer has only one strand." [] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000985 name: double def: "When a nucleotide polymer has two strands that are reverse-complement to one another and pair together." [] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000986 name: topology_attribute def: "The attribute of whether a nucleotide polymer is linear or circular." [] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "topology attribute" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000987 name: linear def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "two-ended" RELATED [] is_a: SO:0000986 ! topology_attribute disjoint_from: SO:0000988 ! circular [Term] id: SO:0000988 name: circular def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "zero-ended" RELATED [] is_a: SO:0000986 ! topology_attribute [Term] id: SO:0000989 name: class_II_RNA def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] synonym: "class II RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000990 name: class_I_RNA def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577. synonym: "class I RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000991 name: genomic_DNA def: "DNA located in the genome and able to be transmitted to the offspring." [BCS:etrwz] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "gDNA" EXACT [] synonym: "genomic DNA" EXACT [] is_a: SO:0000352 ! DNA [Term] id: SO:0000992 name: BAC_cloned_genomic_insert def: "A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome." [] comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006. synonym: "BAC cloned genomic insert" EXACT [] is_a: SO:0000914 ! cloned_genomic_insert intersection_of: SO:0000914 ! cloned_genomic_insert intersection_of: derives_from SO:0000153 ! BAC relationship: derives_from SO:0000153 ! BAC [Term] id: SO:0000993 name: consensus def: "A sequence produced from an aligment algorithm that uses multiple sequences as input." [] comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. is_a: SO:0000905 ! status [Term] id: SO:0000994 name: consensus_region def: "A region that has a known consensus sequence." [] comment: DO not obsolete without considering MGED mapping. synonym: "consensus region" EXACT [] is_a: SO:0001410 ! experimental_feature intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000993 ! consensus relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000995 name: consensus_mRNA def: "An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input." [] comment: DO not obsolete without considering MGED mapping. synonym: "consensus mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000994 ! consensus_region intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000993 ! consensus relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000996 name: predicted_gene def: "A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments." [] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "predicted gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000732 ! predicted relationship: has_quality SO:0000732 ! predicted [Term] id: SO:0000997 name: gene_fragment def: "A portion of a gene that is not the complete gene." [] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "gene fragment" EXACT [] is_a: SO:0000842 ! gene_component_region intersection_of: SO:0000842 ! gene_component_region intersection_of: has_quality SO:0000731 ! fragmentary relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0000998 name: recursive_splice_site def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661] synonym: "recursive splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000999 name: BAC_end def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] comment: Requested by Keith Boroevich December, 2006. synonym: "BAC end" EXACT [] synonym: "BAC end sequence" EXACT [] synonym: "BES" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000153 ! BAC [Term] id: SO:0001000 name: cytosolic_16S_rRNA def: "Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes." [SO:ke] comment: Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 16S ribosomal RNA" EXACT [] synonym: "cytosolic 16S rRNA" RELATED [] synonym: "cytosolic 16S SSU RNA" EXACT [] synonym: "cytosolic rRNA 16S" EXACT [] xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" is_a: SO:0000650 ! cytosolic_SSU_rRNA relationship: derives_from SO:0002237 ! cytosolic_rRNA_16S_gene [Term] id: SO:0001001 name: cytosolic_23S_rRNA def: "Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes." [SO:ke] comment: Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 23S LSU rRNA" EXACT [] synonym: "cytosolic 23S ribosomal RNA" RELATED [] synonym: "cytosolic 23S rRNA" EXACT [] synonym: "cytosolic rRNA 23S" EXACT [] is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002243 ! cytosolic_rRNA_23S_gene [Term] id: SO:0001002 name: cytosolic_25S_rRNA def: "Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes." [PMID:15493135, PMID:2100998, RSC:cb] comment: Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 25S LSU rRNA" EXACT [] synonym: "cytosolic 25S ribosomal RNA" EXACT [] synonym: "cytosolic 25S rRNA" EXACT [] synonym: "cytosolic rRNA 25S" EXACT [] is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002242 ! cytosolic_rRNA_25S_gene [Term] id: SO:0001003 name: solo_LTR def: "A recombination product between the 2 LTR of the same element." [SO:ke] comment: Requested by Hadi Quesneville January 2007. synonym: "solo LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0001004 name: low_complexity def: "When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases." [] synonym: "low complexity" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0001005 name: low_complexity_region def: "A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides." [] synonym: "low complexity region" EXACT [] is_a: SO:0001410 ! experimental_feature intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0001004 ! low_complexity relationship: has_quality SO:0001004 ! low_complexity [Term] id: SO:0001006 name: prophage def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl] xref: http://en.wikipedia.org/wiki/Prophage "wiki" is_a: SO:0000113 ! proviral_region [Term] id: SO:0001007 name: cryptic_prophage def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl] comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site. synonym: "cryptic prophage" EXACT [] xref: http://ecoliwiki.net/colipedia/index.php/Category\:Cryptic_Prophage.w is_a: SO:0000772 ! genomic_island [Term] id: SO:0001008 name: tetraloop def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke] xref: http://en.wikipedia.org/wiki/Tetraloop "wiki" is_a: SO:0000313 ! stem_loop [Term] id: SO:0001009 name: DNA_constraint_sequence def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50] synonym: "DNA constraint" EXACT [] synonym: "DNA constraint sequence" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0001010 name: i_motif def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739] synonym: "i motif" EXACT [] synonym: "short intercalated motif" EXACT [] is_a: SO:0000142 ! DNA_sequence_secondary_structure [Term] id: SO:0001011 name: PNA_oligo def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke] synonym: "peptide nucleic acid" EXACT [] synonym: "PNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001184 ! PNA relationship: has_quality SO:0001184 ! PNA [Term] id: SO:0001012 name: DNAzyme def: "A DNA sequence with catalytic activity." [SO:cb] comment: Added by request from Colin Batchelor. synonym: "catalytic DNA" EXACT [] synonym: "deoxyribozyme" RELATED [] synonym: "DNA enzyme" EXACT [] is_a: SO:0000696 ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001185 ! enzymatic relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0001013 name: MNP def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] synonym: "multiple nucleotide polymorphism" RELATED [] is_a: SO:0002007 ! MNV [Term] id: SO:0001014 name: intron_domain def: "An intronic region that has an attribute." [] comment: Requested by Colin Batchelor, Feb 2007. synonym: "intron domain" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000188 ! intron [Term] id: SO:0001015 name: wobble_base_pair def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617] synonym: "wobble base pair" EXACT [] synonym: "wobble pair" EXACT [] xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0001016 name: internal_guide_sequence def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] synonym: "IGS" EXACT [] synonym: "internal guide sequence" EXACT [] is_a: SO:0001014 ! intron_domain relationship: part_of SO:0000587 ! group_I_intron [Term] id: SO:0001017 name: silent_mutation def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke] comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc. synonym: "silent mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki" xref: loinc:LA6700-4 "Silent" is_a: SO:0001878 ! feature_variant [Term] id: SO:0001018 name: epitope def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb] comment: Requested by Trish Whetzel. xref: http://en.wikipedia.org/wiki/Epitope "wiki" is_a: SO:0000409 ! binding_site [Term] id: SO:0001019 name: copy_number_variation def: "A variation that increases or decreases the copy number of a given region." [SO:ke] subset: SOFA synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" is_a: SO:0000248 ! sequence_length_alteration [Term] id: SO:0001020 name: sequence_variant_affecting_copy_number comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting copy number" EXACT [] synonym: "sequence variant affecting copy number" EXACT [] is_obsolete: true replaced_by: SO:0001563 [Term] id: SO:0001021 name: chromosome_breakpoint alt_id: SO:0001242 def: "A chromosomal region that may sustain a double-strand break, resulting in a recombination event." [] synonym: "aberration breakpoint" EXACT [] synonym: "aberration_junction" EXACT [] synonym: "chromosome breakpoint" EXACT [] synonym: "INSDC_feature:misc_recomb" BROAD [] synonym: "INSDC_qualifier:chromosome_breakpoint" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0001022 name: inversion_breakpoint def: "The point within a chromosome where an inversion begins or ends." [SO:cb] synonym: "inversion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001023 name: allele def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] synonym: "allelomorph" EXACT [] xref: http://en.wikipedia.org/wiki/Allele "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000704 ! gene [Term] id: SO:0001024 name: haplotype def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Haplotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000355 ! haplotype_block [Term] id: SO:0001025 name: polymorphic_sequence_variant def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop] synonym: "polymorphic sequence variant" EXACT [] is_a: SO:0001023 ! allele [Term] id: SO:0001026 name: genome def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genome "wiki" is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0001235 ! replicon relationship: has_part SO:0001235 ! replicon [Term] id: SO:0001027 name: genotype def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0001026 ! genome [Term] id: SO:0001028 name: diplotype def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop] is_a: SO:0001507 ! variant_collection [Term] id: SO:0001029 name: direction_attribute def: "The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse)." [] synonym: "direction attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001030 name: forward def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001031 name: reverse def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001032 name: mitochondrial_DNA def: "DNA belonging to the genome of a mitochondria." [] comment: This terms is used by MO. synonym: "mitochondrial DNA" EXACT [] synonym: "mtDNA" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki" is_a: SO:0000737 ! mitochondrial_sequence intersection_of: SO:0000737 ! mitochondrial_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001033 name: chloroplast_DNA def: "DNA belonging to the genome of a chloroplast, a photosynthetic plastid." [] comment: This term is used by MO. synonym: "chloroplast DNA" EXACT [] is_a: SO:0000745 ! chloroplast_sequence intersection_of: SO:0000745 ! chloroplast_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001034 name: miRtron def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma] comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns. is_a: SO:0001014 ! intron_domain relationship: has_part SO:0001244 ! pre_miRNA [Term] id: SO:0001035 name: piRNA def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:piRNA" EXACT [] synonym: "piwi-associated RNA" EXACT [] xref: http://en.wikipedia.org/wiki/PiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0001036 name: arginyl_tRNA def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke] synonym: "arginyl tRNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript [Term] id: SO:0001037 name: mobile_genetic_element def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] subset: SOFA synonym: "INSDC_feature:mobile_element" EXACT [] synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0001234 ! mobile relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0001038 name: extrachromosomal_mobile_genetic_element def: "An MGE that is not integrated into the host chromosome." [SO:ke] synonym: "extrachromosomal mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001039 name: integrated_mobile_genetic_element def: "An MGE that is integrated into the host chromosome." [SO:ke] subset: SOFA synonym: "integrated mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001040 name: integrated_plasmid def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke] synonym: "integrated plasmid" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element intersection_of: SO:0001039 ! integrated_mobile_genetic_element intersection_of: derives_from SO:0000155 ! plasmid relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0001041 name: viral_sequence def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke] comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. synonym: "viral sequence" EXACT [] synonym: "virus sequence" EXACT [] is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element is_a: SO:0001235 ! replicon [Term] id: SO:0001042 name: phage_sequence def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke] synonym: "bacteriophage" EXACT [] synonym: "phage" EXACT [] synonym: "phage sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki" is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001043 name: attCtn_site def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at] synonym: "attCtn site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000371 ! conjugative_transposon [Term] id: SO:0001044 name: nuclear_mt_pseudogene def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp] comment: Definition change requested by Val, 3172757. synonym: "nuclear mitochondrial pseudogene" EXACT [] synonym: "nuclear mt pseudogene" EXACT [] synonym: "NUMT" EXACT [] xref: http://en.wikipedia.org/wiki/Numt "wikipedia" is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001045 name: cointegrated_plasmid def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at] synonym: "cointegrated plasmid" EXACT [] synonym: "cointegrated replicon" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0001046 name: IRLinv_site def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRLinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001047 name: IRRinv_site def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRRinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001048 name: inversion_site_part def: "A region located within an inversion site." [SO:ke] comment: A term created to allow the parts of an inversion site have an is_a path back to the root. synonym: "inversion site part" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0001049 name: defective_conjugative_transposon def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane] synonym: "defective conjugative transposon" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0001050 name: repeat_fragment def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke] comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats. synonym: "repeat fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001649 ! nested_repeat [Term] id: SO:0001051 name: nested_region is_obsolete: true [Term] id: SO:0001052 name: nested_repeat is_obsolete: true [Term] id: SO:0001053 name: nested_transposon is_obsolete: true [Term] id: SO:0001054 name: transposon_fragment def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke] synonym: "transposon fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001648 ! nested_transposon [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] comment: Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:transcriptional_cis_regulatory_region" EXACT [] synonym: "transcription-control region" EXACT [] synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region def: "A regulatory_region that modulates splicing." [SO:ke] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "splicing regulatory region" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001057 name: enhanceosome is_obsolete: true [Term] id: SO:0001058 name: promoter_targeting_sequence def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] comment: Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field. synonym: "promoter targeting sequence" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region is_obsolete: true [Term] id: SO:0001059 name: sequence_alteration alt_id: SO:1000004 alt_id: SO:1000007 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] comment: Merged with partially characterized change in nucleotide sequence. subset: SOFA synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_feature:variation" EXACT [] synonym: "INSDC_note:sequence_alteration" EXACT [] synonym: "partially characterised change in DNA sequence" NARROW [] synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] synonym: "sequence alteration" EXACT [] synonym: "sequence variation" RELATED [] synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] is_a: SO:0002072 ! sequence_comparison [Term] id: SO:0001060 name: sequence_variant def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "sequence variant" EXACT [] synonym: "VAAST:sequence_variant" EXACT VAR [] [Term] id: SO:0001061 name: propeptide_cleavage_site alt_id: BS:00063 def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "propeptide cleavage site" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0001062 name: propeptide alt_id: BS:00077 def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "INSDC_feature:propeptide" EXACT [] synonym: "propep" RELATED [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Propeptide "wiki" is_a: SO:0100011 ! cleaved_peptide_region relationship: derives_from SO:0002250 ! propeptide_region_of_CDS [Term] id: SO:0001063 name: immature_peptide_region alt_id: BS:00129 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "immature peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001064 name: active_peptide alt_id: BS:00076 def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual] comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length. subset: biosapiens synonym: "active peptide" EXACT [] synonym: "peptide" BROAD [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Peptide "wiki" is_a: SO:0000419 ! mature_protein_region [Term] id: SO:0001066 name: compositionally_biased_region_of_peptide alt_id: BS:00068 def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "compbias" RELATED [uniprot:feature_type] synonym: "compositional bias" RELATED [] synonym: "compositionally biased" RELATED [] synonym: "compositionally biased region of peptide" RELATED [] synonym: "compositionally_biased_region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001067 name: polypeptide_motif alt_id: BS:00032 def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "motif" BROAD [uniprot:feature_type] synonym: "polypeptide motif" EXACT [] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001068 name: polypeptide_repeat alt_id: BS:00070 def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "polypeptide repeat" EXACT [] synonym: "repeat" RELATED [uniprot:feature_type] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001070 name: polypeptide_structural_region alt_id: BS:00337 def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "polypeptide structural region" EXACT [] synonym: "structural_region" RELATED [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001071 name: membrane_structure alt_id: BS:00128 def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "membrane structure" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001072 name: extramembrane_polypeptide_region alt_id: BS:00154 def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "extramembrane" RELATED BS [] synonym: "extramembrane polypeptide region" EXACT [] synonym: "extramembrane_region" RELATED BS [] synonym: "topo_dom" RELATED BS [uniprot:feature_type] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001073 name: cytoplasmic_polypeptide_region alt_id: BS:00145 def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "cytoplasm_location" EXACT BS [] synonym: "cytoplasmic polypeptide region" EXACT [] synonym: "inside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001074 name: non_cytoplasmic_polypeptide_region alt_id: BS:00144 def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb] comment: This could be inside an organelle within the cell. subset: biosapiens synonym: "non cytoplasmic polypeptide region" EXACT [] synonym: "non_cytoplasm_location" EXACT BS [] synonym: "outside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001075 name: intramembrane_polypeptide_region alt_id: BS:00156 def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] subset: biosapiens synonym: "intramembrane" RELATED BS [] synonym: "intramembrane polypeptide region" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001076 name: membrane_peptide_loop alt_id: BS:00155 def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "membrane peptide loop" EXACT [] synonym: "membrane_loop" RELATED BS [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001077 name: transmembrane_polypeptide_region alt_id: BS:00158 def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] subset: biosapiens synonym: "transmem" RELATED BS [uniprot:feature_type] synonym: "transmembrane" RELATED BS [] synonym: "transmembrane polypeptide region" EXACT [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001078 name: polypeptide_secondary_structure alt_id: BS:00003 def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] comment: Biosapien term was secondary_structure. subset: biosapiens synonym: "2nary structure" RELATED BS [] synonym: "polypeptide secondary structure" EXACT [] synonym: "secondary structure" RELATED BS [] synonym: "secondary structure region" RELATED BS [] synonym: "secondary_structure" RELATED BS [] xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001079 name: polypeptide_structural_motif alt_id: BS:0000338 def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide structural motif" RELATED [] synonym: "structural_motif" RELATED BS [] xref: http://en.wikipedia.org/wiki/Structural_motif "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001080 name: coiled_coil alt_id: BS:00041 def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "coiled" RELATED BS [uniprot:feature_type] synonym: "coiled coil" EXACT [] xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki" is_a: SO:0001079 ! polypeptide_structural_motif [Term] id: SO:0001081 name: helix_turn_helix alt_id: BS:00147 def: "A motif comprising two helices separated by a turn." [EBIBS:GAR] subset: biosapiens synonym: "helix turn helix" EXACT [] synonym: "helix-turn-helix" EXACT [] synonym: "HTH" RELATED BS [] is_a: SO:0001079 ! polypeptide_structural_motif relationship: has_part SO:0001114 ! peptide_helix relationship: has_part SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001082 name: polypeptide_sequencing_information alt_id: BS:00125 def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "sequencing_information" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0001083 name: non_adjacent_residues alt_id: BS:00182 def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "non consecutive" EXACT [] synonym: "non_cons" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001084 name: non_terminal_residue alt_id: BS:00072 def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "non terminal" EXACT [] synonym: "non_ter" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001085 name: sequence_conflict alt_id: BS:00069 def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "conflict" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001086 name: sequence_uncertainty alt_id: BS:00181 def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "INSDC_feature:unsure" EXACT [] synonym: "unsure" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001087 name: cross_link alt_id: BS:00178 def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "cross link" EXACT [] synonym: "crosslink" RELATED [] is_obsolete: true [Term] id: SO:0001088 name: disulfide_bond alt_id: BS:00028 def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual] comment: 2 discreet & joined. subset: biosapiens synonym: "disulfid" RELATED [] synonym: "disulfide" RELATED [] synonym: "disulfide bond" RELATED [] synonym: "disulphide" EXACT [] synonym: "disulphide bond" RELATED [] is_obsolete: true [Term] id: SO:0001089 name: post_translationally_modified_region alt_id: BS:00052 def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mod_res" EXACT [uniprot:feature_type] synonym: "modified residue" EXACT [] synonym: "post_translational_modification" EXACT [] xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki" is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001090 name: covalent_binding_site alt_id: BS:00246 def: "Binding involving a covalent bond." [EBIBS:GAR] subset: biosapiens synonym: "covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001091 name: non_covalent_binding_site alt_id: BS:00029 def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "binding" RELATED [uniprot:curation] synonym: "binding site" RELATED [] synonym: "non covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001092 name: polypeptide_metal_contact alt_id: BS:00027 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual] comment: Residue is part of a binding site for a metal ion. subset: biosapiens synonym: "metal_binding" RELATED [] is_a: SO:0001656 ! metal_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001093 name: protein_protein_contact alt_id: BS:00131 def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual] subset: biosapiens synonym: "protein protein contact" EXACT [] synonym: "protein protein contact site" EXACT [] synonym: "protein_protein_interaction" RELATED [] xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki" is_a: SO:0000410 ! protein_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001094 name: polypeptide_calcium_ion_contact_site alt_id: BS:00186 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR] comment: Residue involved in contact with calcium. subset: biosapiens synonym: "ca bind" RELATED [] synonym: "ca_bind" EXACT BS [uniprot:feature_type] synonym: "Ca_contact_site" EXACT [] synonym: "polypeptide calcium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001095 name: polypeptide_cobalt_ion_contact_site alt_id: BS:00136 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Co_contact_site" EXACT [] synonym: "polypeptide cobalt ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001096 name: polypeptide_copper_ion_contact_site alt_id: BS:00146 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Cu_contact_site" EXACT [] synonym: "polypeptide copper ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001097 name: polypeptide_iron_ion_contact_site alt_id: BS:00137 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Fe_contact_site" EXACT [] synonym: "polypeptide iron ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001098 name: polypeptide_magnesium_ion_contact_site alt_id: BS:00187 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mg_contact_site" EXACT [] synonym: "polypeptide magnesium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001099 name: polypeptide_manganese_ion_contact_site alt_id: BS:00140 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mn_contact_site" EXACT [] synonym: "polypeptide manganese ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001100 name: polypeptide_molybdenum_ion_contact_site alt_id: BS:00141 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mo_contact_site" EXACT [] synonym: "polypeptide molybdenum ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001101 name: polypeptide_nickel_ion_contact_site alt_id: BS:00142 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR] subset: biosapiens synonym: "Ni_contact_site" EXACT [] synonym: "polypeptide nickel ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001102 name: polypeptide_tungsten_ion_contact_site alt_id: BS:00143 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide tungsten ion contact site" EXACT [] synonym: "W_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001103 name: polypeptide_zinc_ion_contact_site alt_id: BS:00185 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide zinc ion contact site" EXACT [] synonym: "Zn_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001104 name: catalytic_residue alt_id: BS:00026 def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "act_site" RELATED [uniprot:feature_type] synonym: "active site residue" EXACT [] synonym: "catalytic residue" EXACT [] is_a: SO:0001237 ! amino_acid relationship: part_of SO:0100019 ! polypeptide_catalytic_motif [Term] id: SO:0001105 name: polypeptide_ligand_contact alt_id: BS:00157 def: "Residues which interact with a ligand." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide ligand contact" EXACT [] synonym: "protein-ligand interaction" RELATED [] is_a: SO:0001657 ! ligand_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001106 name: asx_motif alt_id: BS:00202 def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001107 name: beta_bulge alt_id: BS:00208 def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge" EXACT [] xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001108 name: beta_bulge_loop alt_id: BS:00209 def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001109 name: beta_bulge_loop_five alt_id: BS:00210 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop five" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001110 name: beta_bulge_loop_six alt_id: BS:00211 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop six" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001111 name: beta_strand alt_id: BS:00042 def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "strand" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001112 name: antiparallel_beta_strand alt_id: BS:0000341 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "antiparallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001113 name: parallel_beta_strand alt_id: BS:00151 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "parallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001114 name: peptide_helix alt_id: BS:00152 def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "helix" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001115 name: left_handed_peptide_helix alt_id: BS:00222 def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix-l" RELATED [] synonym: "left handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001116 name: right_handed_peptide_helix alt_id: BS:0000339 def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix" RELATED BS [] synonym: "right handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001117 name: alpha_helix alt_id: BS:00040 def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "a-helix" RELATED BS [] synonym: "helix" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001118 name: pi_helix alt_id: BS:00153 def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "pi helix" EXACT [] xref: http://en.wikipedia.org/wiki/Pi_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001119 name: three_ten_helix alt_id: BS:0000340 def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "3(10) helix" EXACT [] synonym: "3-10 helix" EXACT [] synonym: "310 helix" EXACT [] synonym: "three ten helix" EXACT [] xref: http://en.wikipedia.org/wiki/310_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001120 name: polypeptide_nest_motif alt_id: BS:00223 def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest" RELATED BS [] synonym: "nest_motif" EXACT [] synonym: "polypeptide nest motif" RELATED [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001121 name: polypeptide_nest_left_right_motif alt_id: BS:00224 def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_left_right" EXACT [] synonym: "nest_lr" EXACT [] synonym: "polypeptide nest left right motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001122 name: polypeptide_nest_right_left_motif alt_id: BS:00225 def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_right_left" EXACT [] synonym: "nest_rl" EXACT [] synonym: "polypeptide nest right left motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001123 name: schellmann_loop alt_id: BS:00226 def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "paperclip" RELATED BS [] synonym: "paperclip loop" RELATED [] synonym: "schellmann loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001124 name: schellmann_loop_seven alt_id: BS:00228 def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop seven" EXACT [] synonym: "seven-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001125 name: schellmann_loop_six alt_id: BS:00227 def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop six" EXACT [] synonym: "six-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001126 name: serine_threonine_motif alt_id: BS:00229 def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine motif" EXACT [] synonym: "st motif" EXACT [] synonym: "st_motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001127 name: serine_threonine_staple_motif alt_id: BS:00230 def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine threonine staple motif" EXACT [] synonym: "st_staple" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001128 name: polypeptide_turn_motif alt_id: BS:00148 def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type] comment: Range. subset: biosapiens synonym: "turn" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001129 name: asx_turn_left_handed_type_one alt_id: BS:00206 def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type one" EXACT [] synonym: "asx_turn_il" RELATED [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001130 name: asx_turn_left_handed_type_two alt_id: BS:00204 def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type two" EXACT [] synonym: "asx_turn_iil" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001131 name: asx_turn_right_handed_type_two alt_id: BS:00205 def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn right handed type two" EXACT [] synonym: "asx_turn_iir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001132 name: asx_turn_right_handed_type_one alt_id: BS:00207 def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn type right handed type one" EXACT [] synonym: "asx_turn_ir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001133 name: beta_turn alt_id: BS:00212 def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001134 name: beta_turn_left_handed_type_one alt_id: BS:00215 def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type one" EXACT [] synonym: "beta_turn_il" EXACT [] synonym: "type I' beta turn" EXACT [] synonym: "type I' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001135 name: beta_turn_left_handed_type_two alt_id: BS:00213 def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type two" EXACT [] synonym: "beta_turn_iil" EXACT [] synonym: "type II' beta turn" EXACT [] synonym: "type II' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001136 name: beta_turn_right_handed_type_one alt_id: BS:00216 def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type one" EXACT [] synonym: "beta_turn_ir" EXACT [] synonym: "type I beta turn" EXACT [] synonym: "type I turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001137 name: beta_turn_right_handed_type_two alt_id: BS:00214 def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type two" EXACT [] synonym: "beta_turn_iir" EXACT [] synonym: "type II beta turn" EXACT [] synonym: "type II turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001138 name: gamma_turn alt_id: BS:00219 def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001139 name: gamma_turn_classic alt_id: BS:00220 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "classic gamma turn" EXACT [] synonym: "gamma turn classic" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001140 name: gamma_turn_inverse alt_id: BS:00221 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn inverse" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001141 name: serine_threonine_turn alt_id: BS:00231 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine turn" EXACT [] synonym: "st_turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001142 name: st_turn_left_handed_type_one alt_id: BS:00234 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type one" EXACT [] synonym: "st_turn_il" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001143 name: st_turn_left_handed_type_two alt_id: BS:00232 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type two" EXACT [] synonym: "st_turn_iil" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001144 name: st_turn_right_handed_type_one alt_id: BS:00235 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type one" EXACT [] synonym: "st_turn_ir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001145 name: st_turn_right_handed_type_two alt_id: BS:00233 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type two" EXACT [] synonym: "st_turn_iir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001146 name: polypeptide_variation_site alt_id: BS:00336 def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. subset: biosapiens synonym: "sequence_variations" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001147 name: natural_variant_site alt_id: BS:00071 def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "natural_variant" BROAD [] synonym: "sequence variation" BROAD [] synonym: "variant" BROAD [uniprot:feature_type] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001148 name: mutated_variant_site alt_id: BS:00036 def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mutagen" EXACT BS [uniprot:feature_type] synonym: "mutagenesis" EXACT [] synonym: "mutated_site" EXACT [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001149 name: alternate_sequence_site alt_id: BS:00073 alt_id: SO:0001065 def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "alternative_sequence" EXACT [] synonym: "isoform" NARROW [] synonym: "sequence variation" NARROW [] synonym: "var_seq" EXACT [uniprot:feature_type] synonym: "varsplic" NARROW [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001150 name: beta_turn_type_six def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb] subset: biosapiens synonym: "beta turn type six" EXACT [] synonym: "cis-proline loop" EXACT [] synonym: "type VI beta turn" EXACT [] synonym: "type VI turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001151 name: beta_turn_type_six_a def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six a" EXACT [] synonym: "type VIa beta turn" EXACT [] synonym: "type VIa turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001152 name: beta_turn_type_six_a_one def: "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees." [PMID:27428516] subset: biosapiens synonym: "beta turn type six a one" EXACT [] synonym: "type VIa1 beta turn" EXACT [] synonym: "type VIa1 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001153 name: beta_turn_type_six_a_two def: "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees." [PMID:27428516] subset: biosapiens synonym: "beta turn type six a two" EXACT [] synonym: "type VIa2 beta turn" EXACT [] synonym: "type VIa2 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001154 name: beta_turn_type_six_b def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six b" EXACT [] synonym: "type VIb beta turn" EXACT [] synonym: "type VIb turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001155 name: beta_turn_type_eight def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type eight" EXACT [] synonym: "type VIII beta turn" EXACT [] synonym: "type VIII turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001156 name: DRE_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576] comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. synonym: "DRE motif" EXACT [] synonym: "NDM4" EXACT [] synonym: "WATCGATW_motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001157 name: DMv4_motif def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941\:12537576] synonym: "directional motif v4" EXACT [] synonym: "DMv4" EXACT [] synonym: "DMv4 motif" EXACT [] synonym: "motif 1 element" EXACT [] synonym: "promoter motif 1" EXACT [] synonym: "YGGTCACATR" NARROW [] is_a: SO:0001659 ! promoter_element [Term] id: SO:0001158 name: E_box_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576\:16827941] synonym: "AWCAGCTGWT" NARROW [] synonym: "E box motif" EXACT [] synonym: "generic E box motif" EXACT [] synonym: "NDM5" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001159 name: DMv5_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941] synonym: "directional motif v5" EXACT [] synonym: "DMv5" EXACT [] synonym: "DMv5 motif" EXACT [] synonym: "KTYRGTATWTTT" NARROW [] synonym: "promoter motif 6" RELATED [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001160 name: DMv3_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576\:16827941] synonym: "directional motif v3" EXACT [] synonym: "DMv3" EXACT [] synonym: "DMv3 motif" EXACT [] synonym: "KNNCAKCNCTRNY" NARROW [] synonym: "promoter motif 7" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001161 name: DMv2_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941] synonym: "directional motif v2" EXACT [] synonym: "DMv2" EXACT [] synonym: "DMv2 motif" EXACT [] synonym: "MKSYGGCARCGSYSS" NARROW [] synonym: "promoter motif 8" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001162 name: MTE def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576\:15231738, PMID:16858867] synonym: "CSARCSSAACGS" NARROW [] synonym: "motif ten element" EXACT [] synonym: "motif_ten_element" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0001163 name: INR1_motif def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941] synonym: "directional motif p3" EXACT [] synonym: "directional promoter motif 3" EXACT [] synonym: "DMp3" EXACT [] synonym: "INR1 motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001164 name: DPE1_motif def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941] synonym: "directional motif 5" EXACT [] synonym: "directional promoter motif 5" RELATED [] synonym: "DMp5" EXACT [] synonym: "DPE1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001165 name: DMv1_motif def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941] synonym: "directional promoter motif v1" RELATED [] synonym: "DMv1" RELATED [] synonym: "DMv1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001166 name: GAGA_motif def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] synonym: "GAGA" EXACT [] synonym: "GAGA motif" EXACT [] synonym: "NDM1" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001167 name: NDM2_motif def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] synonym: "NDM2" EXACT [] synonym: "NDM2 motif" EXACT [] synonym: "non directional promoter motif 2" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001168 name: NDM3_motif def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] synonym: "NDM3" EXACT [] synonym: "NDM3 motif" EXACT [] synonym: "non directional motif 3" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001169 name: ds_RNA_viral_sequence def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke] synonym: "double stranded RNA virus sequence" EXACT [] synonym: "ds RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001170 name: polinton def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396] synonym: "maverick element" RELATED [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0001171 name: rRNA_21S def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb] comment: This term has been merged into mt_LSU_rRNA (SO:0002345) as part of reorganization of rRNA child terms 10 June 2021. Requested by EBI. See GitHub Issue #493. synonym: "21S LSU rRNA" EXACT [] synonym: "21S ribosomal RNA" EXACT [] synonym: "21S rRNA" EXACT [] synonym: "rRNA 21S" EXACT [] is_obsolete: true replaced_by: SO:0002345 [Term] id: SO:0001172 name: tRNA_region def: "A region of a tRNA." [RSC:cb] synonym: "tRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000253 ! tRNA [Term] id: SO:0001173 name: anticodon_loop def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207] synonym: "anti-codon loop" EXACT [] synonym: "anticodon loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001174 name: anticodon def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb] synonym: "anti-codon" EXACT [] xref: http://en.wikipedia.org/wiki/Anticodon "wiki" is_a: SO:0001172 ! tRNA_region relationship: part_of SO:0001173 ! anticodon_loop [Term] id: SO:0001175 name: CCA_tail def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207] synonym: "CCA sequence" EXACT [] synonym: "CCA tail" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001176 name: DHU_loop def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920] synonym: "D loop" RELATED [] synonym: "DHU loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001177 name: T_loop def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207] synonym: "T loop" EXACT [] synonym: "TpsiC loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001178 name: pyrrolysine_tRNA_primary_transcript def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb] synonym: "pyrrolysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0001179 name: U3_snoRNA def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012] comment: The definition is most of the old definition for snoRNA (SO:0000275). synonym: "small nucleolar RNA U3" EXACT [] synonym: "snoRNA U3" EXACT [] synonym: "U3 small nucleolar RNA" EXACT [] synonym: "U3 snoRNA" EXACT [] xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki" is_a: SO:0000593 ! C_D_box_snoRNA [Term] id: SO:0001180 name: AU_rich_element def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223] synonym: "ARE" RELATED [] synonym: "AU rich element" EXACT [] synonym: "AU-rich element" EXACT [] xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001181 name: Bruno_response_element def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231] comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B. synonym: "BRE" RELATED [] synonym: "Bruno response element" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001182 name: iron_responsive_element def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843] synonym: "IRE" EXACT [] synonym: "iron responsive element" EXACT [] xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0001183 name: morpholino_backbone def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. synonym: "morpholino backbone" EXACT [] xref: http://en.wikipedia.org/wiki/Morpholino "wiki" is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001184 name: PNA def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb] comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead. synonym: "peptide nucleic acid" RELATED [] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001185 name: enzymatic def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001186 name: ribozymic def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead. is_a: SO:0001185 ! enzymatic [Term] id: SO:0001187 name: pseudouridylation_guide_snoRNA def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] comment: Has RNA pseudouridylation guide activity (GO:0030558). synonym: "pseudouridylation guide snoRNA" EXACT [] is_a: SO:0000594 ! H_ACA_box_snoRNA [Term] id: SO:0001188 name: LNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010] comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001189 name: LNA_oligo def: "An oligo composed of LNA residues." [RSC:cb] synonym: "LNA oligo" EXACT [] synonym: "locked nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001188 ! LNA relationship: has_quality SO:0001188 ! LNA [Term] id: SO:0001190 name: TNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019] comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001191 name: TNA_oligo def: "An oligo composed of TNA residues." [RSC:cb] synonym: "threose nucleic acid" EXACT [] synonym: "TNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001190 ! TNA relationship: has_quality SO:0001190 ! TNA [Term] id: SO:0001192 name: GNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015] comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001193 name: GNA_oligo def: "An oligo composed of GNA residues." [RSC:cb] synonym: "glycerol nucleic acid" EXACT [] synonym: "glycol nucleic acid" EXACT [] synonym: "GNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001192 ! GNA relationship: has_quality SO:0001192 ! GNA [Term] id: SO:0001194 name: R_GNA def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016] comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead. synonym: "R GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001195 name: R_GNA_oligo def: "An oligo composed of (R)-GNA residues." [RSC:cb] synonym: "(R)-glycerol nucleic acid" EXACT [] synonym: "(R)-glycol nucleic acid" EXACT [] synonym: "R GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001194 ! R_GNA relationship: has_quality SO:0001194 ! R_GNA [Term] id: SO:0001196 name: S_GNA def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017] comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead. synonym: "S GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001197 name: S_GNA_oligo def: "An oligo composed of (S)-GNA residues." [RSC:cb] synonym: "(S)-glycerol nucleic acid" EXACT [] synonym: "(S)-glycol nucleic acid" EXACT [] synonym: "S GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001196 ! S_GNA relationship: has_quality SO:0001196 ! S_GNA [Term] id: SO:0001198 name: ds_DNA_viral_sequence def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke] synonym: "double stranded DNA virus" EXACT [] synonym: "ds DNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001199 name: ss_RNA_viral_sequence def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke] synonym: "single strand RNA virus" EXACT [] synonym: "ss RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001200 name: negative_sense_ssRNA_viral_sequence def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke] synonym: "negative sense single stranded RNA virus" RELATED [] synonym: "negative sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001201 name: positive_sense_ssRNA_viral_sequence def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke] synonym: "positive sense single stranded RNA virus" RELATED [] synonym: "positive sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001202 name: ambisense_ssRNA_viral_sequence def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke] synonym: "ambisense single stranded RNA virus" EXACT [] synonym: "ambisense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001203 name: RNA_polymerase_promoter def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] comment: Term merged with promoter SO:0000167 in August 2020 as part of GREEKC initiative. See GitHub Issue 492 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/492) synonym: "RNA polymerase promoter" EXACT [] is_obsolete: true replaced_by: SO:0000167 [Term] id: SO:0001204 name: Phage_RNA_Polymerase_Promoter def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC. synonym: "Phage RNA Polymerase Promoter" EXACT [] is_a: SO:0002311 ! viral_promoter [Term] id: SO:0001205 name: SP6_RNA_Polymerase_Promoter def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "SP6 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001206 name: T3_RNA_Polymerase_Promoter def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T3 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001207 name: T7_RNA_Polymerase_Promoter def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T7 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001208 name: five_prime_EST def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "5' EST" EXACT [] synonym: "five prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001209 name: three_prime_EST def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "3' EST" EXACT [] synonym: "three prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001210 name: translational_frameshift def: "The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [http://www.insdc.org/files/feature_table.html, SO:ke] comment: Added synonym 'ribosomal_slippage' on Feb 1, 2021, a term in INSDC and GenBank. See GitHub Issue #522. synonym: "INSDC_qualifier:ribosomal_slippage" EXACT [] synonym: "ribosomal frameshift" EXACT [] synonym: "ribosomal slippage" EXACT [] synonym: "translational frameshift" EXACT [] xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki" is_a: SO:0000836 ! mRNA_region [Term] id: SO:0001211 name: plus_1_translational_frameshift def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 1 ribosomal frameshift" EXACT [] synonym: "plus 1 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001212 name: plus_2_translational_frameshift def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 2 ribosomal frameshift" EXACT [] synonym: "plus 2 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001213 name: group_III_intron def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794] comment: GO:0000374. synonym: "group III intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0001214 name: noncoding_region_of_exon def: "The maximal intersection of exon and UTR." [SO:ke] comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. subset: SOFA synonym: "noncoding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001215 name: coding_region_of_exon def: "The region of an exon that encodes for protein sequence." [SO:ke] comment: An exon containing either a start or stop codon will be partially coding and partially non coding. subset: SOFA synonym: "coding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001216 name: endonuclease_spliced_intron def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] synonym: "endonuclease spliced intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0001217 name: protein_coding_gene def: "A gene that codes for an RNA that can be translated into a protein." [] subset: Alliance_of_Genome_Resources synonym: "protein coding gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000010 ! protein_coding relationship: has_quality SO:0000010 ! protein_coding [Term] id: SO:0001218 name: transgenic_insertion def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] synonym: "transgenic insertion" EXACT [] is_a: SO:0000667 ! insertion intersection_of: SO:0000667 ! insertion intersection_of: has_quality SO:0000781 ! transgenic relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0001219 name: retrogene def: "A gene that has been produced as the product of a reverse transcriptase mediated event." [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000569 ! retrotransposed relationship: has_quality SO:0000569 ! retrotransposed [Term] id: SO:0001220 name: silenced_by_RNA_interference def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb] comment: RNA interference is GO:0016246. synonym: "silenced by RNA interference" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001221 name: silenced_by_histone_modification def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb] comment: Histone modification is GO:0016570. synonym: "silenced by histone modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001222 name: silenced_by_histone_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb] comment: Histone methylation is GO:0016571. synonym: "silenced by histone methylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001223 name: silenced_by_histone_deacetylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb] comment: Histone deacetylation is GO:0016573. synonym: "silenced by histone deacetylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001224 name: gene_silenced_by_RNA_interference def: "A gene that is silenced by RNA interference." [SO:xp] synonym: "gene silenced by RNA interference" EXACT [] synonym: "RNA interference silenced gene" EXACT [] synonym: "RNAi silenced gene" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000127 ! silenced_gene intersection_of: has_quality SO:0001220 ! silenced_by_RNA_interference relationship: has_quality SO:0001220 ! silenced_by_RNA_interference [Term] id: SO:0001225 name: gene_silenced_by_histone_modification def: "A gene that is silenced by histone modification." [SO:xp] synonym: "gene silenced by histone modification" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000127 ! silenced_gene intersection_of: has_quality SO:0001221 ! silenced_by_histone_modification relationship: has_quality SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001226 name: gene_silenced_by_histone_methylation def: "A gene that is silenced by histone methylation." [SO:xp] synonym: "gene silenced by histone methylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: has_quality SO:0001222 ! silenced_by_histone_methylation relationship: has_quality SO:0001222 ! silenced_by_histone_methylation [Term] id: SO:0001227 name: gene_silenced_by_histone_deacetylation def: "A gene that is silenced by histone deacetylation." [SO:xp] synonym: "gene silenced by histone deacetylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: has_quality SO:0001223 ! silenced_by_histone_deacetylation relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation [Term] id: SO:0001228 name: dihydrouridine def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb] synonym: " D" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki" xref: RNAMOD:051 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001229 name: pseudouridine def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb] comment: The free molecule is CHEBI:17802. synonym: " Y" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki" xref: RNAMOD:050 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001230 name: inosine def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb] comment: The free molecule is CHEBI:17596. synonym: "I" RELATED [] synonym: "RNAMOD:017" RELATED [] xref: http://en.wikipedia.org/wiki/Inosine "wiki" is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001231 name: seven_methylguanine def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb] comment: The free molecule is CHEBI:2274. synonym: "7-methylguanine" EXACT [] synonym: "seven methylguanine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001232 name: ribothymidine def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb] comment: The free molecule is CHEBI:30832. is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001233 name: methylinosine def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb] is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001234 name: mobile def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb] xref: http://en.wikipedia.org/wiki/Mobile "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001235 name: replicon def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] subset: SOFA xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001236 name: base def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001237 name: amino_acid def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] comment: Probably in the future this will cross reference to Chebi. synonym: "amino acid" EXACT [] xref: http://en.wikipedia.org/wiki/Amino_acid "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0001238 name: major_TSS def: "The tanscription start site that is most frequently used for transcription of a gene." [] synonym: "major transcription start site" EXACT [] synonym: "major TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001239 name: minor_TSS def: "A tanscription start site that is not the most frequently used for transcription of a gene." [] synonym: "minor TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001240 name: TSS_region def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] comment: Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528 synonym: "TSS region" EXACT [] is_obsolete: true replaced_by: SO:0000167 [Term] id: SO:0001241 name: encodes_alternate_transcription_start_sites def: "A gene that has multiple possible transcription start sites." [] synonym: "encodes alternate transcription start sites" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0001243 name: miRNA_primary_transcript_region def: "A part of an miRNA primary_transcript." [SO:ke] synonym: "miRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0001244 name: pre_miRNA def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke] synonym: "pre-miRNA" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region [Term] id: SO:0001245 name: miRNA_stem def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA stem" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001246 name: miRNA_loop def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA loop" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001247 name: synthetic_oligo def: "An oligo composed of synthetic nucleotides." [SO:ke] synonym: "synthetic oligo" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0001248 name: assembly def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001249 name: fragment_assembly def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] synonym: "fragment assembly" EXACT [] synonym: "physical map" EXACT [] is_a: SO:0001248 ! assembly [Term] id: SO:0001250 name: fingerprint_map def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] synonym: "BACmap" EXACT [] synonym: "fingerprint map" EXACT [] synonym: "FPC" EXACT [] synonym: "FPCmap" EXACT [] synonym: "restriction map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000412 ! restriction_fragment [Term] id: SO:0001251 name: STS_map def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke] synonym: "STS map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001252 name: RH_map def: "A radiation hybrid map is a physical map." [SO:ke] synonym: "radiation hybrid map" EXACT [] synonym: "RH map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001253 name: sonicate_fragment def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke] synonym: "sonicate fragment" EXACT [] is_a: SO:0000143 ! assembly_component [Term] id: SO:0001254 name: polyploid def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke] xref: http://en.wikipedia.org/wiki/Polyploid "wiki" is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0001255 name: autopolyploid def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001256 name: allopolyploid def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001257 name: homing_endonuclease_binding_site def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke] synonym: "homing endonuclease binding site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0001258 name: octamer_motif def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662] comment: Nature. 1986 Oct 16-22;323(6089):640-3. synonym: "octamer motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001259 name: apicoplast_chromosome def: "A chromosome originating in an apicoplast." [SO:xp] synonym: "apicoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000743 ! apicoplast_sequence relationship: has_origin SO:0000743 ! apicoplast_sequence [Term] id: SO:0001260 name: sequence_collection def: "A collection of discontinuous sequences." [SO:ke] synonym: "sequence collection" EXACT [] [Term] id: SO:0001261 name: overlapping_feature_set def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA. synonym: "overlapping feature set" EXACT [] is_a: SO:0000703 ! experimental_result_region [Term] id: SO:0001262 name: overlapping_EST_set def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke] synonym: "overlapping EST set" EXACT [] is_a: SO:0001261 ! overlapping_feature_set relationship: has_part SO:0000345 ! EST [Term] id: SO:0001263 name: ncRNA_gene def: "A gene that encodes a non-coding RNA." [] subset: Alliance_of_Genome_Resources synonym: "ncRNA gene" EXACT [] synonym: "non-coding RNA gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001264 name: gRNA_gene def: "A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system." [] synonym: "gRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000979 ! gRNA_encoding relationship: has_quality SO:0000979 ! gRNA_encoding [Term] id: SO:0001265 name: miRNA_gene alt_id: SO:0001270 def: "A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression." [] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. synonym: "miRNA gene" EXACT [] synonym: "stRNA gene" EXACT [] synonym: "stRNA_gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene intersection_of: SO:0002342 ! sncRNA_gene intersection_of: has_quality SO:0000571 ! miRNA_encoding intersection_of: has_quality SO:0000656 ! stRNA_encoding relationship: has_quality SO:0000571 ! miRNA_encoding relationship: has_quality SO:0000656 ! stRNA_encoding [Term] id: SO:0001266 name: scRNA_gene def: "A gene encoding a small noncoding RNA that is generally found only in the cytoplasm." [] synonym: "scRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000575 ! scRNA_encoding relationship: has_quality SO:0000575 ! scRNA_encoding [Term] id: SO:0001267 name: snoRNA_gene def: "A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs." [] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. Added additional children of snoRNA on 18 Nov 2021 at the request of Steven Marygold. See GitHub Issue #519. synonym: "snoRNA gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene intersection_of: SO:0002342 ! sncRNA_gene intersection_of: has_quality SO:0000578 ! snoRNA_encoding relationship: has_quality SO:0000578 ! snoRNA_encoding [Term] id: SO:0001268 name: snRNA_gene def: "A gene that encodes a small nuclear RNA." [http://en.wikipedia.org/wiki/Small_nuclear_RNA] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. synonym: "small nuclear RNA gene" EXACT [] synonym: "snRNA gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene [Term] id: SO:0001269 name: SRP_RNA_gene def: "A gene that encodes a signal recognition particle (SRP) RNA." [] synonym: "SRP RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000642 ! SRP_RNA_encoding relationship: has_quality SO:0000642 ! SRP_RNA_encoding [Term] id: SO:0001271 name: tmRNA_gene def: "A bacterial RNA with both tRNA and mRNA like properties." [] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. synonym: "tmRNA gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene intersection_of: SO:0002342 ! sncRNA_gene intersection_of: has_quality SO:0000659 ! tmRNA_encoding relationship: has_quality SO:0000659 ! tmRNA_encoding [Term] id: SO:0001272 name: tRNA_gene def: "A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA." [] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. synonym: "tRNA gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene intersection_of: SO:0002342 ! sncRNA_gene intersection_of: has_quality SO:0000663 ! tRNA_encoding relationship: has_quality SO:0000663 ! tRNA_encoding [Term] id: SO:0001273 name: modified_adenosine def: "A modified adenine is an adenine base feature that has been altered." [SO:ke] synonym: "modified adenosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001274 name: modified_inosine def: "A modified inosine is an inosine base feature that has been altered." [SO:ke] synonym: "modified inosine" EXACT [] is_a: SO:0001230 ! inosine [Term] id: SO:0001275 name: modified_cytidine def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke] synonym: "modified cytidine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001276 name: modified_guanosine def: "A guanosine base that has been modified." [] synonym: "modified guanosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001277 name: modified_uridine def: "A uridine base that has been modified." [] synonym: "modified uridine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001278 name: one_methylinosine def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylinosine" EXACT [] synonym: "m1I" EXACT RNAMOD [] synonym: "one methylinosine" EXACT [] xref: RNAMOD:018 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001279 name: one_two_prime_O_dimethylinosine def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylinosine" EXACT [] synonym: "m'Im" EXACT RNAMOD [] synonym: "one two prime O dimethylinosine" EXACT [] xref: RNAMOD:019 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001280 name: two_prime_O_methylinosine def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylinosine" EXACT [] synonym: "Im" EXACT RNAMOD [] synonym: "two prime O methylinosine" EXACT [] xref: RNAMOD:081 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001281 name: three_methylcytidine def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylcytidine" EXACT [] synonym: "m3C" EXACT RNAMOD [] synonym: "three methylcytidine" EXACT [] xref: RNAMOD:020 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001282 name: five_methylcytidine def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylcytidine" EXACT [] synonym: "five methylcytidine" EXACT [] synonym: "m5C" EXACT RNAMOD [] xref: RNAMOD:021 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001283 name: two_prime_O_methylcytidine def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylcytidine" EXACT [] synonym: "Cm" EXACT RNAMOD [] synonym: "two prime O methylcytidine" EXACT [] xref: RNAMOD:022 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001284 name: two_thiocytidine def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiocytidine" EXACT [] synonym: "s2C" EXACT RNAMOD [] synonym: "two thiocytidine" EXACT [] xref: RNAMOD:023 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001285 name: N4_acetylcytidine def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4C" EXACT RNAMOD [] synonym: "N4 acetylcytidine" EXACT [] synonym: "N4-acetylcytidine" EXACT [] xref: RNAMOD:024 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001286 name: five_formylcytidine def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formylcytidine" EXACT [] synonym: "f5C" EXACT RNAMOD [] synonym: "five formylcytidine" EXACT [] xref: RNAMOD:025 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001287 name: five_two_prime_O_dimethylcytidine def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethylcytidine" EXACT [] synonym: "five two prime O dimethylcytidine" EXACT [] synonym: "m5Cm" EXACT RNAMOD [] xref: RNAMOD:026 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001288 name: N4_acetyl_2_prime_O_methylcytidine def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4Cm" EXACT RNAMOD [] synonym: "N4 acetyl 2 prime O methylcytidine" EXACT [] synonym: "N4-acetyl-2'-O-methylcytidine" EXACT [] xref: RNAMOD:027 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001289 name: lysidine def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "k2C" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Lysidine "wiki" xref: RNAMOD:028 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001290 name: N4_methylcytidine def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4C" EXACT RNAMOD [] synonym: "N4 methylcytidine" EXACT [] synonym: "N4-methylcytidine" EXACT [] xref: RNAMOD:082 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001291 name: N4_2_prime_O_dimethylcytidine def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4Cm" EXACT RNAMOD [] synonym: "N4 2 prime O dimethylcytidine" EXACT [] synonym: "N4,2'-O-dimethylcytidine" EXACT [] xref: RNAMOD:083 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001292 name: five_hydroxymethylcytidine def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxymethylcytidine" EXACT [] synonym: "five hydroxymethylcytidine" EXACT [] synonym: "hm5C" EXACT RNAMOD [] xref: RNAMOD:084 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001293 name: five_formyl_two_prime_O_methylcytidine def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formyl-2'-O-methylcytidine" EXACT [] synonym: "f5Cm" EXACT RNAMOD [] synonym: "five formyl two prime O methylcytidine" EXACT [] xref: RNAMOD:095 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001294 name: N4_N4_2_prime_O_trimethylcytidine def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m42Cm" EXACT RNAMOD [] synonym: "N4,N4,2'-O-trimethylcytidine" EXACT [] xref: RNAMOD:107 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001295 name: one_methyladenosine def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyladenosine" EXACT [] synonym: "m1A" EXACT RNAMOD [] synonym: "one methyladenosine" EXACT [] xref: RNAMOD:001 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001296 name: two_methyladenosine def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methyladenosine" EXACT [] synonym: "m2A" EXACT RNAMOD [] synonym: "two methyladenosine" EXACT [] xref: RNAMOD:002 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001297 name: N6_methyladenosine def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6A" EXACT RNAMOD [] synonym: "N6 methyladenosine" EXACT [] synonym: "N6-methyladenosine" EXACT [] xref: RNAMOD:003 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001298 name: two_prime_O_methyladenosine def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyladenosine" EXACT [] synonym: "Am" EXACT RNAMOD [] synonym: "two prime O methyladenosine" EXACT [] xref: RNAMOD:004 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001299 name: two_methylthio_N6_methyladenosine def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-methyladenosine" EXACT [] synonym: "ms2m6A" EXACT RNAMOD [] synonym: "two methylthio N6 methyladenosine" EXACT [] xref: RNAMOD:005 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001300 name: N6_isopentenyladenosine def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "i6A" EXACT RNAMOD [] synonym: "N6 isopentenyladenosine" EXACT [] synonym: "N6-isopentenyladenosine" EXACT [] xref: RNAMOD:006 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001301 name: two_methylthio_N6_isopentenyladenosine def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-isopentenyladenosine" EXACT [] synonym: "ms2i6A" EXACT RNAMOD [] synonym: "two methylthio N6 isopentenyladenosine" EXACT [] xref: RNAMOD:007 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001302 name: N6_cis_hydroxyisopentenyl_adenosine def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "io6A" EXACT RNAMOD [] synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT [] synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT [] xref: RNAMOD:008 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001303 name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT [] synonym: "ms2io6A" EXACT RNAMOD [] synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT [] xref: RNAMOD:009 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001304 name: N6_glycinylcarbamoyladenosine def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "g6A" EXACT RNAMOD [] synonym: "N6 glycinylcarbamoyladenosine" EXACT [] synonym: "N6-glycinylcarbamoyladenosine" EXACT [] xref: RNAMOD:010 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001305 name: N6_threonylcarbamoyladenosine def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-threonylcarbamoyladenosine" EXACT [] synonym: "t6A" EXACT RNAMOD [] xref: RNAMOD:011 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001306 name: two_methylthio_N6_threonyl_carbamoyladenosine def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT [] synonym: "ms2t6A" EXACT RNAMOD [] synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT [] xref: RNAMOD:012 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001307 name: N6_methyl_N6_threonylcarbamoyladenosine def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6t6A" EXACT RNAMOD [] synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT [] xref: RNAMOD:013 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001308 name: N6_hydroxynorvalylcarbamoyladenosine def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "hn6A" EXACT RNAMOD [] synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT [] synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT [] xref: RNAMOD:014 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001309 name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT [] synonym: "ms2hn6A" EXACT RNAMOD [] synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT [] xref: RNAMOD:015 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001310 name: two_prime_O_ribosyladenosine_phosphate def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosyladenosine (phosphate)" EXACT [] synonym: "Ar(p)" EXACT RNAMOD [] synonym: "two prime O ribosyladenosine phosphate" EXACT [] xref: RNAMOD:016 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001311 name: N6_N6_dimethyladenosine def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62A" EXACT RNAMOD [] synonym: "N6,N6-dimethyladenosine" EXACT [] xref: RNAMOD:080 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001312 name: N6_2_prime_O_dimethyladenosine def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6Am" EXACT RNAMOD [] synonym: "N6 2 prime O dimethyladenosine" EXACT [] synonym: "N6,2'-O-dimethyladenosine" EXACT [] xref: RNAMOD:088 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001313 name: N6_N6_2_prime_O_trimethyladenosine def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62Am" EXACT RNAMOD [] synonym: "N6,N6,2'-O-trimethyladenosine" EXACT [] xref: RNAMOD:089 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001314 name: one_two_prime_O_dimethyladenosine def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethyladenosine" EXACT [] synonym: "m1Am" EXACT RNAMOD [] synonym: "one two prime O dimethyladenosine" EXACT [] xref: RNAMOD:097 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001315 name: N6_acetyladenosine def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "ac6A" EXACT RNAMOD [] synonym: "N6 acetyladenosine" EXACT [] synonym: "N6-acetyladenosine" EXACT [] xref: RNAMOD:102 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001316 name: seven_deazaguanosine def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-deazaguanosine" RELATED [] synonym: "seven deazaguanosine" EXACT [] is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001317 name: queuosine def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: " Q" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Queuosine "wiki" xref: RNAMOD:043 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001318 name: epoxyqueuosine def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "eQ" EXACT RNAMOD [] xref: RNAMOD:044 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001319 name: galactosyl_queuosine def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "galactosyl queuosine" EXACT [] synonym: "galactosyl-queuosine" EXACT [] synonym: "galQ" EXACT RNAMOD [] xref: RNAMOD:045 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001320 name: mannosyl_queuosine def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "mannosyl queuosine" EXACT [] synonym: "mannosyl-queuosine" EXACT [] synonym: "manQ" EXACT RNAMOD [] xref: RNAMOD:046 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001321 name: seven_cyano_seven_deazaguanosine def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-cyano-7-deazaguanosine" EXACT [] synonym: "preQ0" EXACT RNAMOD [] synonym: "seven cyano seven deazaguanosine" EXACT [] xref: RNAMOD:047 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001322 name: seven_aminomethyl_seven_deazaguanosine def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-aminomethyl-7-deazaguanosine" EXACT [] synonym: "preQ1" EXACT RNAMOD [] synonym: "seven aminomethyl seven deazaguanosine" EXACT [] xref: RNAMOD:048 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001323 name: archaeosine def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "G+" EXACT RNAMOD [] xref: RNAMOD:049 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001324 name: one_methylguanosine def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylguanosine" EXACT [] synonym: "m1G" EXACT RNAMOD [] synonym: "one methylguanosine" EXACT [] xref: RNAMOD:029 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001325 name: N2_methylguanosine def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2G" EXACT RNAMOD [] synonym: "N2 methylguanosine" EXACT [] synonym: "N2-methylguanosine" EXACT [] xref: RNAMOD:030 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001326 name: seven_methylguanosine def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "7-methylguanosine" EXACT [] synonym: "m7G" EXACT RNAMOD [] synonym: "seven methylguanosine" EXACT [] xref: RNAMOD:031 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001327 name: two_prime_O_methylguanosine def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylguanosine" EXACT [] synonym: "Gm" EXACT RNAMOD [] synonym: "two prime O methylguanosine" EXACT [] xref: RNAMOD:032 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001328 name: N2_N2_dimethylguanosine def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22G" EXACT RNAMOD [] synonym: "N2,N2-dimethylguanosine" EXACT [] xref: RNAMOD:033 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001329 name: N2_2_prime_O_dimethylguanosine def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2Gm" EXACT RNAMOD [] synonym: "N2 2 prime O dimethylguanosine" EXACT [] synonym: "N2,2'-O-dimethylguanosine" EXACT [] xref: RNAMOD:034 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001330 name: N2_N2_2_prime_O_trimethylguanosine def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22Gmv" EXACT RNAMOD [] synonym: "N2,N2,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:035 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001331 name: two_prime_O_ribosylguanosine_phosphate def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosylguanosine (phosphate)" EXACT [] synonym: "Gr(p)" EXACT RNAMOD [] synonym: "two prime O ribosylguanosine phosphate" EXACT [] xref: RNAMOD:036 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001332 name: wybutosine def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "yW" EXACT RNAMOD [] xref: RNAMOD:037 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001333 name: peroxywybutosine def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "o2yW" EXACT RNAMOD [] xref: RNAMOD:038 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001334 name: hydroxywybutosine def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW" EXACT RNAMOD [] xref: RNAMOD:039 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001335 name: undermodified_hydroxywybutosine def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW*" EXACT RNAMOD [] synonym: "undermodified hydroxywybutosine" EXACT [] xref: RNAMOD:040 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001336 name: wyosine def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "IMG" EXACT RNAMOD [] xref: RNAMOD:041 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001337 name: methylwyosine def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mimG" EXACT RNAMOD [] xref: RNAMOD:042 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001338 name: N2_7_dimethylguanosine def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7G" EXACT RNAMOD [] synonym: "N2 7 dimethylguanosine" EXACT [] synonym: "N2,7-dimethylguanosine" EXACT [] xref: RNAMOD:090 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001339 name: N2_N2_7_trimethylguanosine def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,2,7G" EXACT RNAMOD [] synonym: "N2,N2,7-trimethylguanosine" EXACT [] xref: RNAMOD:091 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001340 name: one_two_prime_O_dimethylguanosine def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylguanosine" EXACT [] synonym: "m1Gm" EXACT RNAMOD [] synonym: "one two prime O dimethylguanosine" EXACT [] xref: RNAMOD:096 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001341 name: four_demethylwyosine def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-demethylwyosine" EXACT [] synonym: "four demethylwyosine" EXACT [] synonym: "imG-14" EXACT RNAMOD [] xref: RNAMOD:100 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001342 name: isowyosine def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "imG2" EXACT RNAMOD [] xref: RNAMOD:101 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001343 name: N2_7_2prirme_O_trimethylguanosine def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7Gm" EXACT RNAMOD [] synonym: "N2 7 2prirme O trimethylguanosine" EXACT [] synonym: "N2,7,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:106 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001344 name: five_methyluridine def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyluridine" EXACT [] synonym: "five methyluridine" EXACT [] synonym: "m5U" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki" xref: RNAMOD:052 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001345 name: two_prime_O_methyluridine def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyluridine" EXACT [] synonym: "two prime O methyluridine" EXACT [] synonym: "Um" EXACT RNAMOD [] xref: RNAMOD:053 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001346 name: five_two_prime_O_dimethyluridine def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethyluridine" EXACT [] synonym: "five two prime O dimethyluridine" EXACT [] synonym: "m5Um" EXACT RNAMOD [] xref: RNAMOD:054 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001347 name: one_methylpseudouridine def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylpseudouridine" EXACT [] synonym: "m1Y" EXACT RNAMOD [] synonym: "one methylpseudouridine" EXACT [] xref: RNAMOD:055 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001348 name: two_prime_O_methylpseudouridine def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylpseudouridine" EXACT [] synonym: "two prime O methylpseudouridine" EXACT [] synonym: "Ym" EXACT RNAMOD [] xref: RNAMOD:056 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001349 name: two_thiouridine def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiouridine" EXACT [] synonym: "s2U" EXACT RNAMOD [] synonym: "two thiouridine" EXACT [] xref: RNAMOD:057 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001350 name: four_thiouridine def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-thiouridine" EXACT [] synonym: "four thiouridine" EXACT [] synonym: "s4U" EXACT RNAMOD [] xref: RNAMOD:058 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001351 name: five_methyl_2_thiouridine def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyl-2-thiouridine" EXACT [] synonym: "five methyl 2 thiouridine" EXACT [] synonym: "m5s2U" EXACT RNAMOD [] xref: RNAMOD:059 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001352 name: two_thio_two_prime_O_methyluridine def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thio-2'-O-methyluridine" EXACT [] synonym: "s2Um" EXACT RNAMOD [] synonym: "two thio two prime O methyluridine" EXACT [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001353 name: three_three_amino_three_carboxypropyl_uridine def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT [] synonym: "acp3U" EXACT RNAMOD [] xref: RNAMOD:061 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001354 name: five_hydroxyuridine def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxyuridine" EXACT [] synonym: "five hydroxyuridine" EXACT [] synonym: "ho5U" EXACT RNAMOD [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001355 name: five_methoxyuridine def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxyuridine" EXACT [] synonym: "five methoxyuridine" EXACT [] synonym: "mo5U" EXACT RNAMOD [] xref: RNAMOD:063 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001356 name: uridine_five_oxyacetic_acid def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "cmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid" EXACT [] synonym: "uridine five oxyacetic acid" EXACT [] xref: RNAMOD:064 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001357 name: uridine_five_oxyacetic_acid_methyl_ester def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mcmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid methyl ester" EXACT [] synonym: "uridine five oxyacetic acid methyl ester" EXACT [] xref: RNAMOD:065 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001358 name: five_carboxyhydroxymethyl_uridine def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine" EXACT [] synonym: "chm5U" EXACT RNAMOD [] synonym: "five carboxyhydroxymethyl uridine" EXACT [] xref: RNAMOD:066 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001359 name: five_carboxyhydroxymethyl_uridine_methyl_ester def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT [] synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT [] synonym: "mchm5U" EXACT RNAMOD [] xref: RNAMOD:067 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001360 name: five_methoxycarbonylmethyluridine def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyluridine" EXACT [] synonym: "five methoxycarbonylmethyluridine" EXACT [] synonym: "mcm5U" EXACT RNAMOD [] xref: RNAMOD:068 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001361 name: five_methoxycarbonylmethyl_two_prime_O_methyluridine def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT [] synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT [] synonym: "mcm5Um" EXACT RNAMOD [] xref: RNAMOD:069 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001362 name: five_methoxycarbonylmethyl_two_thiouridine def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT [] synonym: "five methoxycarbonylmethyl two thiouridine" EXACT [] synonym: "mcm5s2U" EXACT RNAMOD [] xref: RNAMOD:070 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001363 name: five_aminomethyl_two_thiouridine def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-aminomethyl-2-thiouridine" EXACT [] synonym: "five aminomethyl two thiouridine" EXACT [] synonym: "nm5s2U" EXACT RNAMOD [] xref: RNAMOD:071 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001364 name: five_methylaminomethyluridine def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyluridine" EXACT [] synonym: "five methylaminomethyluridine" EXACT [] synonym: "mnm5U" EXACT RNAMOD [] xref: RNAMOD:072 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001365 name: five_methylaminomethyl_two_thiouridine def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-thiouridine" EXACT [] synonym: "five methylaminomethyl two thiouridine" EXACT [] synonym: "mnm5s2U" EXACT RNAMOD [] xref: RNAMOD:073 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001366 name: five_methylaminomethyl_two_selenouridine def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-selenouridine" EXACT [] synonym: "five methylaminomethyl two selenouridine" EXACT [] synonym: "mnm5se2U" EXACT RNAMOD [] xref: RNAMOD:074 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001367 name: five_carbamoylmethyluridine def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyluridine" EXACT [] synonym: "five carbamoylmethyluridine" EXACT [] synonym: "ncm5U" EXACT RNAMOD [] xref: RNAMOD:075 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001368 name: five_carbamoylmethyl_two_prime_O_methyluridine def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT [] synonym: "five carbamoylmethyl two prime O methyluridine" EXACT [] synonym: "ncm5Um" EXACT RNAMOD [] xref: RNAMOD:076 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001369 name: five_carboxymethylaminomethyluridine def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyluridine" EXACT [] synonym: "cmnm5U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyluridine" EXACT [] xref: RNAMOD:077 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001370 name: five_carboxymethylaminomethyl_two_prime_O_methyluridine def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT [] synonym: "cmnm5Um" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT [] xref: RNAMOD:078 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001371 name: five_carboxymethylaminomethyl_two_thiouridine def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT [] synonym: "cmnm5s2U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two thiouridine" EXACT [] xref: RNAMOD:079 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001372 name: three_methyluridine def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methyluridine" EXACT [] synonym: "m3U" EXACT RNAMOD [] synonym: "three methyluridine" EXACT [] xref: RNAMOD:085 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001373 name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT [] synonym: "m1acp3Y" EXACT RNAMOD [] xref: RNAMOD:086 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001374 name: five_carboxymethyluridine def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethyluridine" EXACT [] synonym: "cm5U" EXACT RNAMOD [] synonym: "five carboxymethyluridine" EXACT [] xref: RNAMOD:087 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001375 name: three_two_prime_O_dimethyluridine def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3,2'-O-dimethyluridine" EXACT [] synonym: "m3Um" EXACT RNAMOD [] synonym: "three two prime O dimethyluridine" EXACT [] xref: RNAMOD:092 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001376 name: five_methyldihydrouridine def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyldihydrouridine" EXACT [] synonym: "five methyldihydrouridine" EXACT [] synonym: "m5D" EXACT RNAMOD [] xref: RNAMOD:093 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001377 name: three_methylpseudouridine def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylpseudouridine" EXACT [] synonym: "m3Y" EXACT RNAMOD [] synonym: "three methylpseudouridine" EXACT [] xref: RNAMOD:094 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001378 name: five_taurinomethyluridine def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyluridine" EXACT [] synonym: "five taurinomethyluridine" EXACT [] synonym: "tm5U" EXACT RNAMOD [] xref: RNAMOD:098 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001379 name: five_taurinomethyl_two_thiouridine def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyl-2-thiouridine" EXACT [] synonym: "five taurinomethyl two thiouridine" EXACT [] synonym: "tm5s2U" EXACT RNAMOD [] xref: RNAMOD:099 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001380 name: five_isopentenylaminomethyl_uridine def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)uridine" EXACT [] synonym: "five isopentenylaminomethyl uridine" EXACT [] synonym: "inm5U" EXACT RNAMOD [] xref: RNAMOD:103 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001381 name: five_isopentenylaminomethyl_two_thiouridine def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT [] synonym: "five isopentenylaminomethyl two thiouridine" EXACT [] synonym: "inm5s2U" EXACT RNAMOD [] xref: RNAMOD:104 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001382 name: five_isopentenylaminomethyl_two_prime_O_methyluridine def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT [] synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT [] synonym: "inm5Um" EXACT RNAMOD [] xref: RNAMOD:105 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001383 name: histone_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke] synonym: "histone binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0001384 name: CDS_fragment def: "A portion of a CDS that is not the complete CDS." [] synonym: "CDS fragment" EXACT [] synonym: "incomplete CDS" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000731 ! fragmentary relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0001385 name: modified_amino_acid_feature def: "A post translationally modified amino acid feature." [SO:ke] synonym: "modified amino acid feature" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001386 name: modified_glycine def: "A post translationally modified glycine amino acid feature." [SO:ke] synonym: "ModGly" EXACT AAMOD [] synonym: "modified glycine" EXACT [] xref: MOD:00908 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001387 name: modified_L_alanine def: "A post translationally modified alanine amino acid feature." [SO:ke] synonym: "ModAla" EXACT AAMOD [] synonym: "modified L alanine" EXACT [] synonym: "modified L-alanine" EXACT [] xref: MOD:00901 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001388 name: modified_L_asparagine def: "A post translationally modified asparagine amino acid feature." [SO:ke] synonym: "ModAsn" EXACT AAMOD [] synonym: "modified L asparagine" EXACT [] synonym: "modified L-asparagine" EXACT [] xref: MOD:00903 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001389 name: modified_L_aspartic_acid def: "A post translationally modified aspartic acid amino acid feature." [SO:ke] synonym: "ModAsp" EXACT AAMOD [] synonym: "modified L aspartic acid" EXACT [] synonym: "modified L-aspartic acid" EXACT [] xref: MOD:00904 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001390 name: modified_L_cysteine def: "A post translationally modified cysteine amino acid feature." [SO:ke] synonym: "ModCys" EXACT AAMOD [] synonym: "modified L cysteine" EXACT [] synonym: "modified L-cysteine" EXACT [] xref: MOD:00905 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001391 name: modified_L_glutamic_acid def: "A post translationally modified glutamic acid." [] synonym: "ModGlu" EXACT AAMOD [] synonym: "modified L glutamic acid" EXACT [] synonym: "modified L-glutamic acid" EXACT [] xref: MOD:00906 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001392 name: modified_L_threonine def: "A post translationally modified threonine amino acid feature." [SO:ke] synonym: "modified L threonine" EXACT [] synonym: "modified L-threonine" EXACT [] synonym: "ModThr" EXACT AAMOD [] xref: MOD:00917 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001393 name: modified_L_tryptophan def: "A post translationally modified tryptophan amino acid feature." [SO:ke] synonym: "modified L tryptophan" EXACT [] synonym: "modified L-tryptophan" EXACT [] synonym: "ModTrp" EXACT AAMOD [] xref: MOD:00918 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001394 name: modified_L_glutamine def: "A post translationally modified glutamine amino acid feature." [SO:ke] synonym: "ModGln" EXACT [] synonym: "modified L glutamine" EXACT [] synonym: "modified L-glutamine" EXACT [] xref: MOD:00907 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001395 name: modified_L_methionine def: "A post translationally modified methionine amino acid feature." [SO:ke] synonym: "modified L methionine" EXACT [] synonym: "modified L-methionine" EXACT [] synonym: "ModMet" EXACT AAMOD [] xref: MOD:00913 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001396 name: modified_L_isoleucine def: "A post translationally modified isoleucine amino acid feature." [SO:ke] synonym: "modified L isoleucine" EXACT [] synonym: "modified L-isoleucine" EXACT [] synonym: "ModIle" EXACT AAMOD [] xref: MOD:00910 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001397 name: modified_L_phenylalanine def: "A post translationally modified phenylalanine amino acid feature." [SO:ke] synonym: "modified L phenylalanine" EXACT [] synonym: "modified L-phenylalanine" EXACT [] synonym: "ModPhe" EXACT AAMOD [] xref: MOD:00914 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001398 name: modified_L_histidine def: "A post translationally modified histidine amino acid feature." [SO:ke] synonym: "ModHis" EXACT [] synonym: "modified L histidine" EXACT [] synonym: "modified L-histidine" EXACT [] xref: MOD:00909 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001399 name: modified_L_serine def: "A post translationally modified serine amino acid feature." [SO:ke] synonym: "modified L serine" EXACT [] synonym: "modified L-serine" EXACT [] synonym: "MosSer" EXACT AAMOD [] xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104" is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001400 name: modified_L_lysine def: "A post translationally modified lysine amino acid feature." [SO:ke] synonym: "modified L lysine" EXACT [] synonym: "modified L-lysine" EXACT [] synonym: "ModLys" EXACT AAMOD [] xref: MOD:00912 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001401 name: modified_L_leucine def: "A post translationally modified leucine amino acid feature." [SO:ke] synonym: "modified L leucine" EXACT [] synonym: "modified L-leucine " EXACT [] synonym: "ModLeu" EXACT AAMOD [] xref: MOD:00911 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001402 name: modified_L_selenocysteine def: "A post translationally modified selenocysteine amino acid feature." [SO:ke] synonym: "modified L selenocysteine" EXACT [] synonym: "modified L-selenocysteine" EXACT [] xref: MOD:01158 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001403 name: modified_L_valine def: "A post translationally modified valine amino acid feature." [SO:ke] synonym: "modified L valine" EXACT [] synonym: "modified L-valine" EXACT [] synonym: "ModVal" EXACT AAMOD [] xref: MOD:00920 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001404 name: modified_L_proline def: "A post translationally modified proline amino acid feature." [SO:ke] synonym: "modified L proline" EXACT [] synonym: "modified L-proline " EXACT [] synonym: "ModPro" EXACT AAMOD [] xref: MOD:00915 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001405 name: modified_L_tyrosine def: "A post translationally modified tyrosine amino acid feature." [SO:ke] synonym: "modified L tyrosine" EXACT [] synonym: "modified L-tyrosine" EXACT [] synonym: "ModTry" EXACT AAMOD [] xref: MOD:00919 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001406 name: modified_L_arginine def: "A post translationally modified arginine amino acid feature." [SO:ke] synonym: "ModArg" EXACT AAMOD [] synonym: "modified L arginine" EXACT [] synonym: "modified L-arginine" EXACT [] xref: MOD:00902 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001407 name: peptidyl def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0001408 name: cleaved_for_gpi_anchor_region def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh] synonym: "cleaved for gpi anchor region" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0001409 name: biomaterial_region def: "A region which is intended for use in an experiment." [SO:cb] subset: SOFA synonym: "biomaterial region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001410 name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] synonym: "INSDC_misc_feature" BROAD [] synonym: "INSDC_note:biological_region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region def: "A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping." [PMID:32782014, SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001413 name: translocation_breakpoint def: "The point within a chromosome where a translocation begins or ends." [SO:cb] synonym: "translocation breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001414 name: insertion_breakpoint def: "The point within a chromosome where a insertion begins or ends." [SO:cb] synonym: "insertion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001415 name: deletion_breakpoint def: "The point within a chromosome where a deletion begins or ends." [SO:cb] synonym: "deletion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001416 name: five_prime_flanking_region def: "A flanking region located five prime of a specific region." [SO:chado] synonym: "5' flanking region" RELATED [] synonym: "five prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001417 name: three_prime_flanking_region def: "A flanking region located three prime of a specific region." [SO:chado] synonym: "3' flanking region" RELATED [] synonym: "three prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001418 name: transcribed_fragment def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke] comment: Term requested by the MODencode group. synonym: "transcribed fragment" EXACT [] synonym: "transfrag" RELATED [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001419 name: cis_splice_site def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] subset: SOFA synonym: "cis splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001420 name: trans_splice_site def: "Primary transcript region bordering trans-splice junction." [SO:ke] subset: SOFA synonym: "trans splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001421 name: splice_junction def: "The boundary between an intron and an exon." [SO:ke] synonym: "splice boundary" EXACT [] synonym: "splice junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0001422 name: conformational_switch def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke] comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999. synonym: "polypeptide conformational switch" EXACT [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001423 name: dye_terminator_read def: "A read produced by the dye terminator method of sequencing." [SO:ke] synonym: "dye terminator read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001424 name: pyrosequenced_read def: "A read produced by pyrosequencing technology." [SO:ke] comment: An example is a read produced by Roche 454 technology. synonym: "pyorsequenced read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001425 name: ligation_based_read def: "A read produced by ligation based sequencing technologies." [SO:ke] comment: An example of this kind of read is one produced by ABI SOLiD. synonym: "ligation based read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001426 name: polymerase_synthesis_read def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke] comment: An example is a read produced by Illumina technology. synonym: "polymerase synthesis read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001427 name: cis_regulatory_frameshift_element def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "cis regulatory frameshift element" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001428 name: expressed_sequence_assembly def: "A sequence assembly derived from expressed sequences." [SO:ke] comment: From tracker [ 2372385 ] expressed_sequence_assembly. synonym: "expressed sequence assembly" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0001429 name: DNA_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] synonym: "DNA binding site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0001431 name: cryptic_gene def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] synonym: "cryptic gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000976 ! cryptic relationship: has_quality SO:0000976 ! cryptic [Term] id: SO:0001432 name: sequence_variant_affecting_polyadenylation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting polyadenylation" RELATED [] synonym: "sequence variant affecting polyadenylation" EXACT [] is_obsolete: true replaced_by: SO:0001545 [Term] id: SO:0001433 name: three_prime_RACE_clone def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw] synonym: "3' RACE clone" RELATED [] is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0001434 name: cassette_pseudogene def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke] comment: Requested by the Trypanosome community. synonym: "cassette pseudogene" EXACT [] synonym: "cassette type psedogene" RELATED [] is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001435 name: alanine def: "A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG)." [] comment: A place holder for a cross product with chebi. synonym: "A" EXACT aa1 [] synonym: "Ala" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001436 name: valine def: "A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG)." [] comment: A place holder for a cross product with chebi. synonym: "V" EXACT aa1 [] synonym: "Val" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001437 name: leucine def: "A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG." [] comment: A place holder for a cross product with chebi. synonym: "L" EXACT aa1 [] synonym: "Leu" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001438 name: isoleucine def: "A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA)." [] comment: A place holder for a cross product with chebi. synonym: "I" EXACT aa1 [] synonym: "Ile" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001439 name: proline def: "A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG)." [] comment: A place holder for a cross product with chebi. synonym: "P" EXACT aa1 [] synonym: "Pro" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001440 name: tryptophan def: "A non-polar, hydorophobic amino acid encoded by the codon TGG." [] comment: A place holder for a cross product with chebi. synonym: "Trp" EXACT aa3 [] synonym: "W" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001441 name: phenylalanine def: "A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC." [] comment: A place holder for a cross product with chebi. synonym: "F" EXACT aa1 [] synonym: "Phe" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001442 name: methionine def: "A non-polar, hydorophobic amino acid encoded by the codon ATG." [] comment: A place holder for a cross product with chebi. synonym: "M" EXACT aa1 [] synonym: "Met" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001443 name: glycine def: "A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG)." [] comment: A place holder for a cross product with chebi. synonym: "G" EXACT aa1 [] synonym: "Gly" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001444 name: serine def: "A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC." [] comment: A place holder for a cross product with chebi. synonym: "S" EXACT aa1 [] synonym: "Ser" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001445 name: threonine def: "A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG)." [] comment: A place holder for a cross product with chebi. synonym: "T" EXACT aa1 [] synonym: "Thr" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001446 name: tyrosine def: "A polar, hydorophilic amino acid encoded by the codons TAT and TAC." [] comment: A place holder for a cross product with chebi. synonym: "Tyr" EXACT aa3 [] synonym: "Y" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001447 name: cysteine def: "A polar amino acid encoded by the codons TGT and TGC." [] comment: A place holder for a cross product with chebi. synonym: "C" EXACT aa1 [] synonym: "Cys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001448 name: glutamine def: "A polar, hydorophilic amino acid encoded by the codons CAA and CAG. " [] comment: A place holder for a cross product with chebi. synonym: "Gln" EXACT aa3 [] synonym: "Q" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001449 name: asparagine def: "A polar, hydorophilic amino acid encoded by the codons AAT and AAC." [] comment: A place holder for a cross product with chebi. synonym: "Asn" EXACT aa3 [] synonym: "N" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001450 name: lysine def: "A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG." [] comment: A place holder for a cross product with chebi. synonym: "K" EXACT aa1 [] synonym: "Lys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001451 name: arginine def: "A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG." [] comment: A place holder for a cross product with chebi. synonym: "Arg" EXACT aa3 [] synonym: "R" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001452 name: histidine def: "A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC." [] comment: A place holder for a cross product with chebi. synonym: "H" EXACT aa1 [] synonym: "His" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001453 name: aspartic_acid def: "A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC." [] comment: A place holder for a cross product with chebi. synonym: "Asp" EXACT aa3 [] synonym: "aspartic acid" EXACT [] synonym: "D" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001454 name: glutamic_acid def: "A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG." [] comment: A place holder for a cross product with chebi. synonym: "E" EXACT aa1 [] synonym: "Glu" EXACT aa3 [] synonym: "glutamic acid" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001455 name: selenocysteine def: "A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts." [PMID:23275319] comment: A place holder for a cross product with chebi. synonym: "Sec" EXACT aa3 [] synonym: "U" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001456 name: pyrrolysine def: "A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts." [PMID:15788401] comment: A place holder for a cross product with chebi. synonym: "O" EXACT aa1 [] synonym: "Pyl" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001457 name: transcribed_cluster def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "transcribed cluster" EXACT [] synonym: "unigene cluster" RELATED [] is_a: SO:0001410 ! experimental_feature relationship: has_part SO:0000695 ! reagent [Term] id: SO:0001458 name: unigene_cluster def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "unigene cluster" RELATED [] is_a: SO:0001457 ! transcribed_cluster [Term] id: SO:0001459 name: CRISPR def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd] synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT [] synonym: "CRISPR element" EXACT [] xref: http:en.wikipedia.org/wiki/CRISPR is_a: SO:0000314 ! direct_repeat [Term] id: SO:0001460 name: insulator_binding_site def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] comment: See tracker ID 2060908. synonym: "insulator binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000627 ! insulator [Term] id: SO:0001461 name: enhancer_binding_site def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] synonym: "enhancer binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000165 ! enhancer [Term] id: SO:0001462 name: contig_collection def: "A collection of contigs." [SO:ke] comment: See tracker ID: 2138359. synonym: "contig collection" EXACT [] is_a: SO:0001085 ! sequence_conflict is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001085 ! sequence_conflict intersection_of: has_part SO:0000149 ! contig relationship: has_part SO:0000149 ! contig [Term] id: SO:0001463 name: lincRNA def: "Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand." [http://www.gencodegenes.org/gencode_biotypes.html, PMID:19182780, PMID:23463798, SO:ke] synonym: "large intervening non-coding RNA" EXACT [] synonym: "long intergenic non-coding RNA" EXACT [] synonym: "long intervening non-coding RNA" EXACT [] is_a: SO:0001877 ! lncRNA [Term] id: SO:0001464 name: UST def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw] synonym: "UTR sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001465 name: three_prime_UST def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw] synonym: "3' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001466 name: five_prime_UST def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw] synonym: "5' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001467 name: RST def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "RACE sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001468 name: three_prime_RST def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "3' RST" EXACT [] is_a: SO:0001467 ! RST [Term] id: SO:0001469 name: five_prime_RST def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "5' RST" RELATED [] is_a: SO:0001467 ! RST [Term] id: SO:0001470 name: UST_match def: "A match against an UST sequence." [SO:nlw] synonym: "UST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001471 name: RST_match def: "A match against an RST sequence." [SO:nlw] synonym: "RST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001472 name: primer_match def: "A nucleotide match to a primer sequence." [SO:nlw] synonym: "primer match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0001473 name: miRNA_antiguide def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke] synonym: "miRNA antiguide " EXACT [] synonym: "miRNA passenger strand" EXACT [] synonym: "miRNA star" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region created_by: kareneilbeck creation_date: 2009-05-27T03:35:43Z [Term] id: SO:0001474 name: trans_splice_junction def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke] synonym: "trans-splice junction" EXACT [] is_a: SO:0000699 ! junction created_by: kareneilbeck creation_date: 2009-07-13T04:50:49Z [Term] id: SO:0001475 name: outron def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke] is_a: SO:0000835 ! primary_transcript_region created_by: kareneilbeck creation_date: 2009-07-14T11:36:08Z [Term] id: SO:0001476 name: natural_plasmid def: "A plasmid that occurs naturally." [SO:xp] synonym: "natural plasmid" EXACT [] is_a: SO:0000155 ! plasmid is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element intersection_of: SO:0000155 ! plasmid intersection_of: has_quality SO:0000782 ! natural relationship: has_quality SO:0000782 ! natural created_by: kareneilbeck creation_date: 2009-09-01T03:43:06Z [Term] id: SO:0001477 name: gene_trap_construct def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] synonym: "gene trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:49:09Z [Term] id: SO:0001478 name: promoter_trap_construct def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] synonym: "promoter trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:52:01Z [Term] id: SO:0001479 name: enhancer_trap_construct def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] synonym: "enhancer trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:53:26Z [Term] id: SO:0001480 name: PAC_end def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh] synonym: "PAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000154 ! PAC created_by: kareneilbeck creation_date: 2009-09-09T05:18:12Z [Term] id: SO:0001481 name: RAPD def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh] synonym: "Random Amplification Polymorphic DNA" EXACT [] is_a: SO:0000006 ! PCR_product created_by: kareneilbeck creation_date: 2009-09-09T05:26:10Z [Term] id: SO:0001482 name: shadow_enhancer def: "An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene." [PMID:22083793] synonym: "shadow enhancer" EXACT [] is_a: SO:0000165 ! enhancer created_by: kareneilbeck creation_date: 2009-09-09T05:29:29Z [Term] id: SO:0001483 name: SNV def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] subset: SOFA synonym: "single nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2009-10-08T11:37:49Z [Term] id: SO:0001484 name: X_element_combinatorial_repeat def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html] comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:x_element_combinatorial_repeat" EXACT [] synonym: "X element combinatorial repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T11:03:37Z [Term] id: SO:0001485 name: Y_prime_element def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http\://www.yeastgenome.org/help/glossary.html] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:Y_prime_element" EXACT [] synonym: "Y prime element" EXACT [] synonym: "Y' element" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T12:08:57Z [Term] id: SO:0001486 name: standard_draft def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126] synonym: "standard draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:48:32Z [Term] id: SO:0001487 name: high_quality_draft def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126] synonym: "high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:52:36Z [Term] id: SO:0001488 name: improved_high_quality_draft def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126] synonym: "improved high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:54:35Z [Term] id: SO:0001489 name: annotation_directed_improved_draft def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126] synonym: "annotation directed improvement" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:57:10Z [Term] id: SO:0001490 name: noncontiguous_finished def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126] synonym: "non contiguous finished" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:01:07Z [Term] id: SO:0001491 name: finished_genome def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126] synonym: "finished" EXACT [] synonym: "finished genome" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:04:43Z [Term] id: SO:0001492 name: intronic_regulatory_region def: "A regulatory region that is part of an intron." [SO:ke] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "intronic regulatory region" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region relationship: part_of SO:0000188 ! intron created_by: kareneilbeck creation_date: 2009-11-08T02:48:02Z [Term] id: SO:0001493 name: centromere_DNA_Element_I def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEI" EXACT [] synonym: "Centromere DNA Element I" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:47:23Z [Term] id: SO:0001494 name: centromere_DNA_Element_II def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEII" EXACT [] synonym: "centromere DNA Element II" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:51:26Z [Term] id: SO:0001495 name: centromere_DNA_Element_III def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEIII" EXACT [] synonym: "centromere DNA Element III" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:54:47Z [Term] id: SO:0001496 name: telomeric_repeat def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065] comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739. synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:telomeric_repeat" EXACT [] synonym: "telomeric repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-09T06:00:42Z [Term] id: SO:0001497 name: X_element def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434] comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.\n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1. synonym: "X element" RELATED [] synonym: "X element core sequence" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T10:56:54Z [Term] id: SO:0001498 name: YAC_end def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke] synonym: "YAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000152 ! YAC created_by: kareneilbeck creation_date: 2009-11-19T11:07:18Z [Term] id: SO:0001499 name: whole_genome_sequence_status def: "The status of whole genome sequence." [DOI:10.1126] comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms. synonym: "whole genome sequence status" EXACT [] is_a: SO:0000905 ! status created_by: kareneilbeck creation_date: 2009-10-23T12:47:47Z [Term] id: SO:0001500 name: heritable_phenotypic_marker def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] synonym: "heritable phenotypic marker" EXACT [] synonym: "phenotypic marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2009-12-07T01:50:55Z [Term] id: SO:0001501 name: peptide_collection def: "A collection of peptide sequences." [BBOP:nlw] comment: Term requested via tracker ID: 2910829. synonym: "peptide collection" EXACT [] synonym: "peptide set" EXACT [] is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0000104 ! polypeptide relationship: has_part SO:0000104 ! polypeptide created_by: kareneilbeck creation_date: 2009-12-11T10:58:58Z [Term] id: SO:0001502 name: high_identity_region def: "An experimental feature with high sequence identity to another sequence." [SO:ke] comment: Requested by tracker ID: 2902685. synonym: "high identity region" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2009-12-11T11:06:05Z [Term] id: SO:0001503 name: processed_transcript def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen] comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI. synonym: "processed transcript" EXACT [] is_a: SO:0000673 ! transcript created_by: kareneilbeck creation_date: 2009-12-21T05:37:14Z [Term] id: SO:0001504 name: assortment_derived_variation def: "A chromosome variation derived from an event during meiosis." [SO:ke] synonym: "assortment derived variation" RELATED [] is_a: SO:0000240 ! chromosome_variation created_by: kareneilbeck creation_date: 2010-03-02T05:03:18Z [Term] id: SO:0001505 name: reference_genome def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] synonym: "reference genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:10:03Z [Term] id: SO:0001506 name: variant_genome def: "A collection of sequences (often chromosomes) of an individual." [SO:ke] synonym: "variant genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:11:25Z [Term] id: SO:0001507 name: variant_collection def: "A collection of one or more sequences of an individual." [SO:ke] synonym: "variant collection" RELATED [] is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0001059 ! sequence_alteration relationship: has_part SO:0001059 ! sequence_alteration created_by: kareneilbeck creation_date: 2010-03-03T02:13:28Z [Term] id: SO:0001508 name: alteration_attribute def: "An attribute of alteration of one or more chromosomes." [] synonym: "alteration attribute" EXACT [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:53:23Z [Term] id: SO:0001509 name: chromosomal_variation_attribute def: "An attribute of a change in the structure or number of a chromosomes." [] synonym: "chromosomal variation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:54:30Z [Term] id: SO:0001510 name: intrachromosomal def: "A change in chromosomes that occurs between two separate chromosomes." [] is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:25Z [Term] id: SO:0001511 name: interchromosomal def: "A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes." [] is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:43Z [Term] id: SO:0001512 name: insertion_attribute def: "A quality of a chromosomal insertion,." [SO:ke] synonym: "insertion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:56Z [Term] id: SO:0001513 name: tandem def: "An insertion of extension of a tandem repeat." [] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:37Z [Term] id: SO:0001514 name: direct def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:49Z [Term] id: SO:0001515 name: inverted def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:40Z [Term] id: SO:0001516 name: free def: "The quality of a duplication where the new region exists independently of the original." [SO:ke] is_a: SO:0001523 ! duplication_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:51Z [Term] id: SO:0001517 name: inversion_attribute def: "When a region of a chromosome is changed to the reverse order without duplication or deletion." [] synonym: "inversion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:10Z [Term] id: SO:0001518 name: pericentric def: "An inversion event that includes the centromere." [] is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:24Z [Term] id: SO:0001519 name: paracentric def: "An inversion event that does not include the centromere." [] is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:35Z [Term] id: SO:0001520 name: translocaton_attribute def: "An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [] synonym: "translocation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:47Z [Term] id: SO:0001521 name: reciprocal def: "When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials." [] is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:34Z [Term] id: SO:0001522 name: insertional def: "When a translocation is simply moving genetic material from one chromosome to another." [] is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:51Z [Term] id: SO:0001523 name: duplication_attribute def: "An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [] synonym: "duplication attribute" RELATED [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-05T01:56:33Z [Term] id: SO:0001524 name: chromosomally_aberrant_genome def: "When a genome contains an abnormal amount of chromosomes." [] synonym: "chromosomally aberrant genome" RELATED [] is_a: SO:0001506 ! variant_genome created_by: kareneilbeck creation_date: 2010-03-05T02:21:00Z [Term] id: SO:0001525 name: assembly_error_correction def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke] synonym: "assembly error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:16:31Z [Term] id: SO:0001526 name: base_call_error_correction def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke] synonym: "base call error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:18:07Z [Term] id: SO:0001527 name: peptide_localization_signal def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] subset: SOFA synonym: "localization signal" RELATED [] synonym: "peptide localization signal" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2010-03-11T02:15:05Z [Term] id: SO:0001528 name: nuclear_localization_signal def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] synonym: "NLS" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia" is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:16:38Z [Term] id: SO:0001529 name: endosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] synonym: "endosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:20:58Z [Term] id: SO:0001530 name: lysosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] synonym: "lysosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:24:10Z [Term] id: SO:0001531 name: nuclear_export_signal def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] synonym: "NES" EXACT [] synonym: "nuclear export signal" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_export_signal is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:25:25Z [Term] id: SO:0001532 name: recombination_signal_sequence def: "A region recognized by a recombinase." [SO:ke] synonym: "recombination signal sequence" RELATED [] xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia" is_a: SO:0000299 ! specific_recombination_site created_by: kareneilbeck creation_date: 2010-03-11T03:16:47Z [Term] id: SO:0001533 name: cryptic_splice_site def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke] synonym: "cryptic splice signal" RELATED [] synonym: "cryptic splice site" EXACT [] is_a: SO:0000162 ! splice_site created_by: kareneilbeck creation_date: 2010-03-11T03:25:06Z [Term] id: SO:0001534 name: nuclear_rim_localization_signal def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke] synonym: "nuclear rim localization signal" RELATED [] xref: PMID:16027110 is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T03:31:30Z [Term] id: SO:0001535 name: P_TIR_transposon def: "A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain." [PMID:6309410, SO:ke] comment: Moved from under DNA_transposon (SO:0000182) by Dave Sant as per request from GitHub issue #488 on June 25, 2020 synonym: "DTP transposon" EXACT [] synonym: "P element" EXACT [] synonym: "P TIR transposon" EXACT [] synonym: "P transposable element" EXACT [] synonym: "P-element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: kareneilbeck creation_date: 2010-03-12T03:40:33Z [Term] id: SO:0001536 name: functional_effect_variant def: "A variant whereby the effect is evaluated with respect to a reference." [SO:ke] comment: Updated after request from Lea Starita, lea.starita@gmail.com from the NCBI. synonym: "functional effect variant" EXACT [] synonym: "functional variant" EXACT [] is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:30:25Z [Term] id: SO:0001537 name: structural_variant def: "A sequence variant that changes one or more structural features." [SO:ke] synonym: "Jannovar:structural_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "structural variant" RELATED [] synonym: "VAT:svOverlap" EXACT VAR [] xref: http://vat.gersteinlab.org/formats.php "VAT" is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:31:01Z [Term] id: SO:0001538 name: transcript_function_variant def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript function variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2010-03-22T11:32:58Z [Term] id: SO:0001539 name: translational_product_function_variant def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke] synonym: "translational product variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2010-03-22T11:46:15Z [Term] id: SO:0001540 name: level_of_transcript_variant def: "A sequence variant which alters the level of a transcript." [SO:ke] synonym: "level of transcript variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:07Z [Term] id: SO:0001541 name: decreased_transcript_level_variant def: "A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "decreased transcript level" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:47Z [Term] id: SO:0001542 name: increased_transcript_level_variant def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "increased transcript level variant" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:17Z [Term] id: SO:0001543 name: transcript_processing_variant def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript processing variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:48Z [Term] id: SO:0001544 name: editing_variant def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke] synonym: "editing variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:25Z [Term] id: SO:0001545 name: polyadenylation_variant def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke] synonym: "polyadenylation variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:40Z [Term] id: SO:0001546 name: transcript_stability_variant def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript stability variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:01Z [Term] id: SO:0001547 name: decreased_transcript_stability_variant def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke] synonym: "decrease transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:23Z [Term] id: SO:0001548 name: increased_transcript_stability_variant def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke] synonym: "increased transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:39Z [Term] id: SO:0001549 name: transcription_variant def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcription variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:26Z [Term] id: SO:0001550 name: rate_of_transcription_variant def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "rate of transcription variant" EXACT [] is_a: SO:0001549 ! transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:50Z [Term] id: SO:0001551 name: increased_transcription_rate_variant def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "increased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:17Z [Term] id: SO:0001552 name: decreased_transcription_rate_variant def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "decreased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:43Z [Term] id: SO:0001553 name: translational_product_level_variant def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke] synonym: "translational product level variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:32Z [Term] id: SO:0001554 name: polypeptide_function_variant def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke] synonym: "polypeptide function variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:54Z [Term] id: SO:0001555 name: decreased_translational_product_level def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke] synonym: "decrease translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:54:25Z [Term] id: SO:0001556 name: increased_translational_product_level def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke] synonym: "increase translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:55:25Z [Term] id: SO:0001557 name: polypeptide_gain_of_function_variant def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide gain of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:12Z [Term] id: SO:0001558 name: polypeptide_localization_variant def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide localization variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:37Z [Term] id: SO:0001559 name: polypeptide_loss_of_function_variant def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide loss of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:58Z [Term] id: SO:0001560 name: inactive_ligand_binding_site def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke] synonym: "inactive ligand binding site" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:00Z [Term] id: SO:0001561 name: polypeptide_partial_loss_of_function def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide partial loss of function" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:32Z [Term] id: SO:0001562 name: polypeptide_post_translational_processing_variant def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide post translational processing variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:59:06Z [Term] id: SO:0001563 name: copy_number_change def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke] synonym: "copy number change" EXACT [] is_a: SO:0002160 ! sequence_length_variant created_by: kareneilbeck creation_date: 2010-03-22T02:27:33Z [Term] id: SO:0001564 name: gene_variant def: "A sequence variant where the structure of the gene is changed." [SO:ke] synonym: "gene structure variant" EXACT [] synonym: "Jannovar:gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:GENE" EXACT VAR [] synonym: "VAAST:gene_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:01Z [Term] id: SO:0001565 name: gene_fusion def: "A sequence variant whereby a two genes have become joined." [SO:ke] synonym: "gene fusion" EXACT [] is_a: SO:0001564 ! gene_variant is_a: SO:0001882 ! feature_fusion created_by: kareneilbeck creation_date: 2010-03-22T02:28:28Z [Term] id: SO:0001566 name: regulatory_region_variant def: "A sequence variant located within a regulatory region." [SO:ke] comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl. synonym: "Jannovar:regulatory_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "regulatory region variant" EXACT [] synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "snpEff:REGULATION" EXACT VAR [] synonym: "VEP:regulatory_region_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:48Z [Term] id: SO:0001567 name: stop_retained_variant def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke] synonym: "Jannovar:stop_retained_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:NON_SYNONYMOUS_STOP" EXACT VAR [] synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR [] synonym: "stop retained variant" EXACT [] synonym: "VAAST:stop_retained" EXACT VAR [] synonym: "VAAST:stop_retained_variant" EXACT VAR [] synonym: "VEP:stop_retained_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001819 ! synonymous_variant created_by: kareneilbeck creation_date: 2010-04-19T05:02:30Z [Term] id: SO:0001568 name: splicing_variant def: "A sequence variant that changes the process of splicing." [SO:ke] synonym: "Jannovar:splicing_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "splicing variant" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:22Z [Term] id: SO:0001569 name: cryptic_splice_site_variant def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "cryptic splice site activation" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:41Z [Term] id: SO:0001570 name: cryptic_splice_acceptor def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke] synonym: "cryptic splice acceptor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:11Z [Term] id: SO:0001571 name: cryptic_splice_donor def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke] synonym: "cryptic splice donor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:35Z [Term] id: SO:0001572 name: exon_loss_variant def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke] synonym: "exon loss" EXACT [] synonym: "Jannovar:exon_loss_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:EXON_DELETED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:09Z [Term] id: SO:0001573 name: intron_gain_variant def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "intron gain" EXACT [] synonym: "intron gain variant" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:25Z [Term] id: SO:0001574 name: splice_acceptor_variant def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke] synonym: "Jannovar:splice_acceptor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:splice-acceptor" EXACT VAR [] synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR [] synonym: "splice acceptor variant" EXACT [] synonym: "VAAST:splice_acceptor_variant" EXACT VAR [] synonym: "VEP:splice_acceptor_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:52Z [Term] id: SO:0001575 name: splice_donor_variant def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke] synonym: "Jannovar:splice_donor_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:splice-donor" EXACT VAR [] synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR [] synonym: "splice donor variant" EXACT [] synonym: "VAAST:splice_donor_variant" EXACT VAR [] synonym: "VEP:splice_donor_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:10Z [Term] id: SO:0001576 name: transcript_variant def: "A sequence variant that changes the structure of the transcript." [SO:ke] synonym: "Jannovar:transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:TRANSCRIPT" EXACT VAR [] synonym: "transcript variant" EXACT [] synonym: "VAAST:transcript_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:41Z [Term] id: SO:0001577 name: complex_transcript_variant def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. synonym: "complex change in transcript" EXACT [] synonym: "complex transcript variant" EXACT [] synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "Seattleseq:codingComplex" RELATED VAR [] synonym: "Seattleseq:codingComplex-near-splice" RELATED VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:33:03Z [Term] id: SO:0001578 name: stop_lost def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke] comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon. synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:stop_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:stop-lost" EXACT VAR [] synonym: "Seattleseq:stop-lost-near-splice" RELATED VAR [] synonym: "snpEff:STOP_LOST" EXACT VAR [] synonym: "stop codon lost" EXACT [] synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "VAAST:stop_lost" EXACT VAR [] synonym: "VAT:removedStop" EXACT VAR [] synonym: "VEP:stop_lost" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001907 ! feature_elongation is_a: SO:0001992 ! nonsynonymous_variant created_by: kareneilbeck creation_date: 2010-03-23T03:46:42Z [Term] id: SO:0001579 name: transcript_sequence_variant synonym: "transcript sequence variant" EXACT [] is_obsolete: true [Term] id: SO:0001580 name: coding_sequence_variant alt_id: SO:0001581 def: "A sequence variant that changes the coding sequence." [SO:ke] synonym: "coding sequence variant" EXACT [] synonym: "coding variant" EXACT [] synonym: "codon variant" EXACT [] synonym: "codon_variant" EXACT [] synonym: "Jannovar:coding_sequence_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:coding" EXACT VAR [] synonym: "snpEff:CDS" EXACT VAR [] synonym: "snpEff:CODON_CHANGE" RELATED VAR [] synonym: "VAAST:coding_sequence_variant" EXACT VAR [] synonym: "VEP:coding_sequence_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001791 ! exon_variant is_a: SO:0001968 ! coding_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:34:36Z [Term] id: SO:0001582 name: initiator_codon_variant def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke] comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called. synonym: "initiatior codon variant" EXACT [] synonym: "initiator codon change" EXACT [] synonym: "Jannovar:initiator_codon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:NON_SYNONYMOUS_START" RELATED VAR [] synonym: "VAT:startOverlap" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: loinc:LA6695-6 "Initiating Methionine" is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:18Z [Term] id: SO:0001583 name: missense_variant alt_id: SO:0001584 alt_id: SO:0001783 def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke] comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution. synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:missense_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "missense codon" EXACT [] synonym: "Seattleseq:missense" EXACT VAR [] synonym: "Seattleseq:missense-near-splice" RELATED VAR [] synonym: "snpEff:NON_SYNONYMOUS_CODING" EXACT VAR [] synonym: "VAAST:missense_variant" EXACT VAR [] synonym: "VAAST:non_synonymous_codon" RELATED VAR [] synonym: "VAT:nonsynonymous" EXACT VAR [] synonym: "VEP:missense_variant" EXACT VAR [] xref: http://en.wikipedia.org/wiki/Missense_mutation xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences xref: loinc:LA6698-0 "Missense" is_a: SO:0001992 ! nonsynonymous_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:49Z [Term] id: SO:0001585 name: conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke] synonym: "conservative missense codon" EXACT [] synonym: "conservative missense variant" EXACT [] synonym: "neutral missense codon" RELATED [] synonym: "quiet missense codon" RELATED [] is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:36:40Z [Term] id: SO:0001586 name: non_conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke] synonym: "non conservative missense codon" EXACT [] synonym: "non conservative missense variant" EXACT [] is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:37:16Z [Term] id: SO:0001587 name: stop_gained def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide." [SO:ke] comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence). synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:stop_gained" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "nonsense codon" EXACT [] synonym: "Seattleseq:stop-gained" EXACT VAR [] synonym: "Seattleseq:stop-gained-near-splice" RELATED VAR [] synonym: "snpEff:STOP_GAINED" EXACT VAR [] synonym: "stop codon gained" RELATED [] synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "VAAST:stop_gained" EXACT VAR [] synonym: "VAT:prematureStop" EXACT VAR [] synonym: "VEP:stop_gained" EXACT VAR [] xref: http://ensembl.org/info/genome/variation/prediction/predicted_data.html xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: loinc:LA6699-8 "Nonsense" is_a: SO:0001906 ! feature_truncation is_a: SO:0001992 ! nonsynonymous_variant created_by: kareneilbeck creation_date: 2010-03-22T02:37:52Z [Term] id: SO:0001589 name: frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift. synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "ANNOVAR:frameshift substitution" RELATED [] synonym: "frameshift variant" EXACT [] synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "Jannovar:frameshift_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:frameshift" EXACT VAR [] synonym: "Seattleseq:frameshift-near-splice" RELATED VAR [] synonym: "snpEff:FRAME_SHIFT" EXACT VAR [] synonym: "VAAST:frameshift_variant" EXACT VAR [] synonym: "VAT:deletionFS" NARROW VAR [] synonym: "VAT:insertionFS" NARROW VAR [] synonym: "VEP:frameshift_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences xref: loinc:LA6694-9 "Frameshift" is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:19Z [Term] id: SO:0001590 name: terminator_codon_variant alt_id: SO:0001625 def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke] comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon. synonym: "terminal codon variant" EXACT [] synonym: "terminal_codon_variant" EXACT [] synonym: "terminator codon variant" EXACT [] synonym: "VAT:endOverlap" EXACT VAR [] xref: http://vat.gersteinlab.org/formats.php "VAT" xref: loinc:LA6700-2 "Stop Codon Mutation" is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:37Z [Term] id: SO:0001591 name: frame_restoring_variant def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] synonym: "frame restoring variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:09Z [Term] id: SO:0001592 name: minus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "-1 frameshift variant" EXACT [] synonym: "minus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:30Z [Term] id: SO:0001593 name: minus_2_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward." [] synonym: "-2 frameshift variant" EXACT [] synonym: "minus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:52Z [Term] id: SO:0001594 name: plus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "+1 frameshift variant" EXACT [] synonym: "plus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:06Z [Term] id: SO:0001595 name: plus_2_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward." [] synonym: "+2 frameshift variant" EXACT [] synonym: "plus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:23Z [Term] id: SO:0001596 name: transcript_secondary_structure_variant def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke] synonym: "transcript secondary structure variant" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:18Z [Term] id: SO:0001597 name: compensatory_transcript_secondary_structure_variant def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke] synonym: "compensatory transcript secondary structure variant" EXACT [] is_a: SO:0001596 ! transcript_secondary_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:54Z [Term] id: SO:0001598 name: translational_product_structure_variant def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke] synonym: "translational product structure variant" EXACT [] is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:17Z [Term] id: SO:0001599 name: 3D_polypeptide_structure_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "3D polypeptide structure variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:46Z [Term] id: SO:0001600 name: complex_3D_structural_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "complex 3D structural variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:13Z [Term] id: SO:0001601 name: conformational_change_variant def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke] synonym: "conformational change variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:48Z [Term] id: SO:0001602 name: complex_change_of_translational_product_variant def: "A variant that changes the translational product with respect to the reference." [] synonym: "complex change of translational product variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T02:46:54Z [Term] id: SO:0001603 name: polypeptide_sequence_variant def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke] synonym: "polypeptide sequence variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:13Z [Term] id: SO:0001604 name: amino_acid_deletion def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke] synonym: "amino acid deletion" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:36Z [Term] id: SO:0001605 name: amino_acid_insertion def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke] synonym: "amino acid insertion" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:56Z [Term] id: SO:0001606 name: amino_acid_substitution def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke] synonym: "amino acid substitution" EXACT [] synonym: "VAAST:amino_acid_substitution" EXACT VAR [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:48:17Z [Term] id: SO:0001607 name: conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke] synonym: "conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:48:57Z [Term] id: SO:0001608 name: non_conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke] synonym: "non conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:49:23Z [Term] id: SO:0001609 name: elongated_polypeptide def: "An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS." [SO:ke] synonym: "elongated polypeptide" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:49:52Z [Term] id: SO:0001610 name: elongated_polypeptide_C_terminal def: "An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS." [SO:ke] synonym: "elongated polypeptide C terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide relationship: derives_from SO:0002229 ! CDS_three_prime_extension created_by: kareneilbeck creation_date: 2010-03-22T02:50:20Z [Term] id: SO:0001611 name: elongated_polypeptide_N_terminal def: "An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS." [SO:ke] synonym: "elongated polypeptide N terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide relationship: derives_from SO:0002228 ! CDS_five_prime_extension created_by: kareneilbeck creation_date: 2010-03-22T02:50:31Z [Term] id: SO:0001612 name: elongated_in_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated in frame polypeptide C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:05Z [Term] id: SO:0001613 name: elongated_out_of_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated polypeptide out of frame C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:20Z [Term] id: SO:0001614 name: elongated_in_frame_polypeptide_N_terminal_elongation def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated in frame polypeptide N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:49Z [Term] id: SO:0001615 name: elongated_out_of_frame_polypeptide_N_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated out of frame N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:52:05Z [Term] id: SO:0001616 name: polypeptide_fusion def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke] synonym: "polypeptide fusion" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:52:43Z [Term] id: SO:0001617 name: polypeptide_truncation def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke] synonym: "polypeptide truncation" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:53:07Z [Term] id: SO:0001618 name: inactive_catalytic_site def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke] synonym: "inactive catalytic site" EXACT [] is_a: SO:0001560 ! inactive_ligand_binding_site created_by: kareneilbeck creation_date: 2010-03-22T03:06:14Z [Term] id: SO:0001619 name: non_coding_transcript_variant def: "A transcript variant of a non coding RNA gene." [SO:ke] comment: Within non-coding gene - Located within a gene that does not code for a protein. synonym: "ANNOVAR:ncRNA" NARROW VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/] synonym: "Jannovar:non_coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "nc transcript variant" EXACT [] synonym: "non coding transcript variant" EXACT [] synonym: "VEP:non_coding_transcript_variant" EXACT VAR [] synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:23Z [Term] id: SO:0001620 name: mature_miRNA_variant def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke] comment: EBI term: Within mature miRNA - Located within a microRNA. synonym: "mature miRNA variant" EXACT [] synonym: "snpEff:MICRO_RNA" EXACT VAR [] synonym: "VEP:mature_miRNA_variant" EXACT VAR [] synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001619 ! non_coding_transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:58Z [Term] id: SO:0001621 name: NMD_transcript_variant def: "A variant in a transcript that is the target of nonsense-mediated mRNA decay." [SO:ke] synonym: "NMD transcript variant" EXACT [] synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "Nonsense mediated decay transcript variant" EXACT [] synonym: "VEP:NMD_transcript_variant" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:20:40Z [Term] id: SO:0001622 name: UTR_variant def: "A transcript variant that is located within the UTR." [SO:ke] synonym: "UTR variant" EXACT [] synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001791 ! exon_variant is_a: SO:0001968 ! coding_transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:22:58Z [Term] id: SO:0001623 name: 5_prime_UTR_variant def: "A UTR variant of the 5' UTR." [SO:ke] comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region). synonym: "5'UTR variant" EXACT [] synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "five prime UTR variant" EXACT [] synonym: "Jannovar:5_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:5-prime-UTR" EXACT VAR [] synonym: "snpEff:UTR_5_PRIME" EXACT VAR [] synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "VAAST:5_prime_UTR_variant" EXACT VAR [] synonym: "VAAST:five_prime_UTR_variant" EXACT VAR [] synonym: "VEP:5_prime_UTR_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:29Z [Term] id: SO:0001624 name: 3_prime_UTR_variant def: "A UTR variant of the 3' UTR." [SO:ke] comment: EBI term 3prime UTR variations - In 3prime UTR. synonym: "3'UTR variant" EXACT [] synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:3_prime_utr_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:3-prime-UTR" EXACT VAR [] synonym: "snpEff:UTR_3_PRIME" EXACT VAR [] synonym: "three prime UTR variant" EXACT [] synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "VAAST:3_prime_UTR_variant" EXACT VAR [] synonym: "VAAST:three_prime_UTR_variant" EXACT VAR [] synonym: "VEP:3_prime_UTR_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:54Z [Term] id: SO:0001626 name: incomplete_terminal_codon_variant def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke] comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown. synonym: "incomplete terminal codon variant" EXACT [] synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "VEP:incomplete_terminal_codon_variant" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-23T03:51:15Z [Term] id: SO:0001627 name: intron_variant def: "A transcript variant occurring within an intron." [SO:ke] comment: EBI term: Intronic variations - In intron. synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "intron variant" EXACT [] synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "Jannovar:intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:intron" EXACT VAR [] synonym: "Seattleseq:intron-near-splice" RELATED VAR [] synonym: "snpEff:INTRON" EXACT VAR [] synonym: "VAAST:intron_variant" EXACT VAR [] synonym: "VEP:intron_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T03:52:38Z [Term] id: SO:0001628 name: intergenic_variant def: "A sequence variant located in the intergenic region, between genes." [SO:ke] comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript. synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "intergenic variant" EXACT [] synonym: "Jannovar:intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:intergenic" EXACT VAR [] synonym: "snpEff:INTERGENIC" EXACT VAR [] synonym: "VEP:intergenic_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-23T05:07:37Z [Term] id: SO:0001629 name: splice_site_variant def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger. synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "splice site variant" EXACT [] synonym: "VAT:spliceOverlap" EXACT VAR [] xref: http://vat.gersteinlab.org/formats.php "VAT" is_a: SO:0001568 ! splicing_variant is_a: SO:0001627 ! intron_variant created_by: kareneilbeck creation_date: 2010-03-24T09:42:00Z [Term] id: SO:0001630 name: splice_region_variant def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron. synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:splice_region_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:SPLICE_SITE_BRANCH" RELATED VAR [] synonym: "snpEff:SPLICE_SITE_BRANCH_U12" RELATED VAR [] synonym: "snpEff:SPLICE_SITE_REGION" EXACT VAR [] synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "VAAST:splice_region_variant" EXACT VAR [] synonym: "VEP:splice_region_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-24T09:46:02Z [Term] id: SO:0001631 name: upstream_gene_variant def: "A sequence variant located 5' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "Jannovar:upstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:UPSTREAM" EXACT VAR [] synonym: "upstream gene variant" EXACT [] synonym: "VEP:upstream_gene_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:13Z [Term] id: SO:0001632 name: downstream_gene_variant def: "A sequence variant located 3' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "downstream gene variant" EXACT [] synonym: "Jannovar:downstream_gene_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:DOWNSTREAM" EXACT VAR [] synonym: "VEP:downstream_gene_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:38Z [Term] id: SO:0001633 name: 5KB_downstream_variant def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke] comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript. synonym: "5KB downstream variant" EXACT [] synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "Seattleseq:downstream-gene" EXACT VAR [] synonym: "within 5KB downstream" RELATED [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0001632 ! downstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:16Z [Term] id: SO:0001634 name: 500B_downstream_variant def: "A sequence variant located within a half KB of the end of a gene." [SO:ke] synonym: "500B downstream variant" EXACT [] synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001632 ! downstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:42Z [Term] id: SO:0001635 name: 5KB_upstream_variant def: "A sequence variant located within 5KB 5' of a gene." [SO:ke] comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript. synonym: "5kb upstream variant" EXACT [] synonym: "Seattleseq:upstream-gene" EXACT VAR [] synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0001631 ! upstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:06Z [Term] id: SO:0001636 name: 2KB_upstream_variant def: "A sequence variant located within 2KB 5' of a gene." [SO:ke] synonym: "2KB upstream variant" EXACT [] synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001631 ! upstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:22Z [Term] id: SO:0001637 name: rRNA_gene def: "A gene that encodes for ribosomal RNA." [SO:ke] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "rDNA" EXACT [] synonym: "rRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:10:32Z [Term] id: SO:0001638 name: piRNA_gene def: "A gene that encodes for an piwi associated RNA." [SO:ke] comment: Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. synonym: "piRNA gene" EXACT [] is_a: SO:0002342 ! sncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:11:36Z [Term] id: SO:0001639 name: RNase_P_RNA_gene def: "A gene that encodes an RNase P RNA." [SO:ke] comment: Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533. synonym: "RNase P RNA gene" EXACT [] is_a: SO:0002180 ! enzymatic_RNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:23Z [Term] id: SO:0001640 name: RNase_MRP_RNA_gene def: "A gene that encodes a RNase_MRP_RNA." [SO:ke] comment: Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533. synonym: "RNase MRP RNA gene" RELATED [] is_a: SO:0002180 ! enzymatic_RNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:58Z [Term] id: SO:0001641 name: lincRNA_gene def: "A gene that encodes a long, intervening non-coding RNA." [http://www.gencodegenes.org/gencode_biotypes.html, PMID:23463798, SO:ke] synonym: "lincRNA gene" EXACT [] is_a: SO:0002127 ! lncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:14:24Z [Term] id: SO:0001642 name: mathematically_defined_repeat def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill] comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.). synonym: "mathematically defined repeat" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-05-03T11:50:14Z [Term] id: SO:0001643 name: telomerase_RNA_gene def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] synonym: "Telomerase RNA component" EXACT [] synonym: "telomerase RNA gene" EXACT [] synonym: "TERC" EXACT [] xref: http:http\://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia" is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-05-18T05:26:38Z [Term] id: SO:0001644 name: targeting_vector def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] synonym: "targeting vector" RELATED [] is_a: SO:0000440 ! vector_replicon is_a: SO:0000804 ! engineered_region intersection_of: SO:0000440 ! vector_replicon intersection_of: has_part SO:0000853 ! homologous_region intersection_of: has_quality SO:0000783 ! engineered relationship: has_part SO:0000853 ! homologous_region relationship: has_quality SO:0000783 ! engineered created_by: kareneilbeck creation_date: 2010-05-28T02:05:25Z [Term] id: SO:0001645 name: genetic_marker def: "A measurable sequence feature that varies within a population." [SO:db] synonym: "genetic marker" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-05-28T02:33:07Z [Term] id: SO:0001646 name: DArT_marker def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke] synonym: "DArT marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2010-05-28T02:34:43Z [Term] id: SO:0001647 name: kozak_sequence def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] subset: SOFA synonym: "kozak consensus" EXACT [] synonym: "kozak consensus sequence" EXACT [] synonym: "kozak sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" is_a: SO:0000139 ! ribosome_entry_site created_by: kareneilbeck creation_date: 2010-06-07T03:12:20Z [Term] id: SO:0001648 name: nested_transposon def: "A transposon that is disrupted by the insertion of another element." [SO:ke] synonym: "nested transposon" EXACT [] is_a: SO:0000101 ! transposable_element created_by: kareneilbeck creation_date: 2010-06-23T03:22:57Z [Term] id: SO:0001649 name: nested_repeat def: "A repeat that is disrupted by the insertion of another element." [SO:ke] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:nested" EXACT [] synonym: "nested repeat" EXACT [] is_a: SO:0000657 ! repeat_region created_by: kareneilbeck creation_date: 2010-06-23T03:24:55Z [Term] id: SO:0001650 name: inframe_variant def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "ANNOVAR:nonframeshift substitution" RELATED VAR [] synonym: "cds-indel" EXACT dbsnp [] synonym: "inframe variant" EXACT [] synonym: "VAAST:inframe_variant" EXACT VAR [] is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-07-19T01:24:44Z [Term] id: SO:0001653 name: retinoic_acid_responsive_element def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671] synonym: "RARE" EXACT [] synonym: "retinoic acid responsive element" EXACT [] is_a: SO:0000235 ! TF_binding_site created_by: kareneilbeck creation_date: 2010-08-03T10:46:12Z [Term] id: SO:0001654 name: nucleotide_to_protein_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] subset: SOFA synonym: "nucleotide to protein binding site" RELATED [] is_a: SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:26:05Z [Term] id: SO:0001655 name: nucleotide_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] comment: See GO:0000166 : nucleotide binding. synonym: "np_bind" EXACT BS [uniprot:feature] synonym: "nucleotide binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:30:04Z [Term] id: SO:0001656 name: metal_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb] comment: See GO:0046872 : metal ion binding. synonym: "metal binding site" RELATED [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:31:42Z [Term] id: SO:0001657 name: ligand_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke] synonym: "ligand binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:32:58Z [Term] id: SO:0001658 name: nested_tandem_repeat def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF] comment: Tracker ID: 3052459. synonym: "nested tandem repeat" EXACT [] synonym: "NTR" EXACT [] is_a: SO:0001649 ! nested_repeat created_by: kareneilbeck creation_date: 2010-08-26T09:36:16Z [Term] id: SO:0001659 name: promoter_element def: "An element that can exist within the promoter region of a gene." [] comment: Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. synonym: "promoter element" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: overlaps SO:0000235 ! TF_binding_site relationship: part_of SO:0000167 ! promoter created_by: kareneilbeck creation_date: 2010-10-01T11:48:32Z [Term] id: SO:0001660 name: core_eukaryotic_promoter_element def: "An element that only exists within the promoter region of a eukaryotic gene." [GREEKC:cl] synonym: "core eukaryotic promoter element" EXACT [] synonym: "general transcription factor binding site" RELATED [] is_a: SO:0002309 ! core_promoter_element relationship: part_of SO:0002221 ! eukaryotic_promoter created_by: kareneilbeck creation_date: 2010-10-01T11:49:03Z [Term] id: SO:0001661 name: RNA_polymerase_II_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867] synonym: "RNA polymerase II TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:42:12Z [Term] id: SO:0001662 name: RNA_polymerase_III_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke] synonym: "RNA polymerase III TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0000171 ! RNApol_III_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:43:16Z [Term] id: SO:0001663 name: BREd_motif def: "A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867] synonym: "BREd" EXACT [] synonym: "BREd motif" RELATED [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:49:55Z [Term] id: SO:0001664 name: DCE def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867] synonym: "downstream core element" RELATED [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:56:41Z [Term] id: SO:0001665 name: DCE_SI def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke] synonym: "DCE SI" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:10Z [Term] id: SO:0001666 name: DCE_SII def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke] synonym: "DCE SII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:30Z [Term] id: SO:0001667 name: DCE_SIII def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke] synonym: "DCE SIII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:44Z [Term] id: SO:0001668 name: proximal_promoter_element def: "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml] synonym: "proximal promoter element" RELATED [] synonym: "specific transcription factor binding site" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:10:23Z [Term] id: SO:0001669 name: RNApol_II_core_promoter def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] synonym: "RNApol II core promoter" EXACT [] is_a: SO:0000170 ! RNApol_II_promoter created_by: kareneilbeck creation_date: 2010-10-01T03:13:41Z [Term] id: SO:0001670 name: distal_promoter_element def: "A regulatory promoter element that is distal from the TSS." [] synonym: "distal promoter element" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:21:08Z [Term] id: SO:0001671 name: bacterial_RNApol_promoter_sigma_70_element def: "A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription." [] synonym: "bacterial RNA polymerase promoter sigma 70" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:41:34Z [Term] id: SO:0001672 name: bacterial_RNApol_promoter_sigma54_element def: "A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription." [] synonym: "" RELATED [] synonym: "bacterial RNA polymerase promoter sigma54" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:42:37Z [Term] id: SO:0001673 name: minus_12_signal def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 12 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54_element created_by: kareneilbeck creation_date: 2010-10-06T01:44:57Z [Term] id: SO:0001674 name: minus_24_signal def: "A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 24 signal" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54_element created_by: kareneilbeck creation_date: 2010-10-06T01:45:24Z [Term] id: SO:0001675 name: A_box_type_1 def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 1" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:43:43Z [Term] id: SO:0001676 name: A_box_type_2 def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 2" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 created_by: kareneilbeck creation_date: 2010-10-06T05:44:18Z [Term] id: SO:0001677 name: intermediate_element def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659] synonym: "IE" EXACT [] synonym: "intermediate element" RELATED [] is_a: SO:0001660 ! core_eukaryotic_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:52:03Z [Term] id: SO:0001678 name: regulatory_promoter_element def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] synonym: "regulatory promoter element" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2010-10-07T04:39:48Z [Term] id: SO:0001679 name: transcription_regulatory_region def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] comment: Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527. subset: SOFA synonym: "transcription regulatory region" EXACT [] is_obsolete: true created_by: kareneilbeck creation_date: 2010-10-12T03:49:35Z [Term] id: SO:0001680 name: translation_regulatory_region def: "A regulatory region that is involved in the control of the process of translation." [SO:ke] synonym: "translation regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:52:45Z [Term] id: SO:0001681 name: recombination_regulatory_region def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke] synonym: "recombination regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:53:35Z [Term] id: SO:0001682 name: replication_regulatory_region def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:replication_regulatory_region" EXACT [] synonym: "replication regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:54:09Z [Term] id: SO:0001683 name: sequence_motif def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] subset: SOFA synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-14T04:13:22Z [Term] id: SO:0001684 name: experimental_feature_attribute def: "An attribute of an experimentally derived feature." [SO:ke] synonym: "experimental feature attribute" RELATED [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:22:23Z [Term] id: SO:0001685 name: score def: "The score of an experimentally derived feature such as a p-value." [SO:ke] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:23:16Z [Term] id: SO:0001686 name: quality_value def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke] synonym: "quality value" RELATED [] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:24:11Z [Term] id: SO:0001687 name: restriction_enzyme_recognition_site def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] synonym: "restriction endonuclease recognition site" EXACT [] synonym: "restriction enzyme recognition site" EXACT [] is_a: SO:0001954 ! restriction_enzyme_region created_by: kareneilbeck creation_date: 2010-10-29T12:29:57Z [Term] id: SO:0001688 name: restriction_enzyme_cleavage_junction def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke] synonym: "restriction enzyme cleavage junction" EXACT [] is_a: SO:0002204 ! nucleotide_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:35:02Z [Term] id: SO:0001689 name: five_prime_restriction_enzyme_junction def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke] synonym: "5' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:36:24Z [Term] id: SO:0001690 name: three_prime_restriction_enzyme_junction def: "The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence." [] synonym: "3' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:37:52Z [Term] id: SO:0001691 name: blunt_end_restriction_enzyme_cleavage_site def: "A restriction enzyme recognition site that, when cleaved, results in no overhangs." [SBOL:jgquinn, SO:ke] synonym: "blunt end restriction enzyme cleavage site" EXACT [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:39:53Z [Term] id: SO:0001692 name: sticky_end_restriction_enzyme_cleavage_site def: "A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'." [] synonym: "sticky end restriction enzyme cleavage site" RELATED [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:40:50Z [Term] id: SO:0001693 name: blunt_end_restriction_enzyme_cleavage_junction def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke] synonym: "blunt end restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:43:14Z [Term] id: SO:0001694 name: single_strand_restriction_enzyme_cleavage_site def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke] synonym: "single strand restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction created_by: kareneilbeck creation_date: 2010-10-29T12:44:48Z [Term] id: SO:0001695 name: restriction_enzyme_single_strand_overhang def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] synonym: "single strand overhang" EXACT [] synonym: "sticky end" RELATED [] is_a: SO:0001954 ! restriction_enzyme_region relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:48:35Z [Term] id: SO:0001696 name: experimentally_defined_binding_region def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke] synonym: "experimentally defined binding region" RELATED [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-11-02T11:39:59Z [Term] id: SO:0001697 name: ChIP_seq_region def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke] synonym: "ChIP seq region" RELATED [] is_a: SO:0001696 ! experimentally_defined_binding_region relationship: contains SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-11-02T11:43:07Z [Term] id: SO:0001698 name: ASPE_primer def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801] synonym: "allele specific primer extension primer" EXACT [] synonym: "ASPE primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:25:21Z [Term] id: SO:0001699 name: dCAPS_primer def: "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033] synonym: "dCAPS primer" EXACT [] synonym: "derived cleaved amplified polymorphic primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:27:09Z [Term] id: SO:0001700 name: histone_modification def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] synonym: "histone modification" EXACT [] synonym: "histone modification site" RELATED [] is_a: SO:0001089 ! post_translationally_modified_region is_a: SO:0001720 ! epigenetically_modified_region intersection_of: SO:0001089 ! post_translationally_modified_region intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-31T10:22:08Z [Term] id: SO:0001701 name: histone_methylation_site def: "A histone modification site where the modification is the methylation of the residue." [SO:ke] synonym: "histone methylation" EXACT [] synonym: "histone methylation site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:02Z [Term] id: SO:0001702 name: histone_acetylation_site def: "A histone modification where the modification is the acylation of the residue." [SO:ke] synonym: "histone acetylation" EXACT [] synonym: "histone acetylation site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:27Z [Term] id: SO:0001703 name: H3K9_acetylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 acetylation site" EXACT [] synonym: "H3K9ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:05Z [Term] id: SO:0001704 name: H3K14_acetylation_site def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K14 acetylation site" EXACT [] synonym: "H3K14ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:53Z [Term] id: SO:0001705 name: H3K4_monomethylation_site def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 mono-methylation site" EXACT [] synonym: "H3K4me1" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:28:14Z [Term] id: SO:0001706 name: H3K4_trimethylation def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 tri-methylation" EXACT [] synonym: "H3K4me3" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:29:12Z [Term] id: SO:0001707 name: H3K9_trimethylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 tri-methylation site" EXACT [] synonym: "H3K9Me3" RELATED [] is_a: SO:0001736 ! H3K9_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:30:34Z [Term] id: SO:0001708 name: H3K27_monomethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2K27 mono-methylation site" EXACT [] synonym: "H2K27Me1" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:31:54Z [Term] id: SO:0001709 name: H3K27_trimethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K27 tri-methylation site" EXACT [] synonym: "H3K27Me3" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:32:41Z [Term] id: SO:0001710 name: H3K79_monomethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 mono-methylation site" EXACT [] synonym: "H3K79me1" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:33:42Z [Term] id: SO:0001711 name: H3K79_dimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 di-methylation site" EXACT [] synonym: "H3K79Me2" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:34:39Z [Term] id: SO:0001712 name: H3K79_trimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 tri-methylation site" EXACT [] synonym: "H3K79Me3" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:35:30Z [Term] id: SO:0001713 name: H4K20_monomethylation_site def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H4K20 mono-methylation site" EXACT [] synonym: "H4K20Me1" RELATED [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:36:43Z [Term] id: SO:0001714 name: H2BK5_monomethylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2BK5 mono-methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:38:12Z [Term] id: SO:0001715 name: ISRE def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021. synonym: "interferon stimulated response element" EXACT [] is_a: SO:0000235 ! TF_binding_site created_by: kareneilbeck creation_date: 2010-04-05T11:15:08Z [Term] id: SO:0001716 name: histone_ubiqitination_site def: "A histone modification site where ubiquitin may be added." [SO:ke] synonym: "histone ubiquitination site" RELATED [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-04-13T10:12:18Z [Term] id: SO:0001717 name: H2B_ubiquitination_site def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke] synonym: "H2BUbiq" RELATED [] is_a: SO:0001716 ! histone_ubiqitination_site created_by: kareneilbeck creation_date: 2010-04-13T10:13:28Z [Term] id: SO:0001718 name: H3K18_acetylation_site def: "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke] synonym: "H3K18 acetylation site" EXACT [] synonym: "H3K18ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:39:35Z [Term] id: SO:0001719 name: H3K23_acetylation_site def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:ke] synonym: "H3K23 acetylation site" EXACT [] synonym: "H3K23ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:42:45Z [Term] id: SO:0001720 name: epigenetically_modified_region def: "A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] comment: Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534. subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0005836 ! regulatory_region intersection_of: SO:0001411 ! biological_region intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0001721 name: H3K27_acylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K27 acylation site" EXACT [] synonym: "H3K27Ac" RELATED [] is_obsolete: true created_by: kareneilbeck creation_date: 2010-04-13T10:44:09Z [Term] id: SO:0001722 name: H3K36_monomethylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] synonym: "H3K36 mono-methylation site" EXACT [] synonym: "H3K36Me1" RELATED [] is_a: SO:0001733 ! H3K36_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:46:32Z [Term] id: SO:0001723 name: H3K36_dimethylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke] synonym: "H3K36 di-methylation site" EXACT [] synonym: "H3K36Me2" RELATED [] is_a: SO:0001733 ! H3K36_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:59:35Z [Term] id: SO:0001724 name: H3K36_trimethylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke] synonym: "H3K36 tri-methylation site" EXACT [] synonym: "H3K36Me3" RELATED [] is_a: SO:0001733 ! H3K36_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:01:58Z [Term] id: SO:0001725 name: H3K4_dimethylation_site def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke] synonym: "H3K4 di-methylation site" EXACT [] synonym: "H3K4Me2" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:03:15Z [Term] id: SO:0001726 name: H3K27_dimethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke] synonym: "H3K27 di-methylation site" EXACT [] synonym: "H3K27Me2" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T01:45:41Z [Term] id: SO:0001727 name: H3K9_monomethylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] synonym: "H3K9 mono-methylation site" EXACT [] synonym: "H3K9Me1" RELATED [] is_a: SO:0001736 ! H3K9_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:06:17Z [Term] id: SO:0001728 name: H3K9_dimethylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke] synonym: "H3K9 di-methylation site" EXACT [] synonym: "H3K9Me2" RELATED [] is_a: SO:0001736 ! H3K9_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:08:19Z [Term] id: SO:0001729 name: H4K16_acetylation_site def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke] synonym: "H4K16 acetylation site" EXACT [] synonym: "H4K16ac" EXACT [] is_a: SO:0001972 ! histone_4_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:09:41Z [Term] id: SO:0001730 name: H4K5_acetylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:ke] synonym: "H4K5 acetylation site" EXACT [] synonym: "H4K5ac" EXACT [] is_a: SO:0001972 ! histone_4_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:13:00Z [Term] id: SO:0001731 name: H4K8_acetylation_site def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated." [SO:KE] synonym: "H4K8 acetylation site" EXACT [] synonym: "H4K8ac" EXACT [] is_a: SO:0001972 ! histone_4_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:14:24Z [Term] id: SO:0001732 name: H3K27_methylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] synonym: "H3K27 methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:26:22Z [Term] id: SO:0001733 name: H3K36_methylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] synonym: "H3K36 methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:27:28Z [Term] id: SO:0001734 name: H3K4_methylation_site def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke] synonym: "H3K4 methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:28:14Z [Term] id: SO:0001735 name: H3K79_methylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] synonym: "H3K79 methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:29:16Z [Term] id: SO:0001736 name: H3K9_methylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] synonym: "H3K9 methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-04-13T11:31:37Z [Term] id: SO:0001737 name: histone_acylation_region def: "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke] synonym: "histone acylation region" RELATED [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-04-13T01:58:21Z [Term] id: SO:0001738 name: H4K_acylation_region def: "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke] synonym: "H4K acylation region" EXACT [] synonym: "H4KAc" RELATED [] is_a: SO:0001737 ! histone_acylation_region created_by: kareneilbeck creation_date: 2010-04-13T02:00:06Z [Term] id: SO:0001739 name: gene_with_non_canonical_start_codon def: "A gene with a start codon other than AUG." [SO:xp] comment: Requested by flybase, Dec 2010. synonym: "gene with non canonical start codon" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: contains SO:0000680 ! non_canonical_start_codon relationship: contains SO:0000680 ! non_canonical_start_codon created_by: kareneilbeck creation_date: 2011-01-10T01:30:31Z [Term] id: SO:0001740 name: gene_with_start_codon_CUG def: "A gene with a translational start codon of CUG." [SO:mc] comment: Requested by flybase, Dec 2010. synonym: "gene with start codon CUG" EXACT [] is_a: SO:0001739 ! gene_with_non_canonical_start_codon created_by: kareneilbeck creation_date: 2011-01-10T01:32:35Z [Term] id: SO:0001741 name: pseudogenic_gene_segment def: "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd] synonym: "pseudogenic gene segment" EXACT [] is_a: SO:3000000 ! gene_segment created_by: batchelorc creation_date: 2011-02-15T05:07:52Z [Term] id: SO:0001742 name: copy_number_gain def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke] subset: DBVAR synonym: "copy number gain" EXACT [] synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] is_a: SO:0001019 ! copy_number_variation created_by: kareneilbeck creation_date: 2011-02-28T01:54:09Z [Term] id: SO:0001743 name: copy_number_loss def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke] subset: DBVAR synonym: "copy number loss" EXACT [] synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] is_a: SO:0001019 ! copy_number_variation created_by: kareneilbeck creation_date: 2011-02-28T01:55:02Z [Term] id: SO:0001744 name: UPD def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM] subset: DBVAR synonym: "uniparental disomy" EXACT [] synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] xref: http:http\://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia" is_a: SO:0001059 ! sequence_alteration created_by: kareneilbeck creation_date: 2011-02-28T02:01:05Z [Term] id: SO:0001745 name: maternal_uniparental_disomy def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm] synonym: "maternal uniparental disomy" EXACT [] is_a: SO:0001744 ! UPD created_by: kareneilbeck creation_date: 2011-02-28T02:03:01Z [Term] id: SO:0001746 name: paternal_uniparental_disomy def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm] synonym: "paternal uniparental disomy" EXACT [] is_a: SO:0001744 ! UPD created_by: kareneilbeck creation_date: 2011-02-28T02:03:30Z [Term] id: SO:0001747 name: open_chromatin_region def: "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb] comment: Requested by John Calley 3125900. synonym: "open chromatin region" EXACT [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2011-02-28T02:21:52Z [Term] id: SO:0001748 name: SL3_acceptor_site def: "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL3 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T02:58:40Z [Term] id: SO:0001749 name: SL4_acceptor_site def: "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL4 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:08:47Z [Term] id: SO:0001750 name: SL5_acceptor_site def: "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL5 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:09:36Z [Term] id: SO:0001751 name: SL6_acceptor_site def: "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL6 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:10:14Z [Term] id: SO:0001752 name: SL7_acceptor_site def: "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL37 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:13:20Z [Term] id: SO:0001753 name: SL8_acceptor_site def: "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL8 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:15:26Z [Term] id: SO:0001754 name: SL9_acceptor_site def: "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL9 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:15:57Z [Term] id: SO:0001755 name: SL10_acceptor_site def: "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL10 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:16:31Z [Term] id: SO:0001756 name: SL11_acceptor_site def: "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL11 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:16:54Z [Term] id: SO:0001757 name: SL12_acceptor_site def: "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL12 acceptor site" EXACT [] is_a: SO:0000709 ! SL2_acceptor_site created_by: kareneilbeck creation_date: 2011-02-28T03:17:23Z [Term] id: SO:0001758 name: duplicated_pseudogene def: "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene] synonym: "duplicated pseudogene" RELATED [] is_a: SO:0001760 ! non_processed_pseudogene created_by: kareneilbeck creation_date: 2011-03-09T09:58:04Z [Term] id: SO:0001759 name: unitary_pseudogene def: "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, http://en.wikipedia.org/wiki/Pseudogene, SO:ke] comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates. synonym: "disabled gene" RELATED [] synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:unitary" EXACT [] synonym: "unitary pseudogene" RELATED [] is_a: SO:0001760 ! non_processed_pseudogene created_by: kareneilbeck creation_date: 2011-03-09T10:04:04Z [Term] id: SO:0001760 name: non_processed_pseudogene def: "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, SO:ke] synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:unprocessed" EXACT [] synonym: "non processed pseudogene" RELATED [] synonym: "unprocessed pseudogene" EXACT [] synonym: "unprocessed_pseudogene" EXACT [] is_a: SO:0000336 ! pseudogene created_by: kareneilbeck creation_date: 2011-03-09T10:54:47Z [Term] id: SO:0001761 name: variant_quality def: "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke] synonym: "variant quality" EXACT [] is_a: SO:0000400 ! sequence_attribute created_by: kareneilbeck creation_date: 2011-03-15T03:40:35Z [Term] id: SO:0001762 name: variant_origin def: "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke] synonym: "variant origin" EXACT [] is_a: SO:0001761 ! variant_quality created_by: kareneilbeck creation_date: 2011-03-15T03:42:13Z [Term] id: SO:0001763 name: variant_frequency def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke] synonym: "variant frequency" EXACT [] is_a: SO:0001761 ! variant_quality created_by: kareneilbeck creation_date: 2011-03-15T03:44:39Z [Term] id: SO:0001764 name: unique_variant def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke] synonym: "unique variant" EXACT [] is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2011-03-15T03:47:20Z [Term] id: SO:0001765 name: rare_variant def: "When a variant from the genomic sequence is rarely found in the general population. The threshold for 'rare' varies between studies." [] synonym: "rare variant" EXACT [] is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2011-03-15T03:48:29Z [Term] id: SO:0001766 name: polymorphic_variant def: "A variant that affects one of several possible alleles at that location, such as the major histocompatibility complex (MHC) genes." [] synonym: "polymorphic variant" EXACT [] is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2011-03-15T03:48:51Z [Term] id: SO:0001767 name: common_variant def: "When a variant from the genomic sequence is commonly found in the general population." [] synonym: "common variant" EXACT [] is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2011-03-15T03:50:36Z [Term] id: SO:0001768 name: fixed_variant def: "When a variant has become fixed in the population so that it is now the only variant." [] synonym: "fixed variant" EXACT [] is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2011-03-15T03:50:53Z [Term] id: SO:0001769 name: variant_phenotype def: "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke] synonym: "variant phenotype" EXACT [] is_a: SO:0001761 ! variant_quality created_by: kareneilbeck creation_date: 2011-03-15T03:53:15Z [Term] id: SO:0001770 name: benign_variant def: "A variant that does not affect the function of the gene or cause disease." [] synonym: "benign variant" EXACT [] is_a: SO:0001769 ! variant_phenotype created_by: kareneilbeck creation_date: 2011-03-15T03:55:40Z [Term] id: SO:0001771 name: disease_associated_variant def: "A variant that has been found to be associated with disease." [] synonym: "disease associated variant" EXACT [] is_a: SO:0001769 ! variant_phenotype created_by: kareneilbeck creation_date: 2011-03-15T04:05:16Z [Term] id: SO:0001772 name: disease_causing_variant def: "A variant that has been found to cause disease." [] synonym: "disease causing variant" EXACT [] is_a: SO:0001769 ! variant_phenotype created_by: kareneilbeck creation_date: 2011-03-15T04:05:46Z [Term] id: SO:0001773 name: lethal_variant def: "A sequence variant where the mutated gene product does not allow for one or more basic functions necessary for survival." [] synonym: "lethal variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2011-03-15T04:06:22Z [Term] id: SO:0001774 name: quantitative_variant def: "A variant within a gene that contributes to a quantitative trait such as height or weight." [] synonym: "quantitative variant" EXACT [] is_a: SO:0001769 ! variant_phenotype created_by: kareneilbeck creation_date: 2011-03-15T04:28:13Z [Term] id: SO:0001775 name: maternal_variant def: "A variant in the genetic material inherited from the mother." [] synonym: "maternal variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:30:23Z [Term] id: SO:0001776 name: paternal_variant def: "A variant in the genetic material inherited from the father." [] synonym: "paternal variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:30:47Z [Term] id: SO:0001777 name: somatic_variant def: "A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body." [] synonym: "somatic variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:31:12Z [Term] id: SO:0001778 name: germline_variant def: "A variant present in the embryo that is carried by every cell in the body." [] synonym: "germline variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:31:46Z [Term] id: SO:0001779 name: pedigree_specific_variant def: "A variant that is found only by individuals that belong to the same pedigree." [] synonym: "pedigree specific variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:32:18Z [Term] id: SO:0001780 name: population_specific_variant def: "A variant found within only speficic populations." [] synonym: "population specific variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:33:05Z [Term] id: SO:0001781 name: de_novo_variant def: "A variant arising in the offspring that is not found in either of the parents." [] synonym: "de novo variant" EXACT [] is_a: SO:0001762 ! variant_origin created_by: kareneilbeck creation_date: 2011-03-15T04:33:34Z [Term] id: SO:0001782 name: TF_binding_site_variant def: "A sequence variant located within a transcription factor binding site." [EBI:fc] synonym: "Jannovar:tf_binding_site_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "TF binding site variant" EXACT [] synonym: "VEP:TF_binding_site_variant" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001566 ! regulatory_region_variant created_by: kareneilbeck creation_date: 2011-03-17T10:59:20Z [Term] id: SO:0001784 name: complex_structural_alteration alt_id: SO:1000146 def: "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke] subset: DBVAR synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "complex chromosomal mutation" EXACT [] synonym: "complex_chromosomal_mutation" EXACT [] is_a: SO:0001785 ! structural_alteration is_a: SO:1000183 ! chromosome_structure_variation created_by: kareneilbeck creation_date: 2011-03-23T03:21:19Z [Term] id: SO:0001785 name: structural_alteration def: "An alteration of the genome that leads to a change in the structure of one or more chromosomes." [] subset: DBVAR synonym: "structural alteration" EXACT [] is_a: SO:0001059 ! sequence_alteration created_by: kareneilbeck creation_date: 2011-03-25T02:27:41Z [Term] id: SO:0001786 name: loss_of_heterozygosity def: "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke] subset: DBVAR synonym: "LOH" EXACT [] synonym: "loss of heterozygosity" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2011-03-25T02:32:58Z [Term] id: SO:0001787 name: splice_donor_5th_base_variant def: "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr] synonym: "splice donor 5th base variant" EXACT [] is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2011-04-05T04:16:28Z [Term] id: SO:0001788 name: U_box def: "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446] synonym: "U-box" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000186 ! LTR_retrotransposon created_by: kareneilbeck creation_date: 2011-04-08T10:39:14Z [Term] id: SO:0001789 name: mating_type_region def: "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke] synonym: "mating type region" EXACT [] xref: http://en.wikipedia.org/wiki/Mating-type_region is_a: SO:0005855 ! gene_group created_by: kareneilbeck creation_date: 2011-04-08T11:14:07Z [Term] id: SO:0001790 name: paired_end_fragment def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke] subset: SOFA synonym: "paired end fragment" EXACT [] is_a: SO:0000143 ! assembly_component created_by: kareneilbeck creation_date: 2011-04-14T01:48:20Z [Term] id: SO:0001791 name: exon_variant def: "A sequence variant that changes exon sequence." [SO:ke] synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "exon variant" EXACT [] synonym: "Jannovar:exon_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:EXON" EXACT VAR [] synonym: "VAAST:exon_variant" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2011-05-06T01:51:17Z [Term] id: SO:0001792 name: non_coding_transcript_exon_variant def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke] synonym: "ANNOVAR:ncRNA_exonic" NARROW VAR [] synonym: "Jannovar:non_coding_transcript_exon_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "non coding transcript exon variant" EXACT [] synonym: "non_coding_transcript_exon_variant" EXACT VAR [] synonym: "Seattleseq:non-coding-exon" EXACT VAR [] synonym: "Seattleseq:non-coding-exon-near-splice" RELATED VAR [] synonym: "snpEff:non_coding_exon_variant" EXACT VAR [] synonym: "VEP:non_coding_transcript_exon_variant" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0001619 ! non_coding_transcript_variant is_a: SO:0001791 ! exon_variant created_by: kareneilbeck creation_date: 2011-05-06T01:51:59Z [Term] id: SO:0001793 name: clone_end def: "A read from an end of the clone sequence." [SO:ke] synonym: "clone end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000151 ! clone created_by: kareneilbeck creation_date: 2011-05-13T11:32:27Z [Term] id: SO:0001794 name: point_centromere def: "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw] synonym: "point centromere" EXACT [] is_a: SO:0000577 ! centromere created_by: kareneilbeck creation_date: 2011-05-31T12:42:35Z [Term] id: SO:0001795 name: regional_centromere def: "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw] synonym: "regional centromere" EXACT [] is_a: SO:0000577 ! centromere created_by: kareneilbeck creation_date: 2011-05-31T12:43:07Z [Term] id: SO:0001796 name: regional_centromere_central_core def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw] synonym: "regional centromere central core" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001795 ! regional_centromere created_by: kareneilbeck creation_date: 2011-05-31T12:56:30Z [Term] id: SO:0001797 name: centromeric_repeat def: "A repeat region found within the modular centromere." [SO:ke] synonym: "centromeric repeat" EXACT [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:centromeric_repeat" EXACT [] is_a: SO:0000657 ! repeat_region created_by: kareneilbeck creation_date: 2011-05-31T12:59:27Z [Term] id: SO:0001798 name: regional_centromere_inner_repeat_region def: "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw] synonym: "lmr repeat" EXACT [] synonym: "lmr1L" EXACT [] synonym: "lmr1R" EXACT [] synonym: "regional centromere inner repeat region" EXACT [] is_a: SO:0001797 ! centromeric_repeat relationship: part_of SO:0001795 ! regional_centromere relationship: part_of SO:0001796 ! regional_centromere_central_core created_by: kareneilbeck creation_date: 2011-05-31T01:01:08Z [Term] id: SO:0001799 name: regional_centromere_outer_repeat_region def: "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw] synonym: "regional centromere outer repeat region" EXACT [] is_a: SO:0001797 ! centromeric_repeat relationship: part_of SO:0001795 ! regional_centromere created_by: kareneilbeck creation_date: 2011-05-31T01:03:23Z [Term] id: SO:0001800 name: tasiRNA def: "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017] synonym: "trans acting small interfering RNA" RELATED [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0001801 ! tasiRNA_primary_transcript created_by: kareneilbeck creation_date: 2011-05-31T03:24:06Z [Term] id: SO:0001801 name: tasiRNA_primary_transcript def: "A primary transcript encoding a tasiRNA." [PMID:16145017] synonym: "tasiRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2011-05-31T03:27:35Z [Term] id: SO:0001802 name: increased_polyadenylation_variant def: "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke] comment: Term requested by M. Dumontier, June 1 2011. synonym: "increased polyadenylation variant" EXACT [] is_a: SO:0001545 ! polyadenylation_variant created_by: kareneilbeck creation_date: 2011-06-01T10:53:12Z [Term] id: SO:0001803 name: decreased_polyadenylation_variant def: "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke] comment: Term requested by M. Dumontier, June 1 2011. synonym: "decreased polyadenylation variant" EXACT [] is_a: SO:0001545 ! polyadenylation_variant created_by: kareneilbeck creation_date: 2011-06-01T10:53:40Z [Term] id: SO:0001804 name: DDB_box def: "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632] comment: Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence. synonym: "DDB box" EXACT [] synonym: "DDB-box" EXACT [] is_a: SO:0001093 ! protein_protein_contact created_by: kareneilbeck creation_date: 2011-06-17T12:10:44Z [Term] id: SO:0001805 name: destruction_box def: "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691] synonym: "D-box" EXACT [] synonym: "destruction box" EXACT [] is_a: SO:0100017 ! polypeptide_conserved_motif created_by: kareneilbeck creation_date: 2011-06-17T12:16:02Z [Term] id: SO:0001806 name: ER_retention_signal def: "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689] synonym: "endoplasmic reticulum retention signal" EXACT [] synonym: "ER retention signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2011-06-17T12:19:49Z [Term] id: SO:0001807 name: KEN_box def: "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916] synonym: "KEN box" EXACT [] is_a: SO:0100017 ! polypeptide_conserved_motif created_by: kareneilbeck creation_date: 2011-06-17T12:24:14Z [Term] id: SO:0001808 name: mitochondrial_targeting_signal def: "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah] synonym: "mitochondrial signal sequence" EXACT [] synonym: "mitochondrial targeting signal" EXACT [] synonym: "MTS" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2011-06-17T12:26:35Z [Term] id: SO:0001809 name: signal_anchor def: "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php] synonym: "signal anchor" EXACT [] synonym: "uncleaved signal peptide" EXACT [] is_a: SO:0000418 ! signal_peptide created_by: kareneilbeck creation_date: 2011-06-17T12:28:53Z [Term] id: SO:0001810 name: PIP_box def: "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646] synonym: "PIP box" EXACT [] is_a: SO:0001093 ! protein_protein_contact created_by: kareneilbeck creation_date: 2011-06-17T12:33:25Z [Term] id: SO:0001811 name: phosphorylation_site def: "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah] synonym: "phosphorylation site" EXACT [] is_a: SO:0001089 ! post_translationally_modified_region created_by: kareneilbeck creation_date: 2011-06-17T12:36:20Z [Term] id: SO:0001812 name: transmembrane_helix def: "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah] synonym: "transmembrane helix" EXACT [] is_a: SO:0001114 ! peptide_helix relationship: part_of SO:0001077 ! transmembrane_polypeptide_region created_by: kareneilbeck creation_date: 2011-06-17T12:39:46Z [Term] id: SO:0001813 name: vacuolar_sorting_signal def: "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah] synonym: "vacuolar sorting signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2011-06-17T12:42:48Z [Term] id: SO:0001814 name: coding_variant_quality def: "An attribute of a coding genomic variant." [] synonym: "coding variant quality" EXACT [] is_a: SO:0001761 ! variant_quality created_by: kareneilbeck creation_date: 2011-06-24T03:32:25Z [Term] id: SO:0001815 name: synonymous def: "A variant that does not lead to any change in the amino acid sequence." [] is_a: SO:0001814 ! coding_variant_quality created_by: kareneilbeck creation_date: 2011-06-24T03:33:16Z [Term] id: SO:0001816 name: non_synonymous def: "A variant that leads to the change of an amino acid within the protein." [] synonym: "non synonymous" RELATED [] is_a: SO:0001814 ! coding_variant_quality created_by: kareneilbeck creation_date: 2011-06-24T03:33:36Z [Term] id: SO:0001817 name: inframe def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke] is_a: SO:0000863 ! mRNA_attribute created_by: kareneilbeck creation_date: 2011-06-24T03:34:03Z [Term] id: SO:0001818 name: protein_altering_variant def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr] synonym: "protein altering variant" EXACT [] synonym: "VEP:protein_altering_variant" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2011-06-24T03:38:02Z [Term] id: SO:0001819 name: synonymous_variant alt_id: SO:0001588 def: "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke] comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term. synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "Jannovar:synonymous_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "Seattleseq:synonymous" EXACT VAR [] synonym: "Seattleseq:synonymous-near-splice" RELATED VAR [] synonym: "silent mutation" RELATED [] synonym: "silent substitution" RELATED [] synonym: "silent_mutation" RELATED [] synonym: "snpEff:SYNONYMOUS_CODING" EXACT VAR [] synonym: "synonymous codon" EXACT [] synonym: "synonymous_coding" EXACT [] synonym: "synonymous_codon" EXACT [] synonym: "VAAST:synonymous_codon" EXACT VAR [] synonym: "VAAST:synonymous_variant" EXACT VAR [] synonym: "VAT:synonymous" EXACT VAR [] synonym: "VEP:synonymous_variant" EXACT VAR [] xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki" xref: http://en.wikipedia.org/wiki/Synonymous_mutation xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2011-06-24T03:38:30Z [Term] id: SO:0001820 name: inframe_indel def: "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke] synonym: "inframe change in CDS length" EXACT [] synonym: "inframe indel" EXACT [] is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2011-06-27T11:25:33Z [Term] id: SO:0001821 name: inframe_insertion alt_id: SO:0001651 def: "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr] synonym: "ANNOVAR:nonframeshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "inframe codon gain" RELATED [] synonym: "inframe increase in CDS length" EXACT [] synonym: "inframe insertion" EXACT [] synonym: "inframe_codon_gain" EXACT [] synonym: "Jannovar:inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEFF:CODON_INSERTION" EXACT VAR [] synonym: "VAT:insertionNFS" EXACT VAR [] synonym: "VEP:inframe_insertion" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001820 ! inframe_indel is_a: SO:0001908 ! internal_feature_elongation created_by: kareneilbeck creation_date: 2011-06-27T11:26:22Z [Term] id: SO:0001822 name: inframe_deletion alt_id: SO:0001652 def: "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr] synonym: "ANNOVAR:nonframeshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "inframe codon loss" RELATED [] synonym: "inframe decrease in CDS length" EXACT [] synonym: "inframe deletion" RELATED [] synonym: "inframe_codon_loss" EXACT [] synonym: "Jannovar:inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:CODON_DELETION" RELATED VAR [] synonym: "VAT:deletionNFS" EXACT VAR [] synonym: "VEP:inframe_deletion" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http://vat.gersteinlab.org/formats.php "VAT" xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001820 ! inframe_indel is_a: SO:0001906 ! feature_truncation created_by: kareneilbeck creation_date: 2011-06-27T11:27:10Z [Term] id: SO:0001823 name: conservative_inframe_insertion def: "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr] synonym: "conservative increase in CDS length" EXACT [] synonym: "conservative inframe insertion" EXACT [] is_a: SO:0001821 ! inframe_insertion created_by: kareneilbeck creation_date: 2011-06-27T11:28:02Z [Term] id: SO:0001824 name: disruptive_inframe_insertion def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr] synonym: "disruptive increase in CDS length" EXACT [] synonym: "disruptive inframe insertion" EXACT [] synonym: "Jannovar:disruptive_inframe_insertion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001821 ! inframe_insertion created_by: kareneilbeck creation_date: 2011-06-27T11:28:37Z [Term] id: SO:0001825 name: conservative_inframe_deletion def: "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr] synonym: "conservative decrease in CDS length" RELATED [] synonym: "conservative inframe deletion" EXACT [] is_a: SO:0001822 ! inframe_deletion created_by: kareneilbeck creation_date: 2011-06-27T11:30:43Z [Term] id: SO:0001826 name: disruptive_inframe_deletion def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr] synonym: "disruptive decrease in CDS length" EXACT [] synonym: "disruptive inframe deletion" EXACT [] synonym: "Jannovar:disruptive_inframe_deletion" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001822 ! inframe_deletion created_by: kareneilbeck creation_date: 2011-06-27T11:31:31Z [Term] id: SO:0001827 name: mRNA_read def: "A sequencer read of an mRNA substrate." [SO:ke] comment: Requested by Bayer Cropscience June, 2011. synonym: "mRNA read" EXACT [] is_a: SO:0000150 ! read created_by: kareneilbeck creation_date: 2011-06-28T04:04:32Z [Term] id: SO:0001828 name: genomic_DNA_read def: "A sequencer read of a genomic DNA substrate." [SO:ke] synonym: "gDNA read" EXACT [] synonym: "gDNA_read" EXACT [] synonym: "genomic DNA read" EXACT [] is_a: SO:0000150 ! read created_by: kareneilbeck creation_date: 2011-06-28T04:06:10Z [Term] id: SO:0001829 name: mRNA_contig def: "A contig composed of mRNA_reads." [SO:ke] comment: Requested by Bayer Cropscience June, 2011. synonym: "mRNA contig" RELATED [] is_a: SO:0000149 ! contig created_by: kareneilbeck creation_date: 2011-06-28T04:07:09Z [Term] id: SO:0001830 name: AFLP_fragment def: "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea] comment: Requested by Bayer Cropscience June, 2011. synonym: "AFLP" EXACT [] synonym: "AFLP fragment" EXACT [] synonym: "AFLP-PCR" EXACT [] synonym: "amplified fragment length polymorphism" EXACT [] synonym: "amplified fragment length polymorphism PCR" EXACT [] xref: http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism "wiki" is_a: SO:0000006 ! PCR_product created_by: kareneilbeck creation_date: 2011-07-14T12:12:35Z [Term] id: SO:0001831 name: protein_hmm_match def: "A match to a protein HMM such as pfam." [SO:ke] synonym: "protein hmm match" EXACT [] is_a: SO:0000349 ! protein_match created_by: kareneilbeck creation_date: 2011-08-11T03:20:27Z [Term] id: SO:0001832 name: immunoglobulin_region def: "A region of immunoglobulin sequence, either constant or variable." [SO:ke] synonym: "immunoglobulin region" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2011-09-01T03:27:20Z [Term] id: SO:0001833 name: V_region def: "The variable region of an immunoglobulin polypeptide sequence." [SO:ke] synonym: "INSDC_feature:V_region" EXACT [] synonym: "V region" EXACT [] is_a: SO:0001832 ! immunoglobulin_region created_by: kareneilbeck creation_date: 2011-09-01T03:28:40Z [Term] id: SO:0001834 name: C_region def: "The constant region of an immunoglobulin polypeptide sequence." [SO:ke] synonym: "C region" EXACT [] is_a: SO:0001832 ! immunoglobulin_region created_by: kareneilbeck creation_date: 2011-09-01T03:29:41Z [Term] id: SO:0001835 name: N_region def: "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke] synonym: "INSDC_feature:N_region" EXACT [] synonym: "N-region" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature created_by: kareneilbeck creation_date: 2011-09-01T03:50:16Z [Term] id: SO:0001836 name: S_region def: "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke] synonym: "INSDC_feature:S_region" EXACT [] synonym: "S region" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature created_by: kareneilbeck creation_date: 2011-09-01T03:52:05Z [Term] id: SO:0001837 name: mobile_element_insertion def: "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga] comment: Requested by the EBI. synonym: "mobile element insertion" EXACT [] is_a: SO:0000667 ! insertion intersection_of: SO:0000667 ! insertion intersection_of: contains SO:0001037 ! mobile_genetic_element relationship: contains SO:0001037 ! mobile_genetic_element created_by: kareneilbeck creation_date: 2011-10-04T12:36:52Z [Term] id: SO:0001838 name: novel_sequence_insertion def: "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th] comment: Requested by the NCBI. synonym: "novel sequence insertion" EXACT [] is_a: SO:0000667 ! insertion created_by: kareneilbeck creation_date: 2011-10-04T01:14:50Z [Term] id: SO:0001839 name: CSL_response_element def: "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542] synonym: "CSL response element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T03:37:43Z [Term] id: SO:0001840 name: GATA_box def: "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208] comment: Changed to is_a SO:0001055 transcriptional_cis_regulatory_region from core_eukaryotic_promoter_element SO:0001660 after Ruth Lovering from GREEKC initiative pointed out that GATA boxes are frequently in enhancer regions, Dave Sant Aug 2020. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021. synonym: "GATA box" EXACT [] synonym: "GATA element" RELATED [] is_a: SO:0000235 ! TF_binding_site created_by: kareneilbeck creation_date: 2011-10-07T03:42:05Z [Term] id: SO:0001841 name: polymorphic_pseudogene def: "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, JAX:hd] comment: This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated. synonym: "polymorphic psuedogene" EXACT [] is_a: SO:0000336 ! pseudogene created_by: kareneilbeck creation_date: 2011-10-07T03:46:57Z [Term] id: SO:0001842 name: AP_1_binding_site def: "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983] synonym: "AP-1 binding site" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T03:54:52Z [Term] id: SO:0001843 name: CRE alt_id: SO:0001900 def: "MERGED DEFINITION:\nTARGET DEFINITION: A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.\n--------------------\nSOURCE DEFINITION: A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:11483355, PMID:11483993, PMID:15448137] comment: New synonym Atf1/Pcr1 recognition motif added in response to Antonia Lock GitHub Issue Request #437, PMID:15716492 synonym: "ATF/CRE site" EXACT [PMID:11483993] synonym: "Atf1/Pcr1 recognition motif" EXACT [] synonym: "cyclic AMP response element" EXACT [] synonym: "M26 binding site" EXACT [] synonym: "m26 site" EXACT [] synonym: "M26_binding_site" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T03:58:48Z [Term] id: SO:0001844 name: CuRE def: "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922] synonym: "copper-response element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:02:51Z [Term] id: SO:0001845 name: DRE def: "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127] synonym: "DNA damage response element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:17:25Z [Term] id: SO:0001846 name: FLEX_element def: "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934] synonym: "FLEX element" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:20:01Z [Term] id: SO:0001847 name: forkhead_motif def: "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092] synonym: "forkhead motif" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:22:06Z [Term] id: SO:0001848 name: homol_D_box def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:21673110, PMID:7501449, PMID:8458332] synonym: "homoID" EXACT [] synonym: "homol D box" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:24:14Z [Term] id: SO:0001849 name: homol_E_box def: "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449] synonym: "homol E box" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:26:09Z [Term] id: SO:0001850 name: HSE def: "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565] synonym: "heat shock element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:29:10Z [Term] id: SO:0001851 name: iron_repressed_GATA_element def: "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681] comment: The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes. synonym: "IDP (GATA)" EXACT [] synonym: "iron repressed GATA element" EXACT [] is_a: SO:0001840 ! GATA_box created_by: kareneilbeck creation_date: 2011-10-07T04:32:42Z [Term] id: SO:0001852 name: mating_type_M_box def: "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811] comment: Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF. synonym: "mating type M-box" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-07T04:39:43Z [Term] id: SO:0001853 name: androgen_response_element def: "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522] synonym: "androgen response element" EXACT [] synonym: "ARE" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2011-10-10T04:52:44Z [Term] id: SO:0001854 name: smFISH_probe def: "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792] synonym: "single molecule fish probe" EXACT [] synonym: "smFISH probe" RELATED [] is_a: SO:0000051 ! probe created_by: kareneilbeck creation_date: 2011-10-10T05:00:30Z [Term] id: SO:0001855 name: MCB def: "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853] synonym: "MluI cell cycle box" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-10T05:09:45Z [Term] id: SO:0001856 name: CCAAT_motif def: "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626] synonym: "CCAAT motif" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-10T05:13:54Z [Term] id: SO:0001857 name: Ace2_UAS def: "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171] synonym: "Ace2 upstream activating sequence" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-10T05:19:10Z [Term] id: SO:0001858 name: TR_box def: "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709] synonym: "TR box" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-10T05:22:13Z [Term] id: SO:0001859 name: STREP_motif def: "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717] synonym: "STREP motif" RELATED [] synonym: "stress-starvation response element of Schizosaccharomyces pombe" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-14T10:25:02Z [Term] id: SO:0001860 name: rDNA_intergenic_spacer_element def: "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). The S. pombe telomeric repeat consensus is TTAC(0-1)A(0-1)G(1-8)." [ISBN:978-0199638901, PMID:9016645] comment: Page 208 of ISBN:978-0199638901 synonym: "rDIS" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2011-10-19T11:23:09Z [Term] id: SO:0001861 name: sterol_regulatory_element def: "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923] synonym: "SRE" BROAD [GO:mah] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-19T03:02:05Z [Term] id: SO:0001862 name: GT_dinucleotide_repeat def: "A dinucleotide repeat region composed of GT repeating elements." [SO:ke] comment: paper:PMID:16043634. synonym: "d(GT)n" EXACT [] is_a: SO:0000290 ! dinucleotide_repeat_microsatellite_feature created_by: kareneilbeck creation_date: 2011-10-19T03:54:37Z [Term] id: SO:0001863 name: GTT_trinucleotide_repeat def: "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke] synonym: "d(GTT)" EXACT [] is_a: SO:0000291 ! trinucleotide_repeat_microsatellite_feature created_by: kareneilbeck creation_date: 2011-10-19T03:56:54Z [Term] id: SO:0001864 name: Sap1_recognition_motif def: "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412] synonym: "Sap1 recognitions site" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2011-10-19T04:24:16Z [Term] id: SO:0001865 name: CDRE_motif def: "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959] synonym: "calcineurin-dependent response element" EXACT [PMID:16928959] synonym: "CDRE motif" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2011-10-20T10:12:19Z [Term] id: SO:0001866 name: BAC_read_contig def: "A contig of BAC reads." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "BAC read contig" EXACT [] is_a: SO:0000149 ! contig intersection_of: SO:0000149 ! contig intersection_of: has_origin SO:0000153 ! BAC relationship: has_origin SO:0000153 ! BAC relationship: part_of SO:0000153 ! BAC created_by: kareneilbeck creation_date: 2012-01-17T02:45:04Z [Term] id: SO:0001867 name: candidate_gene def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "candidate gene" EXACT [] synonym: "target gene" EXACT [] is_a: SO:0000704 ! gene created_by: kareneilbeck creation_date: 2012-01-17T02:53:03Z [Term] id: SO:0001868 name: positional_candidate_gene def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "positional candidate gene" EXACT [] synonym: "positional target gene" RELATED [] is_a: SO:0001867 ! candidate_gene created_by: kareneilbeck creation_date: 2012-01-17T02:54:42Z [Term] id: SO:0001869 name: functional_candidate_gene def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "functional candidate gene" EXACT [] synonym: "functional target gene" EXACT [] is_a: SO:0001867 ! candidate_gene created_by: kareneilbeck creation_date: 2012-01-17T02:57:30Z [Term] id: SO:0001870 name: enhancerRNA def: "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm] synonym: "eRNA" EXACT [] is_a: SO:0000655 ! ncRNA intersection_of: SO:0000655 ! ncRNA intersection_of: transcribed_from SO:0000165 ! enhancer relationship: transcribed_from SO:0000165 ! enhancer created_by: kareneilbeck creation_date: 2012-01-17T03:09:35Z [Term] id: SO:0001871 name: PCB def: "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2012-01-17T03:14:02Z [Term] id: SO:0001872 name: rearrangement_region def: "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416] comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation. synonym: "rearrangement region" EXACT [] is_a: SO:0001411 ! biological_region is_a: SO:0001785 ! structural_alteration created_by: kareneilbeck creation_date: 2012-02-03T04:38:35Z [Term] id: SO:0001873 name: interchromosomal_breakpoint def: "A rearrangement breakpoint between two different chromosomes." [NCBI:th] synonym: "interchromosomal breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint created_by: kareneilbeck creation_date: 2012-02-03T04:43:45Z [Term] id: SO:0001874 name: intrachromosomal_breakpoint def: "A rearrangement breakpoint within the same chromosome." [NCBI:th] synonym: "intrachromosomal breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint created_by: kareneilbeck creation_date: 2012-02-03T04:44:53Z [Term] id: SO:0001875 name: unassigned_supercontig def: "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea] comment: Requested by Bayer Cropscience January, 2012. synonym: "unassigned scaffold" RELATED [] synonym: "unassigned supercontig" EXACT [] is_a: SO:0000148 ! supercontig created_by: kareneilbeck creation_date: 2012-02-14T05:02:20Z [Term] id: SO:0001876 name: partial_genomic_sequence_assembly def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea] comment: Requested by Bayer Cropscience January, 2012. synonym: "partial genomic sequence assembly" EXACT [] synonym: "pseudomolecule" BROAD [] synonym: "sequence assembly with N-gaps" EXACT [] is_a: SO:0000353 ! sequence_assembly created_by: kareneilbeck creation_date: 2012-02-14T05:05:32Z [Term] id: SO:0001877 name: lncRNA def: "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced." [HGNC:mw] {comment="PMID:33353982"} comment: Updated the definition of lncRNA (SO:0001877) from "A non-coding RNA over 200nucleotides in length." to "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced." See GitHub Issue #575 synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:lncRNA" EXACT [] synonym: "lncRNA_transcript" EXACT [] synonym: "long non-coding RNA" EXACT [] xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2012-02-14T05:18:01Z [Term] id: SO:0001878 name: feature_variant def: "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke] comment: Created in conjunction with the EBI. synonym: "feature alteration" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2012-04-03T11:27:27Z [Term] id: SO:0001879 name: feature_ablation def: "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke] comment: Created in conjunction with the EBI. synonym: "feature ablation" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2012-04-03T11:36:48Z [Term] id: SO:0001880 name: feature_amplification def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke] comment: Created in conjunction with the EBI. synonym: "feature amplification" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2012-04-03T11:37:48Z [Term] id: SO:0001881 name: feature_translocation def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke] comment: Created in conjunction with the EBI. synonym: "feature translocation" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2012-04-03T11:38:52Z [Term] id: SO:0001882 name: feature_fusion def: "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke] comment: Created in conjunction with the EBI. synonym: "feature fusion" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2012-04-03T11:39:20Z [Term] id: SO:0001883 name: transcript_translocation def: "A feature translocation where the region contains a transcript." [SO:ke] comment: Created in conjunction with the EBI. synonym: "transcript translocation" EXACT [] is_a: SO:0001881 ! feature_translocation created_by: kareneilbeck creation_date: 2012-04-03T12:29:52Z [Term] id: SO:0001884 name: regulatory_region_translocation def: "A feature translocation where the region contains a regulatory region." [SO:ke] comment: Created in conjunction with the EBI. synonym: "regulatory region translocation" EXACT [] is_a: SO:0001881 ! feature_translocation created_by: kareneilbeck creation_date: 2012-04-03T12:31:04Z [Term] id: SO:0001885 name: TFBS_translocation def: "A feature translocation where the region contains a transcription factor binding site." [SO:ke] comment: Created in conjunction with the EBI. synonym: "TFBS binding site translocation" EXACT [] synonym: "transcription factor binding site translocation" EXACT [] is_a: SO:0001884 ! regulatory_region_translocation created_by: kareneilbeck creation_date: 2012-04-03T12:31:15Z [Term] id: SO:0001886 name: transcript_fusion def: "A feature fusion where the deletion brings together transcript regions." [SO:ke] comment: Created in conjunction with the EBI. synonym: "transcript fusion" EXACT [] is_a: SO:0001882 ! feature_fusion created_by: kareneilbeck creation_date: 2012-04-03T12:34:56Z [Term] id: SO:0001887 name: regulatory_region_fusion def: "A feature fusion where the deletion brings together regulatory regions." [SO:ke] comment: Created in conjunction with the EBI. synonym: "regulatory region fusion" EXACT [] is_a: SO:0001882 ! feature_fusion created_by: kareneilbeck creation_date: 2012-04-03T12:35:58Z [Term] id: SO:0001888 name: TFBS_fusion def: "A fusion where the deletion brings together transcription factor binding sites." [SO:ke] comment: Created in conjunction with the EBI. synonym: "TFBS fusion " EXACT [] synonym: "transcription factor binding site fusion" EXACT [] is_a: SO:0001887 ! regulatory_region_fusion created_by: kareneilbeck creation_date: 2012-04-03T12:36:42Z [Term] id: SO:0001889 name: transcript_amplification def: "A feature amplification of a region containing a transcript." [SO:ke] comment: Created in conjunction with the EBI. synonym: "transcript amplification" EXACT [] synonym: "VEP:transcript_amplification" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001880 ! feature_amplification created_by: kareneilbeck creation_date: 2012-04-03T12:39:23Z [Term] id: SO:0001890 name: transcript_regulatory_region_fusion def: "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke] comment: Created in conjunction with the EBI. synonym: "transcript regulatory region fusion" EXACT [] is_a: SO:0001882 ! feature_fusion created_by: kareneilbeck creation_date: 2012-04-03T12:40:17Z [Term] id: SO:0001891 name: regulatory_region_amplification def: "A feature amplification of a region containing a regulatory region." [SO:ke] comment: Created in conjunction with the EBI. synonym: "regulatory region amplification" EXACT [] synonym: "VEP:regulatory_region_amplification" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001880 ! feature_amplification created_by: kareneilbeck creation_date: 2012-04-03T12:41:28Z [Term] id: SO:0001892 name: TFBS_amplification def: "A feature amplification of a region containing a transcription factor binding site." [SO:ke] comment: Created in conjunction with the EBI. synonym: "TFBS amplification " EXACT [] synonym: "transcription factor binding site amplification" EXACT [] synonym: "VEP:TFBS_amplification" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001891 ! regulatory_region_amplification created_by: kareneilbeck creation_date: 2012-04-03T12:42:48Z [Term] id: SO:0001893 name: transcript_ablation def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke] comment: Created in conjunction with the EBI. synonym: "Jannovar:transcript_ablation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "transcript ablation" EXACT [] synonym: "VEP:transcript_ablation" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001879 ! feature_ablation created_by: kareneilbeck creation_date: 2012-04-03T12:44:19Z [Term] id: SO:0001894 name: regulatory_region_ablation def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke] comment: Created in conjunction with the EBI. synonym: "regulatory region ablation" EXACT [] synonym: "VEP:regulatory_region_ablation" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001879 ! feature_ablation created_by: kareneilbeck creation_date: 2012-04-03T12:45:13Z [Term] id: SO:0001895 name: TFBS_ablation def: "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke] comment: Created in conjunction with the EBI. synonym: "TFBS ablation" EXACT [] synonym: "transcription factor binding site ablation" EXACT [] synonym: "VEP:TFBS_ablation" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001894 ! regulatory_region_ablation created_by: kareneilbeck creation_date: 2012-04-03T12:45:56Z [Term] id: SO:0001896 name: transposable_element_CDS def: "A CDS that is part of a transposable element." [SO:ke] synonym: "transposable element CDS" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: part_of SO:0000101 ! transposable_element relationship: part_of SO:0000101 ! transposable_element created_by: kareneilbeck creation_date: 2012-04-05T01:57:04Z [Term] id: SO:0001897 name: transposable_element_pseudogene def: "A pseudogene contained within a transposable element." [SO:ke] synonym: "transposable element pseudogene" EXACT [] is_a: SO:0000336 ! pseudogene intersection_of: SO:0000336 ! pseudogene intersection_of: part_of SO:0000101 ! transposable_element relationship: part_of SO:0000101 ! transposable_element created_by: kareneilbeck creation_date: 2012-04-05T04:09:45Z [Term] id: SO:0001898 name: dg_repeat def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw] comment: For the S. pombe project - requested by Val Wood. synonym: "dg repeat" EXACT [] is_a: SO:0001797 ! centromeric_repeat relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region created_by: kareneilbeck creation_date: 2012-04-06T11:48:48Z [Term] id: SO:0001899 name: dh_repeat def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw] comment: For the S. pombe project - requested by Val Wood. synonym: "dh repeat" EXACT [] is_a: SO:0001797 ! centromeric_repeat relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region created_by: kareneilbeck creation_date: 2012-04-06T11:50:07Z [Term] id: SO:0001901 name: AACCCT_box def: "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687] synonym: "AACCCT box" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element created_by: kareneilbeck creation_date: 2012-04-06T12:05:24Z [Term] id: SO:0001902 name: splice_region def: "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm] synonym: "splice region" RELATED [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000185 ! primary_transcript created_by: kareneilbeck creation_date: 2012-04-06T12:23:32Z [Term] id: SO:0001904 name: antisense_lncRNA def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999] comment: Relationship is_a SO:0000644 antisense_RNA added 23 April 2021. See GitHub Issue #443 synonym: "antisense lncRNA" RELATED [] synonym: "natural antisense transcript" EXACT [] is_a: SO:0000644 ! antisense_RNA is_a: SO:0001877 ! lncRNA created_by: kareneilbeck creation_date: 2012-04-06T04:36:44Z [Term] id: SO:0001905 name: regional_centromere_outer_repeat_transcript def: "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah] synonym: "centromere outer repeat transcript" EXACT [] synonym: "regional centromere outer repeat region transcript" EXACT [] synonym: "regional_centromere_outer_repeat_region_transcript" EXACT [] is_a: SO:0000185 ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: derives_from SO:0001799 ! regional_centromere_outer_repeat_region relationship: derives_from SO:0001799 ! regional_centromere_outer_repeat_region created_by: kareneilbeck creation_date: 2012-04-11T04:54:22Z [Term] id: SO:0001906 name: feature_truncation def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke] synonym: "feature truncation" EXACT [] synonym: "Jannovar:feature_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "VEP:feature_truncation" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2012-04-12T05:05:28Z [Term] id: SO:0001907 name: feature_elongation def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke] synonym: "feature elongation" EXACT [] synonym: "VEP:feature_elongation" EXACT VAR [] xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2012-04-12T05:05:56Z [Term] id: SO:0001908 name: internal_feature_elongation def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke] synonym: "internal feature elongation" EXACT [] synonym: "Jannovar:internal_feature_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0001907 ! feature_elongation created_by: kareneilbeck creation_date: 2012-04-12T05:06:20Z [Term] id: SO:0001909 name: frameshift_elongation def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke] synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "frameshift elongation" EXACT [] synonym: "Jannovar:frameshift_elongation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0001589 ! frameshift_variant is_a: SO:0001908 ! internal_feature_elongation created_by: kareneilbeck creation_date: 2012-04-12T05:10:05Z [Term] id: SO:0001910 name: frameshift_truncation def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke] synonym: "ANNOVAR:frameshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html] synonym: "frameshift truncation" EXACT [] synonym: "Jannovar:frameshift_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0001589 ! frameshift_variant is_a: SO:0001906 ! feature_truncation created_by: kareneilbeck creation_date: 2012-04-12T05:10:45Z [Term] id: SO:0001911 name: copy_number_increase def: "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke] synonym: "copy number increase" EXACT [] is_a: SO:0001563 ! copy_number_change created_by: kareneilbeck creation_date: 2012-04-13T11:26:32Z [Term] id: SO:0001912 name: copy_number_decrease def: "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke] synonym: "copy number decrease" EXACT [] is_a: SO:0001563 ! copy_number_change created_by: kareneilbeck creation_date: 2012-04-13T11:27:52Z [Term] id: SO:0001913 name: bacterial_RNApol_promoter_sigma_ecf_element def: "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc] comment: Requested by Kevin Clancy - invitrogen -May 2012. synonym: "bacterial RNApol promoter sigma ecf " EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2012-06-11T02:41:33Z [Term] id: SO:0001914 name: rDNA_replication_fork_barrier def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529] comment: Requested by Midori - June 2012. synonym: "DNA spacer replication fork barrier" EXACT [] synonym: "rDNA replication fork barrier" EXACT [] synonym: "RFB" EXACT [] synonym: "RTS1 barrier" EXACT [] synonym: "RTS1 element" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2012-06-11T02:55:02Z [Term] id: SO:0001915 name: transcription_start_cluster def: "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson] synonym: "transcriptional initiation cluster" EXACT [] synonym: "transcriptional start site cluster" EXACT [] synonym: "TSC" EXACT [] synonym: "TSS cluster" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2012-10-17T12:09:50Z [Term] id: SO:0001916 name: CAGE_tag def: "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson] synonym: "CAGE tag" EXACT [] is_a: SO:0000324 ! tag created_by: kareneilbeck creation_date: 2012-10-17T12:36:58Z [Term] id: SO:0001917 name: CAGE_cluster def: "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson] synonym: "CAGE cluster" EXACT [] synonym: "CAGE peak" EXACT [] synonym: "CAGE_peak" EXACT [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:CAGE_cluster" EXACT [] is_a: SO:0001915 ! transcription_start_cluster created_by: kareneilbeck creation_date: 2012-10-17T12:42:03Z [Term] id: SO:0001918 name: 5_methylcytosine def: "A cytosine methylated at the 5 carbon." [SO:rtapella] synonym: "5 methylcytosine" EXACT [] synonym: "5-mC" EXACT [] synonym: "m-5C" EXACT [] synonym: "m5c" EXACT [] xref: http://www.insdc.org/files/feature_table.html#7.4.2 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0000114 ! methylated_cytosine created_by: kareneilbeck creation_date: 2012-10-17T12:46:10Z [Term] id: SO:0001919 name: 4_methylcytosine def: "A cytosine methylated at the 4 nitrogen." [SO:rtapella] synonym: "4-mC" EXACT [] synonym: "4-methylcytosine" EXACT [] synonym: "m-4C" EXACT [] synonym: "m4c" EXACT [] synonym: "N4 methylcytosine" EXACT [] synonym: "N4-methylcytosine" EXACT [] synonym: "N4_methylcytosine" EXACT [] xref: http://www.insdc.org/files/feature_table.html#7.4.2 xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0000114 ! methylated_cytosine created_by: kareneilbeck creation_date: 2012-10-17T12:50:40Z [Term] id: SO:0001920 name: N6_methyladenine def: "An adenine methylated at the 6 nitrogen." [SO:rtapella] synonym: "6-mA" EXACT [] synonym: "6-methyladenine" EXACT [] synonym: "6mA" EXACT [] synonym: "m-6A" EXACT [] synonym: "m6a" EXACT [] synonym: "N6-methyladenine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0000161 ! methylated_adenine created_by: kareneilbeck creation_date: 2012-10-17T12:54:23Z [Term] id: SO:0001921 name: mitochondrial_contig def: "A contig of mitochondria derived sequences." [GMOD:ea] comment: Requested by Bayer Cropscience, October, 2012. synonym: "mitochondrial contig" EXACT [] is_a: SO:0000149 ! contig intersection_of: SO:0000149 ! contig intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! mitochondrial_sequence created_by: kareneilbeck creation_date: 2012-10-31T12:34:38Z [Term] id: SO:0001922 name: mitochondrial_supercontig def: "A scaffold composed of mitochondrial contigs." [GMOD:ea] synonym: "mitochondrial scaffold" EXACT [] synonym: "mitochondrial supercontig" EXACT [] synonym: "mitochondrial_scaffold" EXACT [] is_a: SO:0000148 ! supercontig created_by: kareneilbeck creation_date: 2012-10-31T12:42:45Z [Term] id: SO:0001923 name: TERRA def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915] comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012. synonym: "telomeric repeat containing RNA" RELATED [] is_a: SO:0001927 ! telomeric_transcript created_by: kareneilbeck creation_date: 2012-10-31T01:06:40Z [Term] id: SO:0001924 name: ARRET def: "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915] comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012. is_a: SO:0001927 ! telomeric_transcript created_by: kareneilbeck creation_date: 2012-10-31T01:11:49Z [Term] id: SO:0001925 name: ARIA def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." [PMID:22139915] comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012. is_a: SO:0001927 ! telomeric_transcript created_by: kareneilbeck creation_date: 2012-10-31T01:24:37Z [Term] id: SO:0001926 name: anti_ARRET def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." [PMID:22139915] comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012. synonym: "anti-ARRET" EXACT [] is_a: SO:0001927 ! telomeric_transcript created_by: kareneilbeck creation_date: 2012-10-31T01:40:22Z [Term] id: SO:0001927 name: telomeric_transcript def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915] synonym: "telomeric transcript" EXACT [] is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2012-10-31T01:42:15Z [Term] id: SO:0001928 name: distal_duplication def: "A duplication of the distal region of a chromosome." [SO:bm] comment: This term is used by Complete Genomics in the structural variant analysis files. synonym: "distal duplication" EXACT [] is_a: SO:1000035 ! duplication created_by: kareneilbeck creation_date: 2012-10-31T01:56:44Z [Term] id: SO:0001929 name: mitochondrial_DNA_read def: "A sequencer read of a mitochondrial DNA sample." [GMOD:ea] comment: Requested by Bayer Cropscience, October, 2012. synonym: "mitochondrial DNA read" EXACT [] is_a: SO:0000150 ! read intersection_of: SO:0000150 ! read intersection_of: has_origin SO:0001032 ! mitochondrial_DNA relationship: has_origin SO:0001032 ! mitochondrial_DNA created_by: kareneilbeck creation_date: 2012-11-14T04:39:56Z [Term] id: SO:0001930 name: chloroplast_DNA_read def: "A sequencer read of a chloroplast DNA sample." [GMOD:ea] comment: Requested by Bayer Cropscience, October, 2012. synonym: "chloroplast DNA read" EXACT [] is_a: SO:0000150 ! read intersection_of: SO:0000150 ! read intersection_of: has_origin SO:0001033 ! chloroplast_DNA relationship: has_origin SO:0001033 ! chloroplast_DNA created_by: kareneilbeck creation_date: 2012-11-14T04:43:45Z [Term] id: SO:0001931 name: consensus_gDNA def: "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea] comment: Requested by Bayer Cropscience November, 2012. synonym: "consensus gDNA" EXACT [] synonym: "consensus genomic DNA" EXACT [] is_a: SO:0000994 ! consensus_region created_by: kareneilbeck creation_date: 2012-11-28T12:53:14Z [Term] id: SO:0001932 name: restriction_enzyme_five_prime_single_strand_overhang def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke] synonym: "restriction enzyme five prime single strand overhang" EXACT [] is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang created_by: kareneilbeck creation_date: 2013-03-06T09:50:44Z [Term] id: SO:0001933 name: restriction_enzyme_three_prime_single_strand_overhang def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke] synonym: "restriction enzyme three prime single strand overhang" EXACT [] is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang created_by: kareneilbeck creation_date: 2013-03-06T09:52:14Z [Term] id: SO:0001934 name: monomeric_repeat def: "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke] synonym: "monomeric repeat" EXACT [] is_a: SO:0000705 ! tandem_repeat created_by: kareneilbeck creation_date: 2013-03-06T09:59:15Z [Term] id: SO:0001935 name: H3K20_trimethylation_site def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj] synonym: "H3K20 trimethylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:13:48Z [Term] id: SO:0001936 name: H3K36_acetylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj] synonym: "H3K36 acetylation site" EXACT [] synonym: "H3K36ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:16:55Z [Term] id: SO:0001937 name: H2BK12_acetylation_site def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated." [EBI:nj] synonym: "H2BK12 acetylation site" EXACT [] synonym: "H2BK12ac" EXACT [] is_a: SO:0002143 ! histone_2B_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:19:13Z [Term] id: SO:0001938 name: H2AK5_acetylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj] synonym: "H2AK5 acetylation site" EXACT [] synonym: "H2AK5ac" EXACT [] is_a: SO:0002142 ! histone_2A_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:20:57Z [Term] id: SO:0001939 name: H4K12_acetylation_site def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj] synonym: "H4K12 acetylation site" EXACT [] synonym: "H4K12ac" EXACT [] is_a: SO:0001972 ! histone_4_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:26:15Z [Term] id: SO:0001940 name: H2BK120_acetylation_site def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj, http://dx.doi.org/10.4161/epi.6.5.15623] synonym: "H2BK120 acetylation site" EXACT [] synonym: "H2BK120ac" EXACT [] is_a: SO:0002143 ! histone_2B_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:28:38Z [Term] id: SO:0001941 name: H4K91_acetylation_site def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj] synonym: "H4K91 acetylation site" EXACT [] synonym: "H4K91ac" EXACT [] is_a: SO:0001972 ! histone_4_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:41:04Z [Term] id: SO:0001942 name: H2BK20_acetylation_site def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj] synonym: "H2BK20 acetylation site" EXACT [] synonym: "H2BK20ac" EXACT [] is_a: SO:0002143 ! histone_2B_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:44:31Z [Term] id: SO:0001943 name: H3K4_acetylation_site def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj] synonym: "H3K4 acetylation site" EXACT [] synonym: "H3K4ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:46:32Z [Term] id: SO:0001944 name: H2AK9_acetylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj] synonym: "H2AK9 acetylation site" EXACT [] synonym: "H2AK9ac" EXACT [] is_a: SO:0002142 ! histone_2A_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:48:11Z [Term] id: SO:0001945 name: H3K56_acetylation_site def: "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj] synonym: "H3K56 acetylation site" EXACT [] synonym: "H3K56ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:51:14Z [Term] id: SO:0001946 name: H2BK15_acetylation_site def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj] synonym: "H2BK15 acetylation site" EXACT [] synonym: "H2BK15ac" EXACT [] is_a: SO:0002143 ! histone_2B_acetylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:53:23Z [Term] id: SO:0001947 name: H3R2_monomethylation_site def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj] synonym: " H3R2me1" EXACT [] synonym: "H3R2 monomethylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:57:13Z [Term] id: SO:0001948 name: H3R2_dimethylation_site def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj] synonym: "H3R2 dimethylation site" EXACT [] synonym: "H3R2me2" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T10:59:17Z [Term] id: SO:0001949 name: H4R3_dimethylation_site def: "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj] synonym: "H4R3 dimethylation site" EXACT [] synonym: "H4R3me2" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T11:01:27Z [Term] id: SO:0001950 name: H4K4_trimethylation_site def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj] synonym: " H4K4me3" EXACT [] synonym: "H4K4 trimethylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T11:03:29Z [Term] id: SO:0001951 name: H3K23_dimethylation_site def: "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj] synonym: "H3K23 dimethylation site" EXACT [] synonym: "H3K23me2" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2013-03-06T11:05:33Z [Term] id: SO:0001952 name: promoter_flanking_region def: "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj] synonym: "promoter flanking region" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: kareneilbeck creation_date: 2013-03-06T11:36:25Z [Term] id: SO:0001953 name: restriction_enzyme_assembly_scar def: "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke] is_a: SO:0001954 ! restriction_enzyme_region created_by: kareneilbeck creation_date: 2013-03-06T03:18:11Z [Term] id: SO:0001954 name: restriction_enzyme_region def: "A region related to restriction enzyme function." [SO:ke] comment: Not a great term for annotation, but used to classify the various regions related to restriction enzymes. synonym: "restriction enzyme region" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2013-03-06T03:23:34Z [Term] id: SO:0001955 name: protein_stability_element def: "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke] synonym: "protein stability element" RELATED [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2013-03-06T03:32:47Z [Term] id: SO:0001956 name: protease_site def: "A polypeptide_region that codes for a protease cleavage site." [SO:ke] synonym: "protease site" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2013-03-06T03:36:28Z [Term] id: SO:0001957 name: RNA_stability_element def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke] synonym: "rna stability element" RELATED [] is_obsolete: true created_by: kareneilbeck creation_date: 2013-03-06T03:38:35Z [Term] id: SO:0001958 name: lariat_intron def: "A kind of intron whereby the excision is driven by lariat formation." [SO:ke] comment: Requested by PomBase 3604508. synonym: "lariat intron" EXACT [] is_a: SO:0000188 ! intron created_by: kareneilbeck creation_date: 2013-03-07T10:58:40Z [Term] id: SO:0001959 name: TCT_motif def: "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl] synonym: "polypyrimidine initiator" EXACT [] synonym: "TCT element" EXACT [] is_a: SO:0001660 ! core_eukaryotic_promoter_element created_by: kareneilbeck creation_date: 2013-05-17T04:38:48Z [Term] id: SO:0001960 name: 5_hydroxymethylcytosine def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke] synonym: "5-hmC" EXACT [] synonym: "5-hydroxymethylcytosine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0000114 ! methylated_cytosine created_by: kareneilbeck creation_date: 2013-05-17T05:05:31Z [Term] id: SO:0001961 name: 5_formylcytosine def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke] synonym: "5-fC" EXACT [] synonym: "5-formylcytosine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0001963 ! modified_cytosine created_by: kareneilbeck creation_date: 2013-05-17T05:06:13Z [Term] id: SO:0001962 name: modified_adenine def: "A modified adenine DNA base feature." [SO:ke] is_a: SO:0000305 ! modified_DNA_base created_by: kareneilbeck creation_date: 2013-05-20T01:22:30Z [Term] id: SO:0001963 name: modified_cytosine def: "A modified cytosine DNA base feature." [SO:ke] is_a: SO:0000305 ! modified_DNA_base created_by: kareneilbeck creation_date: 2013-05-20T01:23:47Z [Term] id: SO:0001964 name: modified_guanine def: "A modified guanine DNA base feature." [SO:ke] is_a: SO:0000305 ! modified_DNA_base created_by: kareneilbeck creation_date: 2013-05-20T01:25:31Z [Term] id: SO:0001965 name: 8_oxoguanine def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke] synonym: "8-oxoG" EXACT [] synonym: "8-oxoguanine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0001964 ! modified_guanine created_by: kareneilbeck creation_date: 2013-05-20T01:27:51Z [Term] id: SO:0001966 name: 5_carboxylcytosine def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke] synonym: "5-caC" EXACT [] synonym: "5-carboxycytosine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0001963 ! modified_cytosine created_by: kareneilbeck creation_date: 2013-05-20T01:30:01Z [Term] id: SO:0001967 name: 8_oxoadenine def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke] synonym: "8-oxoA" EXACT [] synonym: "8-oxoadenine" EXACT [] xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf is_a: SO:0001962 ! modified_adenine created_by: kareneilbeck creation_date: 2013-05-20T01:31:05Z [Term] id: SO:0001968 name: coding_transcript_variant def: "A transcript variant of a protein coding gene." [SO:ke] synonym: "coding transcript variant" EXACT [] synonym: "Jannovar:coding_transcript_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2013-05-22T04:34:49Z [Term] id: SO:0001969 name: coding_transcript_intron_variant def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke] synonym: "coding sequence intron variant" EXACT [] synonym: "Jannovar:coding_transcript_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0001627 ! intron_variant is_a: SO:0001968 ! coding_transcript_variant created_by: kareneilbeck creation_date: 2013-05-23T10:54:17Z [Term] id: SO:0001970 name: non_coding_transcript_intron_variant def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke] synonym: "ANNOVAR:ncRNA_intronic" NARROW VAR [] synonym: "Jannovar:non_coding_transcript_intron_variant" NARROW VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "non coding transcript intron variant" EXACT [] is_a: SO:0001619 ! non_coding_transcript_variant is_a: SO:0001627 ! intron_variant created_by: kareneilbeck creation_date: 2013-05-23T10:55:03Z [Term] id: SO:0001971 name: zinc_finger_binding_site def: "A binding site to which a polypeptide will bind with a zinc finger motif, which is characterized by requiring one or more Zinc 2+ ions for stabilized folding." [] synonym: "zinc finger binding site" EXACT [] synonym: "zinc_fing" EXACT BS [] is_a: SO:0001429 ! DNA_binding_site created_by: kareneilbeck creation_date: 2013-07-29T04:41:53Z [Term] id: SO:0001972 name: histone_4_acetylation_site def: "A histone 4 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke] synonym: "H4ac" EXACT [] synonym: "histone 4 acetylation site" EXACT [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2013-07-30T10:43:04Z [Term] id: SO:0001973 name: histone_3_acetylation_site def: "A histone 3 modification where the modification is the acetylation of the residue." [EBI:nj, ISBN:0815341059, SO:ke] synonym: "H3ac" EXACT [] synonym: "histone 3 acetylation site" EXACT [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2013-07-30T10:46:42Z [Term] id: SO:0001974 name: CTCF_binding_site def: "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj] synonym: "CCCTF binding site" EXACT [] synonym: "CTCF binding site" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2013-07-30T10:59:11Z [Term] id: SO:0001975 name: five_prime_sticky_end_restriction_enzyme_cleavage_site def: "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke] comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction. synonym: "five prime sticky end restriction enzyme cleavage site" EXACT [] is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2013-07-30T11:32:16Z [Term] id: SO:0001976 name: three_prime_sticky_end_restriction_enzyme_cleavage_site def: "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke] comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction. synonym: "three prime sticky end restriction enzyme cleavage site" EXACT [] is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2013-07-30T11:37:19Z [Term] id: SO:0001977 name: ribonuclease_site def: "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke] synonym: "ribonuclease site" EXACT [] is_a: SO:0000833 ! transcript_region created_by: kareneilbeck creation_date: 2013-07-30T11:41:06Z [Term] id: SO:0001978 name: signature def: "A region of sequence where developer information is encoded." [SO:ke] comment: Requested by Jackie Quinn for use in synthetic biology. synonym: "DNA signature" EXACT [] is_a: SO:0000804 ! engineered_region created_by: kareneilbeck creation_date: 2013-07-30T11:49:22Z [Term] id: SO:0001979 name: RNA_stability_element def: "A motif that affects the stability of RNA." [PMID:22495308, SO:ke] synonym: "RNA stability element" EXACT [] is_a: SO:0000715 ! RNA_motif created_by: kareneilbeck creation_date: 2013-07-30T03:33:53Z [Term] id: SO:0001980 name: G_box def: "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml] comment: A plant specific region. synonym: "G-box" EXACT [] synonym: "GBF binding sequence" EXACT [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2013-07-30T04:00:50Z [Term] id: SO:0001981 name: L_box def: "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml] synonym: "L-box" EXACT [] synonym: "L-box promoter element" EXACT [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2013-07-30T04:12:19Z [Term] id: SO:0001982 name: I-box def: "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml] synonym: "I-box promoter motif" EXACT [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2013-07-30T04:17:55Z [Term] id: SO:0001983 name: 5_prime_UTR_premature_start_codon_variant def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am] comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia. synonym: "5' UTR premature start codon variant" EXACT [] is_a: SO:0001623 ! 5_prime_UTR_variant created_by: kareneilbeck creation_date: 2013-07-30T04:36:25Z [Term] id: SO:0001984 name: silent_mating_type_cassette_array def: "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah] synonym: "silent mating-type cassette" RELATED [] is_a: SO:0005854 ! gene_cassette_array created_by: kareneilbeck creation_date: 2013-07-31T02:40:38Z [Term] id: SO:0001985 name: Okazaki_fragment def: "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152] comment: Requested by Midori Harris, 2013. synonym: "Okazaki fragment" EXACT [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2013-07-31T02:57:55Z [Term] id: SO:0001986 name: upstream_transcript_variant def: "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr] comment: Requested by Graham Ritchie, EBI/Sanger. synonym: "upstream transcript variant" EXACT [] is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2013-07-31T03:46:14Z [Term] id: SO:0001987 name: downstream_transcript_variant def: "A feature variant, where the alteration occurs downstream of the transcript termination site." [] comment: Requested by Graham Ritchie, EBI/Sanger. synonym: "downstream transcript variant" EXACT [] is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2013-07-31T03:47:51Z [Term] id: SO:0001988 name: 5_prime_UTR_premature_start_codon_gain_variant def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am] synonym: "5 prime UTR premature start codon gain variant" EXACT [] synonym: "Jannovar:5_prime_UTR_premature_start_codon_gain_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:START_GAINED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant created_by: kareneilbeck creation_date: 2013-07-31T03:53:06Z [Term] id: SO:0001989 name: 5_prime_UTR_premature_start_codon_loss_variant def: "A 5' UTR variant where a premature start codon is lost." [SANGER:am] is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant created_by: kareneilbeck creation_date: 2013-07-31T03:56:48Z [Term] id: SO:0001990 name: five_prime_UTR_premature_start_codon_location_variant def: "A 5' UTR variant where a premature start codon is moved." [SANGER:am] is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant created_by: kareneilbeck creation_date: 2013-07-31T03:57:47Z [Term] id: SO:0001991 name: consensus_AFLP_fragment def: "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea] comment: Requested by Bayer Cropscience September, 2013. synonym: "consensus AFLP fragment" EXACT [] synonym: "consensus amplified fragment length polymorphism fragment" EXACT [] is_a: SO:0000994 ! consensus_region created_by: kareneilbeck creation_date: 2013-09-24T10:43:41Z [Term] id: SO:0001992 name: nonsynonymous_variant def: "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke] synonym: "non_synonymous_coding" EXACT [http://ensembl.org/info/docs/variation/index.html] synonym: "nonsynonymous variant" EXACT [] is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2013-10-16T11:47:51Z [Term] id: SO:0001993 name: extended_cis_splice_site def: "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am] comment: Added by Andy Menzies (Sanger). synonym: "extended cis splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site created_by: kareneilbeck creation_date: 2014-01-04T06:20:00Z [Term] id: SO:0001994 name: intron_base_5 def: "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am] synonym: "intron base 5" EXACT [] is_a: SO:0001014 ! intron_domain relationship: part_of SO:0001993 ! extended_cis_splice_site created_by: kareneilbeck creation_date: 2014-01-04T06:26:02Z [Term] id: SO:0001995 name: extended_intronic_splice_region_variant def: "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am] comment: Added by Andy Menzies (Sanger). synonym: "extended intronic splice region variant" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2014-01-04T06:37:27Z [Term] id: SO:0001996 name: extended_intronic_splice_region def: "Region of intronic sequence within 10 bases of an exon." [SANGER:am] synonym: "extended intronic splice region " EXACT [] is_a: SO:0001014 ! intron_domain created_by: kareneilbeck creation_date: 2014-01-04T06:41:23Z [Term] id: SO:0001997 name: subtelomere def: "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al] is_a: SO:0000628 ! chromosomal_structural_element created_by: kareneilbeck creation_date: 2014-01-05T07:02:01Z [Term] id: SO:0001998 name: sgRNA def: "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893] synonym: "gRNA" RELATED [] synonym: "guide RNA" RELATED [] synonym: "small guide RNA" EXACT [] is_a: SO:0000696 ! oligo created_by: kareneilbeck creation_date: 2014-01-05T07:25:08Z [Term] id: SO:0001999 name: mating_type_region_motif def: "DNA motif that is a component of a mating type region." [SO:ke] synonym: "mating type region motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001789 ! mating_type_region created_by: kareneilbeck creation_date: 2014-01-05T07:30:17Z [Term] id: SO:0002001 name: Y_region def: "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd] comment: Requested by Janos Demeter, SGD. synonym: "Y-region" EXACT [] is_a: SO:0001999 ! mating_type_region_motif created_by: kareneilbeck creation_date: 2014-01-05T07:33:30Z [Term] id: SO:0002002 name: Z1_region def: "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd] comment: Requested by Janos Demeter, SGD. synonym: "Z1-region" EXACT [] is_a: SO:0001999 ! mating_type_region_motif created_by: kareneilbeck creation_date: 2014-01-05T07:34:59Z [Term] id: SO:0002003 name: Z2_region def: "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd] comment: Requested by Janos Demeter, SGD. synonym: "Z2-segment" EXACT [] is_a: SO:0001999 ! mating_type_region_motif created_by: kareneilbeck creation_date: 2014-01-05T07:36:45Z [Term] id: SO:0002004 name: ARS_consensus_sequence def: "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd] synonym: "ACS" EXACT [] synonym: "ARS consensus sequence" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000436 ! ARS created_by: kareneilbeck creation_date: 2014-01-05T07:47:48Z [Term] id: SO:0002005 name: DSR_motif def: "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662] comment: Requested by Antonia Locke, (Pombe). synonym: "DSR motif" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2014-01-05T07:51:27Z [Term] id: SO:0002006 name: zinc_repressed_element def: "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh] comment: This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe. synonym: "zinc repressed element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2014-01-05T09:23:27Z [Term] id: SO:0002007 name: MNV def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th] synonym: "multiple nucleotide substitution" EXACT [] synonym: "multiple nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2014-01-13T03:48:40Z [Term] id: SO:0002008 name: rare_amino_acid_variant def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke] comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function. synonym: "Jannovar:rare_amino_acid_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "rare amino acid variant" EXACT [] synonym: "snpEff:RARE_AMINO_ACID" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001586 ! non_conservative_missense_variant created_by: kareneilbeck creation_date: 2014-03-24T02:24:01Z [Term] id: SO:0002009 name: selenocysteine_loss def: "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid." [SO:ke] comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function. synonym: "selenocysteine loss" EXACT [] is_a: SO:0002008 ! rare_amino_acid_variant created_by: kareneilbeck creation_date: 2014-03-24T02:29:44Z [Term] id: SO:0002010 name: pyrrolysine_loss def: "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke] comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function. synonym: "pyrrolysine loss" EXACT [] is_a: SO:0002008 ! rare_amino_acid_variant created_by: kareneilbeck creation_date: 2014-03-24T02:30:16Z [Term] id: SO:0002011 name: intragenic_variant def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke] comment: Requested by Pablo Cingolani, for use in SnpEff. synonym: "intragenic variant" EXACT [] synonym: "Jannovar:intragenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:INTRAGENIC" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2014-03-24T02:33:13Z [Term] id: SO:0002012 name: start_lost def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke] comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts. synonym: "Jannovar:start_lost" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:START_LOST" EXACT VAR [] synonym: "VEP:start_lost" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html xref: http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences is_a: SO:0001582 ! initiator_codon_variant is_a: SO:0001992 ! nonsynonymous_variant created_by: kareneilbeck creation_date: 2014-03-24T02:41:28Z [Term] id: SO:0002013 name: 5_prime_UTR_truncation def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke] synonym: "5 prime UTR truncation" EXACT [] synonym: "Jannovar:5_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:UTR_5_DELETED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001623 ! 5_prime_UTR_variant created_by: kareneilbeck creation_date: 2014-03-25T10:46:42Z [Term] id: SO:0002014 name: 5_prime_UTR_elongation def: "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke] synonym: "5 prime UTR elongation" EXACT [] is_a: SO:0001623 ! 5_prime_UTR_variant created_by: kareneilbeck creation_date: 2014-03-25T10:48:26Z [Term] id: SO:0002015 name: 3_prime_UTR_truncation def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke] synonym: "3 prime UTR truncation" EXACT [] synonym: "Jannovar:3_prime_utr_truncation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:UTR_3_DELETED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001624 ! 3_prime_UTR_variant created_by: kareneilbeck creation_date: 2014-03-25T10:54:50Z [Term] id: SO:0002016 name: 3_prime_UTR_elongation def: "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke] synonym: "3 prime UTR elongation" EXACT [] is_a: SO:0001624 ! 3_prime_UTR_variant created_by: kareneilbeck creation_date: 2014-03-25T10:55:33Z [Term] id: SO:0002017 name: conserved_intergenic_variant def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke] comment: Requested by Uma Paila (UVA) for snpEff. synonym: "conserved intergenic variant" EXACT [] synonym: "Jannovar:conserved_intergenic_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2014-03-25T02:54:39Z [Term] id: SO:0002018 name: conserved_intron_variant def: "A transcript variant occurring within a conserved region of an intron." [SO:ke] comment: Requested by Uma Paila (UVA) for snpEff. synonym: "conserved intron variant" EXACT [] synonym: "Jannovar:conserved_intron_variant" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] synonym: "snpEff:INTRON_CONSERVED" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0001627 ! intron_variant created_by: kareneilbeck creation_date: 2014-03-25T02:58:41Z [Term] id: SO:0002019 name: start_retained_variant def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke] comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation. synonym: "snpEff:SYNONYMOUS_START" EXACT VAR [] is_a: SO:0001582 ! initiator_codon_variant is_a: SO:0001819 ! synonymous_variant created_by: kareneilbeck creation_date: 2014-03-28T10:08:41Z [Term] id: SO:0002020 name: boundary_element def: "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502] comment: Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf). synonym: "boundary element" EXACT [] synonym: "insulator" RELATED [] is_a: SO:0000627 ! insulator created_by: kareneilbeck creation_date: 2014-05-30T14:45:37Z [Term] id: SO:0002021 name: mating_type_region_replication_fork_barrier def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787] comment: Requested by Midori Harris. synonym: "mating type region replication fork barrier" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2014-05-30T14:57:26Z [Term] id: SO:0002022 name: priRNA def: "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al] synonym: "primal small RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2014-05-30T15:01:24Z [Term] id: SO:0002023 name: multiplexing_sequence_identifier def: "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170] synonym: "multiplexing sequence identifier" EXACT [] is_a: SO:0000324 ! tag created_by: kareneilbeck creation_date: 2014-05-30T15:13:16Z [Term] id: SO:0002024 name: W_region alt_id: SO:0002000 def: "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." [SGD:jd] comment: MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD. synonym: "W-region" EXACT [] is_a: SO:0001999 ! mating_type_region_motif created_by: kareneilbeck creation_date: 2014-07-11T13:20:08Z [Term] id: SO:0002025 name: cis_acting_homologous_chromosome_pairing_region def: "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw] comment: Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase. synonym: "cis-acting homologous chromosome pairing region" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2014-07-14T11:40:34Z [Term] id: SO:0002026 name: intein_encoding_region def: "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123] comment: Requested by Janos Demeter 2014. is_a: SO:0000842 ! gene_component_region created_by: kareneilbeck creation_date: 2014-07-14T11:53:21Z [Term] id: SO:0002027 name: uORF def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah] synonym: "regulatory uORF" EXACT [] synonym: "upstream ORF" EXACT [] xref: PMID:26684391 is_a: SO:0000236 ! ORF created_by: kareneilbeck creation_date: 2014-07-14T11:59:23Z [Term] id: SO:0002028 name: sORF def: "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah] synonym: "small ORF" EXACT [] synonym: "smORF" EXACT [] is_a: SO:0000236 ! ORF created_by: kareneilbeck creation_date: 2014-07-14T12:02:33Z [Term] id: SO:0002029 name: tnaORF def: "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw] synonym: "translated nested antisense gene" EXACT [] is_a: SO:0000236 ! ORF created_by: kareneilbeck creation_date: 2014-07-14T12:04:32Z [Term] id: SO:0002030 name: X_region def: "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd] synonym: "x-region" EXACT [] is_a: SO:0001999 ! mating_type_region_motif created_by: kareneilbeck creation_date: 2014-07-14T18:43:21Z [Term] id: SO:0002031 name: shRNA def: "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke] synonym: "short hairpin RNA" EXACT [] synonym: "small hairpin RNA" EXACT [] xref: http:http\:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia" is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2014-10-23T09:16:29Z [Term] id: SO:0002032 name: moR def: "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." [SO:ke] comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015. synonym: "microRNA-offset RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA relationship: part_of SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T13:57:43Z [Term] id: SO:0002033 name: loR def: "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke] comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015. synonym: "loop-origin miRs" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA relationship: part_of SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T14:02:02Z [Term] id: SO:0002034 name: miR_encoding_snoRNA_primary_transcript def: "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:02:13Z [Term] id: SO:0002035 name: lncRNA_primary_transcript def: "A primary transcript encoding a lncRNA." [SO:ke] synonym: "lncRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2015-01-09T15:23:03Z [Term] id: SO:0002036 name: miR_encoding_lncRNA_primary_transcript def: "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding lncRNA primary transcript" EXACT [] is_a: SO:0002035 ! lncRNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:23:48Z [Term] id: SO:0002037 name: miR_encoding_tRNA_primary_transcript def: "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:28:23Z [Term] id: SO:0002038 name: shRNA_primary_transcript def: "A primary transcript encoding an shRNA." [SO:ke] synonym: "shRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2015-01-09T15:30:43Z [Term] id: SO:0002039 name: miR_encoding_shRNA_primary_transcript def: "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding shRNA primary transcript" EXACT [] is_a: SO:0002038 ! shRNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:32:00Z [Term] id: SO:0002040 name: vaultRNA_primary_transcript def: "A primary transcript encoding a vaultRNA." [SO:ke] synonym: "vaultRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2015-01-09T15:33:33Z [Term] id: SO:0002041 name: miR_encoding_vaultRNA_primary_transcript def: "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding vaultRNA primary transcript" EXACT [] is_a: SO:0002040 ! vaultRNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:34:32Z [Term] id: SO:0002042 name: Y_RNA_primary_transcript def: "A primary transcript encoding a Y-RNA." [SO:ke] synonym: "Y-RNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2015-01-09T15:36:51Z [Term] id: SO:0002043 name: miR_encoding_Y_RNA_primary_transcript def: "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] synonym: "miR encoding Y-RNA primary transcript" EXACT [] is_a: SO:0002042 ! Y_RNA_primary_transcript relationship: has_part SO:0001244 ! pre_miRNA created_by: kareneilbeck creation_date: 2015-01-09T15:37:46Z [Term] id: SO:0002044 name: TCS_element def: "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." [PMID:1489142, PMID:20118212, SO:ke] comment: Requested by Rama - SGD. synonym: "TCS element" EXACT [] synonym: "TEA Consensus Sequence " EXACT [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2015-02-09T15:02:53Z [Term] id: SO:0002045 name: pheromone_response_element def: "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke] comment: Requested by Rama, SGD. synonym: "pheromone response element" EXACT [] synonym: "PRE" EXACT [] is_a: SO:0000235 ! TF_binding_site is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2015-02-09T15:05:43Z [Term] id: SO:0002046 name: FRE def: "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke] comment: Requested by Rama, SGD. synonym: "filamentation and invasion response element" EXACT [] is_a: SO:0001461 ! enhancer_binding_site created_by: kareneilbeck creation_date: 2015-02-09T15:09:47Z [Term] id: SO:0002047 name: transcription_pause_site def: "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." [PMID:24789973, SO:ke] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "transcription pause site" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: kareneilbeck creation_date: 2015-02-09T15:32:52Z [Term] id: SO:0002048 name: disabled_reading_frame def: "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." [SGD:se] synonym: "disabled ORF" EXACT [] synonym: "disabled_reading frame" RELATED [] synonym: "dORF" EXACT [] is_a: SO:0000717 ! reading_frame created_by: kareneilbeck creation_date: 2015-02-09T16:15:46Z [Term] id: SO:0002049 name: H3K27_acetylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs] comment: Requested by: Sagar Jain, Richard Scheuermann. synonym: "H3K27 acetylation site" EXACT [] synonym: "H3K27ac" EXACT [] is_a: SO:0001973 ! histone_3_acetylation_site created_by: kareneilbeck creation_date: 2015-05-14T10:17:11Z [Term] id: SO:0002050 name: constitutive_promoter def: "A promoter that allows for continual transcription of gene." [SO:ke] synonym: "constitutive promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: kareneilbeck creation_date: 2015-05-14T10:39:09Z [Term] id: SO:0002051 name: inducible_promoter def: "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke] synonym: "inducible promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: kareneilbeck creation_date: 2015-05-14T10:39:56Z [Term] id: SO:0002052 name: dominant_negative_variant def: "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke] comment: Requested by Deanna Church. synonym: "dominant negative" EXACT [] synonym: "dominant negative variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2015-05-14T11:16:28Z [Term] id: SO:0002053 name: gain_of_function_variant def: "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke] synonym: "gain of function variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2015-05-14T11:20:47Z [Term] id: SO:0002054 name: loss_of_function_variant def: "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke] synonym: "loss of function variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2015-05-14T11:21:29Z [Term] id: SO:0002055 name: null_mutation def: "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke] synonym: "null mutation" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: kareneilbeck creation_date: 2015-05-14T11:21:57Z [Term] id: SO:0002056 name: intronic_splicing_silencer def: "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke] comment: Requested by Javier Diez Perez. synonym: "intronic splicing silencer" EXACT [] synonym: "ISS" EXACT [] is_a: SO:0000625 ! silencer relationship: part_of SO:0000188 ! intron created_by: kareneilbeck creation_date: 2015-05-14T12:24:10Z [Term] id: SO:0002057 name: intronic_splicing_enhancer synonym: "ISE" EXACT [] is_obsolete: true created_by: kareneilbeck creation_date: 2015-05-14T12:28:31Z [Term] id: SO:0002058 name: exonic_splicing_silencer def: "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke] comment: Requested by Javier Diez Perez. synonym: "ESS" EXACT [] synonym: "exonic splicing silencer" EXACT [] is_a: SO:0000625 ! silencer is_a: SO:0000852 ! exon_region created_by: kareneilbeck creation_date: 2015-05-14T12:42:12Z [Term] id: SO:0002059 name: recombination_enhancer def: "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se] synonym: "recombination enhancer" EXACT [] is_a: SO:0001681 ! recombination_regulatory_region created_by: kareneilbeck creation_date: 2015-05-14T13:08:58Z [Term] id: SO:0002060 name: interchromosomal_translocation def: "A translocation where the regions involved are from different chromosomes." [NCBI:th] is_a: SO:1000044 ! chromosomal_translocation created_by: kareneilbeck creation_date: 2015-06-18T11:10:30Z [Term] id: SO:0002061 name: intrachromosomal_translocation def: "A translocation where the regions involved are from the same chromosome." [NCBI:th] is_a: SO:1000044 ! chromosomal_translocation created_by: kareneilbeck creation_date: 2015-06-18T11:10:51Z [Term] id: SO:0002062 name: complex_chromosomal_rearrangement def: "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th] synonym: "complex chromosomal rearrangement" EXACT [] is_a: SO:0001784 ! complex_structural_alteration created_by: kareneilbeck creation_date: 2015-06-18T11:24:55Z [Term] id: SO:0002063 name: Alu_insertion def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th] synonym: "Alu insertion" EXACT [] is_a: SO:0001837 ! mobile_element_insertion created_by: kareneilbeck creation_date: 2015-06-18T11:30:36Z [Term] id: SO:0002064 name: LINE1_insertion def: "An insertion from the Line1 family of mobile elements." [NCBI:th] synonym: "line1 insertion" RELATED [] is_a: SO:0001837 ! mobile_element_insertion relationship: derives_from SO:0002272 ! L1_LINE_retrotransposon created_by: kareneilbeck creation_date: 2015-06-18T11:34:44Z [Term] id: SO:0002065 name: SVA_insertion def: "An insertion of sequence from the SVA family of mobile elements." [NCBI:th] is_a: SO:0001837 ! mobile_element_insertion created_by: kareneilbeck creation_date: 2015-06-18T11:36:12Z [Term] id: SO:0002066 name: mobile_element_deletion def: "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." [NCBI:th] synonym: "mobile element deletion" EXACT [] is_a: SO:0000159 ! deletion created_by: kareneilbeck creation_date: 2015-09-04T13:40:43Z [Term] id: SO:0002067 name: HERV_deletion def: "A deletion of the HERV mobile element with respect to a reference." [NCBI:th] synonym: "HERV deletion" EXACT [] is_a: SO:0002066 ! mobile_element_deletion relationship: derives_from SO:0002268 ! Endogenous_Retrovirus_LTR_retrotransposon created_by: kareneilbeck creation_date: 2015-09-04T13:42:52Z [Term] id: SO:0002068 name: SVA_deletion def: "A deletion of an SVA mobile element." [NCBI:th] synonym: "SVA deletion" EXACT [] is_a: SO:0002066 ! mobile_element_deletion created_by: kareneilbeck creation_date: 2015-09-04T13:45:22Z [Term] id: SO:0002069 name: LINE1_deletion def: "A deletion of a LINE1 mobile element with respect to a reference." [NCBI:th] synonym: "LINE1 deletion" RELATED [] is_a: SO:0002066 ! mobile_element_deletion relationship: derives_from SO:0002272 ! L1_LINE_retrotransposon created_by: kareneilbeck creation_date: 2015-09-04T13:46:26Z [Term] id: SO:0002070 name: Alu_deletion def: "A deletion of an Alu mobile element with respect to a reference." [NCBI:th] is_a: SO:0002066 ! mobile_element_deletion created_by: kareneilbeck creation_date: 2015-09-04T13:47:16Z [Term] id: SO:0002071 name: CDS_supported_by_peptide_spectrum_match def: "A CDS that is supported by proteomics data." [SO:ke] is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data created_by: kareneilbeck creation_date: 2015-10-12T13:25:02Z [Term] id: SO:0002072 name: sequence_comparison def: "A position or feature where two sequences have been compared." [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:sequence_comparison" EXACT [] synonym: "sequence comparison" EXACT [] is_a: SO:0000110 ! sequence_feature created_by: kareneilbeck creation_date: 2015-11-23T14:14:32Z [Term] id: SO:0002073 name: no_sequence_alteration def: "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence." [SO:ke] comment: This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly. synonym: "no sequence alteration" EXACT [] is_a: SO:0002072 ! sequence_comparison created_by: kareneilbeck creation_date: 2015-11-23T14:15:08Z [Term] id: SO:0002074 name: intergenic_1kb_variant def: "A variant that falls in an intergenic region that is 1 kb or less between 2 genes." [SO:ke] comment: This term is added to map to the Annovar annotation 'upstream,downstream' . synonym: "ANNOVAR:upstream;downstream" EXACT VAR [] is_a: SO:0001628 ! intergenic_variant created_by: kareneilbeck creation_date: 2015-11-23T14:24:16Z [Term] id: SO:0002075 name: incomplete_transcript_variant def: "A sequence variant that intersects an incompletely annotated transcript." [SO:ke] comment: This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation.\n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems. synonym: "incomplete transcript variant" EXACT [] xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2015-11-23T14:43:51Z [Term] id: SO:0002076 name: incomplete_transcript_3UTR_variant def: "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript." [SO:ke] synonym: "ANNOVAR:ncRNA_UTR3" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/] synonym: "incomplete transcript 3UTR variant" RELATED [] xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-23T14:45:52Z [Term] id: SO:0002077 name: incomplete_transcript_5UTR_variant def: "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript." [SO:ke] synonym: "ANNOVAR:ncRNA_UTR5" EXACT VAR [http://annovar.openbioinformatics.org/en/latest/user-guide/gene/] synonym: "incomplete transcript 5UTR variant" EXACT [] xref: http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-24T12:39:17Z [Term] id: SO:0002078 name: incomplete_transcript_intronic_variant def: "A sequence variant that intersects the intron of an incompletely annotated transcript." [SO:ke] synonym: "incomplete transcript intronic variant" EXACT [] is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-24T12:51:45Z [Term] id: SO:0002079 name: incomplete_transcript_splice_region_variant def: "A sequence variant that intersects the splice region of an incompletely annotated transcript." [SO:ke] synonym: "incomplete transcript splice region variant" EXACT [] is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-24T12:52:06Z [Term] id: SO:0002080 name: incomplete_transcript_exonic_variant def: "A sequence variant that intersects the exon of an incompletely annotated transcript." [SO:ke] synonym: "incomplete transcript exonic variant" EXACT [] is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-24T12:52:10Z [Term] id: SO:0002081 name: incomplete_transcript_CDS def: "A sequence variant that intersects the coding regions of an incompletely annotated transcript." [SO:ke] synonym: "Seattleseq:coding-notMod3" EXACT VAR [] synonym: "Seattleseq:coding-unknown" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0002075 ! incomplete_transcript_variant created_by: kareneilbeck creation_date: 2015-11-24T15:32:27Z [Term] id: SO:0002082 name: incomplete_transcript_coding_splice_variant def: "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript." [SO:ke] synonym: "incomplete transcript coding splice variant" EXACT [] synonym: "Seattleseq:coding-notMod3-near-splice" EXACT VAR [] synonym: "Seattleseq:coding-unknown-near-splice" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0002079 ! incomplete_transcript_splice_region_variant created_by: kareneilbeck creation_date: 2015-11-24T15:51:06Z [Term] id: SO:0002083 name: 2KB_downstream_variant def: "A sequence variant located within 2KB 3' of a gene." [SO:ke] synonym: "Seattleseq:near-gene-3" EXACT VAR [] xref: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp "Seattleseq" is_a: SO:0001632 ! downstream_gene_variant created_by: kareneilbeck creation_date: 2015-11-24T15:55:49Z [Term] id: SO:0002084 name: exonic_splice_region_variant def: "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary." [SO:ke] synonym: "ANNOVAR:exonic;splicing" EXACT VAR [] synonym: "exonic splice region variant" EXACT [] synonym: "Seattleseq:coding-near-splice" RELATED VAR [] is_a: SO:0001630 ! splice_region_variant created_by: kareneilbeck creation_date: 2015-12-01T14:38:47Z [Term] id: SO:0002085 name: unidirectional_gene_fusion def: "A sequence variant whereby two genes, on the same strand have become joined." [SO:ke] comment: Requested by SNPEFF team. Feb 2016. synonym: "unidirectional gene fusion" EXACT [] is_a: SO:0001565 ! gene_fusion created_by: kareneilbeck creation_date: 2016-02-23T12:16:48Z [Term] id: SO:0002086 name: bidirectional_gene_fusion def: "A sequence variant whereby two genes, on alternate strands have become joined." [SO:ke] comment: Requested by SNPEFF team. Feb 2016. synonym: "bidirectional gene fusion" EXACT [] is_a: SO:0001565 ! gene_fusion created_by: kareneilbeck creation_date: 2016-02-23T12:17:18Z [Term] id: SO:0002087 name: pseudogenic_CDS def: "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." [SO:ke] synonym: "INSDC_feature:CDS" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "pseudogenic CDS" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: part_of SO:0000516 ! pseudogenic_transcript created_by: kareneilbeck creation_date: 2016-02-29T12:58:52Z [Term] id: SO:0002088 name: non_coding_transcript_splice_region_variant def: "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript." [SO:ke] synonym: "ANNOVAR:ncRNA_splicing" NARROW [] is_a: SO:0001619 ! non_coding_transcript_variant is_a: SO:0001630 ! splice_region_variant created_by: kareneilbeck creation_date: 2016-03-07T09:40:46Z [Term] id: SO:0002089 name: 3_prime_UTR_exon_variant def: "A UTR variant of exonic sequence of the 3' UTR." [SO:ke] comment: Requested by visze github tracker ID 346. synonym: "3 prime UTR exon variant" EXACT [] is_a: SO:0001624 ! 3_prime_UTR_variant created_by: kareneilbeck creation_date: 2016-03-07T10:37:04Z [Term] id: SO:0002090 name: 3_prime_UTR_intron_variant def: "A UTR variant of intronic sequence of the 3' UTR." [SO:ke] comment: Requested by visze github tracker ID 346. synonym: "3 prime UTR intron variant" EXACT [] is_a: SO:0001624 ! 3_prime_UTR_variant is_a: SO:0001969 ! coding_transcript_intron_variant created_by: kareneilbeck creation_date: 2016-03-07T10:37:41Z [Term] id: SO:0002091 name: 5_prime_UTR_intron_variant def: "A UTR variant of intronic sequence of the 5' UTR." [SO:ke] comment: Requested by visze github tracker ID 346. synonym: "5 prime UTR intron variant" EXACT [] is_a: SO:0001623 ! 5_prime_UTR_variant is_a: SO:0001969 ! coding_transcript_intron_variant created_by: kareneilbeck creation_date: 2016-03-07T10:38:04Z [Term] id: SO:0002092 name: 5_prime_UTR_exon_variant def: "A UTR variant of exonic sequence of the 5' UTR." [SO:ke] comment: Requested by visze github tracker ID 346. synonym: "5 prime UTR exon variant" EXACT [] is_a: SO:0001623 ! 5_prime_UTR_variant created_by: kareneilbeck creation_date: 2016-03-07T10:38:26Z [Term] id: SO:0002093 name: structural_interaction_variant def: "A variant that impacts the internal interactions of the resulting polypeptide structure." [SO:ke] comment: Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be "interacting" and thus important for protein structure. synonym: "structural interaction variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2016-03-07T11:43:55Z [Term] id: SO:0002094 name: non_allelic_homologous_recombination_region def: "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination." [] synonym: "INSDC_feature:misc_recomb" BROAD [] synonym: "INSDC_qualifier:non_allelic_homologous" EXACT [] synonym: "INSDC_qualifier:non_allelic_homologous_recombination" EXACT [] synonym: "NAHRR" EXACT [] synonym: "non allelic homologous recombination region" EXACT [] is_a: SO:0000339 ! recombination_hotspot created_by: nicole creation_date: 2016-05-17T13:34:12Z [Term] id: SO:0002095 name: scaRNA def: "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs)." [PMC:126017, PMID:27775477, PMID:28869095, SO:nrs] comment: Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509. synonym: "small Cajal body specific RNA" EXACT [] synonym: "small Cajal body-specific RNA" EXACT [] xref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/ is_a: SO:0000275 ! snoRNA created_by: nicole creation_date: 2016-05-19T13:42:45Z [Term] id: SO:0002096 name: short_tandem_repeat_variation def: "A variation that expands or contracts a tandem repeat with regard to a reference." [SO:ke] synonym: "short tandem repeat variation" EXACT [] synonym: "str variation" EXACT [] is_a: SO:0000248 ! sequence_length_alteration created_by: kareneilbeck creation_date: 2016-07-14T16:04:40Z [Term] id: SO:0002097 name: vertebrate_immune_system_pseudogene def: "A pseudogene derived from a vertebrate immune system gene." [SO:ke] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "vertebrate immune system pseudogene" EXACT [] is_a: SO:0000336 ! pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:00:22Z [Term] id: SO:0002098 name: immunoglobulin_pseudogene def: "A pseudogene derived from an immunoglobulin gene." [SO:ke] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "immunoglobulin pseudogene" EXACT [] is_a: SO:0002097 ! vertebrate_immune_system_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:01:47Z [Term] id: SO:0002099 name: T_cell_receptor_pseudogene def: "A pseudogene derived from a T-cell receptor gene." [SO:ke] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. is_a: SO:0002097 ! vertebrate_immune_system_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:02:18Z [Term] id: SO:0002100 name: IG_C_pseudogene def: "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IG C pseudogene" EXACT [] is_a: SO:0002098 ! immunoglobulin_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:05:08Z [Term] id: SO:0002101 name: IG_J_pseudogene def: "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IG J pseudogene" EXACT [] synonym: "IG joining pseudogene" EXACT [] synonym: "IG_joining_pseudogene" EXACT [] synonym: "Immunoglobulin Joining Pseudogene" EXACT [] synonym: "Immunoglobulin_Joining_Pseudogene" EXACT [] is_a: SO:0002098 ! immunoglobulin_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:05:34Z [Term] id: SO:0002102 name: IG_V_pseudogene def: "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IG V pseudogene" EXACT [] synonym: "IG variable pseudogene" EXACT [] synonym: "IG_variable_pseudogene" EXACT [] synonym: "Immunoglobulin variable pseudogene" EXACT [] synonym: "Immunoglobulin_variable_pseudogene" EXACT [] is_a: SO:0002098 ! immunoglobulin_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:05:56Z [Term] id: SO:0002103 name: TR_V_pseudogene def: "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T cell receptor V pseudogene" EXACT [] synonym: "T cell receptor Variable pseudogene" EXACT [] synonym: "T_cell_receptor_V_pseudogene" EXACT [] synonym: "T_cell_receptor_Variable_pseudogene" EXACT [] synonym: "TR V pseudogene" EXACT [] is_a: SO:0002099 ! T_cell_receptor_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:06:29Z [Term] id: SO:0002104 name: TR_J_pseudogene def: "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T cell receptor J pseudogene" EXACT [] synonym: "T cell receptor Joining pseudogene" EXACT [] synonym: "T_cell_receptor_J_pseudogene" EXACT [] synonym: "T_cell_receptor_Joining_pseudogene" EXACT [] synonym: "TR J pseudogene" EXACT [] is_a: SO:0002099 ! T_cell_receptor_pseudogene created_by: kareneilbeck creation_date: 2016-07-15T16:06:51Z [Term] id: SO:0002105 name: translated_processed_pseudogene def: "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "translated processed pseudogene" EXACT [] is_a: SO:0000043 ! processed_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:31:53Z [Term] id: SO:0002106 name: translated_unprocessed_pseudogene def: "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "translated unprocessed pseudogene" EXACT [] synonym: "translated_nonprocessed_pseudogene" EXACT [] is_a: SO:0001760 ! non_processed_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:34:42Z [Term] id: SO:0002107 name: transcribed_unprocessed_pseudogene def: "A unprocessed pseudogene supported by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "transcribed unprocessed pseudogene" EXACT [] synonym: "transcribed_non_processed_pseudogene" EXACT [] is_a: SO:0001760 ! non_processed_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:41:53Z [Term] id: SO:0002108 name: transcribed_unitary_pseudogene def: "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "transcribed unitary pseudogene" EXACT [] is_a: SO:0001759 ! unitary_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:44:26Z [Term] id: SO:0002109 name: transcribed_processed_pseudogene def: "A processed_pseudogene overlapped by locus-specific evidence of transcription." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "transcribed processed pseudogene" EXACT [] is_a: SO:0000043 ! processed_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:45:48Z [Term] id: SO:0002110 name: polymorphic_pseudogene_with_retained_intron def: "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "polymorphic pseudogene with retained intron" EXACT [] is_a: SO:0001841 ! polymorphic_pseudogene created_by: kareneilbeck creation_date: 2016-07-18T12:47:33Z [Term] id: SO:0002111 name: pseudogene_processed_transcript def: "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "pseudogene processed transcript" EXACT [] is_a: SO:0001503 ! processed_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:07:00Z [Term] id: SO:0002112 name: coding_transcript_with_retained_intron def: "A protein coding transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "mRNA with retained intron" RELATED [] is_a: SO:0000120 ! protein_coding_primary_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:09:49Z [Term] id: SO:0002113 name: lncRNA_with_retained_intron def: "A lncRNA transcript containing a retained intron." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "lncRNA with retained intron" EXACT [] synonym: "lncRNA_retained_intron" EXACT [] is_a: SO:0002035 ! lncRNA_primary_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:13:07Z [Term] id: SO:0002114 name: NMD_transcript def: "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "NMD transcript" EXACT [] synonym: "nonsense mediated decay transcript" EXACT [] synonym: "protein_coding_NMD" EXACT [] xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000120 ! protein_coding_primary_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:16:13Z [Term] id: SO:0002115 name: pseudogenic_transcript_with_retained_intron def: "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. synonym: "pseudogene retained intron" EXACT [] is_a: SO:0000185 ! primary_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:19:04Z [Term] id: SO:0002116 name: polymorphic_pseudogene_processed_transcript def: "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "polymorphic pseudogene processed transcript" EXACT [] is_a: SO:0002111 ! pseudogene_processed_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:23:59Z [Term] id: SO:0002117 name: is_obsolete: true created_by: kareneilbeck creation_date: 2016-07-18T14:27:21Z [Term] id: SO:0002118 name: NMD_polymorphic_pseudogene_transcript def: "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Term added as part of collaboration with Gencode, adding biotypes used in annotation. synonym: "NMD polymorphic pseudogene transcript" EXACT [] synonym: "nonsense_mediated_decay_polymorphic_pseudogene" EXACT [] is_a: SO:0002114 ! NMD_transcript created_by: kareneilbeck creation_date: 2016-07-18T14:28:02Z [Term] id: SO:0002119 name: allelic_frequency def: "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population." [SO:ke] comment: Requested by HL7 clinical genomics group. xref: wikipedia:Allele_frequency is_a: SO:0001763 ! variant_frequency created_by: kareneilbeck creation_date: 2016-07-21T11:58:55Z [Term] id: SO:0002120 name: three_prime_overlapping_ncrna def: "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. synonym: "3'_overlapping_ncrna" EXACT [] synonym: "3prime_overlapping_ncRNA" EXACT [] synonym: "three prime overlapping noncoding rna" EXACT [] is_a: SO:0000655 ! ncRNA created_by: nicole creation_date: 2016-08-23T15:48:21Z [Term] id: SO:0002121 name: vertebrate_immune_system_gene def: "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci)." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "immune_gene" EXACT [] is_a: SO:0000704 ! gene created_by: nicole creation_date: 2016-08-23T15:54:51Z [Term] id: SO:0002122 name: immunoglobulin_gene def: "A germline immunoglobulin gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "All_IG_genes" EXACT [] synonym: "IG_genes" EXACT [] is_a: SO:0002121 ! vertebrate_immune_system_gene created_by: nicole creation_date: 2016-08-23T15:56:09Z [Term] id: SO:0002123 name: IG_C_gene def: "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IGC_gene" EXACT [] synonym: "immunoglobulin_C_gene" EXACT [] synonym: "Immunoglobulin_Constant_germline_Gene" EXACT [] is_a: SO:0002122 ! immunoglobulin_gene created_by: nicole creation_date: 2016-08-23T15:57:29Z [Term] id: SO:0002124 name: IG_D_gene def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IGD_gene" EXACT [] synonym: "immunoglobulin_D_gene" EXACT [] synonym: "Immunoglobulin_Diversity_ gene" EXACT [] is_a: SO:0002122 ! immunoglobulin_gene created_by: nicole creation_date: 2016-08-23T15:59:10Z [Term] id: SO:0002125 name: IG_J_gene def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IG_joining_gene" EXACT [] synonym: "immunoglobulin_J_gene" EXACT [] synonym: "Immunoglobulin_Joining_Gene" EXACT [] is_a: SO:0002122 ! immunoglobulin_gene created_by: nicole creation_date: 2016-08-23T16:00:36Z [Term] id: SO:0002126 name: IG_V_gene def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "IG_variable_gene" EXACT [] synonym: "IGV_gene" EXACT [] synonym: "Immunoglobulin_variable_gene" EXACT [] is_a: SO:0002122 ! immunoglobulin_gene created_by: nicole creation_date: 2016-08-23T16:02:09Z [Term] id: SO:0002127 name: lncRNA_gene def: "A gene that encodes a long non-coding RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. synonym: "lnc RNA gene" EXACT [] synonym: "lnc_RNA_gene" EXACT [] synonym: "long_non_coding_RNA_gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: nicole creation_date: 2016-08-23T16:03:33Z [Term] id: SO:0002128 name: mt_rRNA def: "Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Updated definition to be consistent with format of other rRNA definitions on 10 June 2021. Requested by EBI. See GitHub Issue #493. synonym: "mitochondrial rRNA" EXACT [] synonym: "mitochondrial_rRNA" EXACT [] synonym: "Mt rRNA" EXACT [] synonym: "Mt_rRNA" EXACT [] is_a: SO:0000252 ! rRNA created_by: nicole creation_date: 2016-08-23T16:08:59Z [Term] id: SO:0002129 name: mt_tRNA def: "Mitochondrial transfer RNA." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] synonym: "mitochondrial_tRNA" EXACT [] synonym: "Mt_tRNA" EXACT [] is_a: SO:0000253 ! tRNA created_by: nicole creation_date: 2016-08-23T16:10:17Z [Term] id: SO:0002130 name: NSD_transcript def: "A transcript that contains a CDS but has no stop codon before the polyA site is reached." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] synonym: "non_stop_decay_transcript" EXACT [] is_a: SO:0000234 ! mRNA created_by: nicole creation_date: 2016-08-23T16:11:34Z [Term] id: SO:0002131 name: sense_intronic_lncRNA alt_id: SO:0001903 def: "A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579. synonym: "sense intronic lncRNA" EXACT [] synonym: "sense_intronic" EXACT [] synonym: "sense_intronic_lncRNA" EXACT [] synonym: "sense_intronic_non-coding_RNA" EXACT [] is_a: SO:0001877 ! lncRNA created_by: nicole creation_date: 2016-08-23T16:15:02Z [Term] id: SO:0002132 name: sense_overlap_lncRNA def: "A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence." [GENECODE:http\://www.gencodegenes.org/gencode_biotypes.html] comment: Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579. synonym: "sense overlap lncRNA" EXACT [] synonym: "sense_overlap_lncRNA" EXACT [] synonym: "sense_overlapping" EXACT [] is_a: SO:0001877 ! lncRNA created_by: nicole creation_date: 2016-08-23T16:16:13Z [Term] id: SO:0002133 name: T_cell_receptor_gene def: "A T-cell receptor germline gene." [] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "TR_gene" EXACT [] is_a: SO:0002121 ! vertebrate_immune_system_gene created_by: nicole creation_date: 2016-08-23T16:17:12Z [Term] id: SO:0002134 name: TR_C_Gene def: "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T_cell_receptor_C_gene" EXACT [] is_a: SO:0002133 ! T_cell_receptor_gene created_by: nicole creation_date: 2016-08-23T16:19:20Z [Term] id: SO:0002135 name: TR_D_Gene def: "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T_cell_receptor_D_gene" EXACT [] is_a: SO:0002133 ! T_cell_receptor_gene created_by: nicole creation_date: 2016-08-23T16:20:06Z [Term] id: SO:0002136 name: TR_J_Gene def: "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T_cell_receptor_J_gene" EXACT [] is_a: SO:0002133 ! T_cell_receptor_gene created_by: nicole creation_date: 2016-08-23T16:20:36Z [Term] id: SO:0002137 name: TR_V_Gene def: "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] comment: These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT. synonym: "T_cell_receptor_V_gene" EXACT [] is_a: SO:0002133 ! T_cell_receptor_gene created_by: nicole creation_date: 2016-08-23T16:21:04Z [Term] id: SO:0002138 name: predicted_transcript def: "A transcript feature that has been predicted but is not yet validated." [SO:ke] synonym: "predicted transcript" EXACT [] is_a: SO:0000673 ! transcript created_by: nicole creation_date: 2016-08-23T16:27:38Z [Term] id: SO:0002139 name: unconfirmed_transcript def: "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] synonym: "TEC" EXACT [] synonym: "to_be_experimentally_confirmed_transcript" EXACT [] is_a: SO:0002138 ! predicted_transcript created_by: nicole creation_date: 2016-08-23T16:28:07Z [Term] id: SO:0002140 name: early_origin_of_replication def: "An origin of replication that initiates early in S phase." [PMID:23348837, PMID:9115207] synonym: "early origin" EXACT [] synonym: "early origin of replication" EXACT [] synonym: "early replication origin" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2016-09-15T15:53:36Z [Term] id: SO:0002141 name: late_origin_of_replication def: "An origin of replication that initiates late in S phase." [PMID:23348837, PMID:9115207] synonym: "late origin" EXACT [] synonym: "late origin of replication" EXACT [] synonym: "late replication origin" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2016-09-15T15:56:07Z [Term] id: SO:0002142 name: histone_2A_acetylation_site def: "A histone 2A modification where the modification is the acetylation of the residue." [ISBN:0815341059] synonym: "H2Aac" EXACT [] synonym: "histone 2A acetylation site" EXACT [] is_a: SO:0001702 ! histone_acetylation_site created_by: nicole creation_date: 2016-10-25T12:03:46Z [Term] id: SO:0002143 name: histone_2B_acetylation_site def: "A histone 2B modification where the modification is the acetylation of the residue." [ISBN:0815341059] synonym: "H2Bac" EXACT [] synonym: "histone 2B acetylation site" EXACT [] is_a: SO:0001702 ! histone_acetylation_site created_by: nicole creation_date: 2016-10-25T12:04:04Z [Term] id: SO:0002144 name: histone_2AZ_acetylation_site def: "A histone 2AZ modification where the modification is the acetylation of the residue." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.Zac" EXACT [] synonym: "H2AZac" EXACT [] synonym: "histone 2AZ acetylation site" EXACT [] is_a: SO:0002142 ! histone_2A_acetylation_site created_by: nicole creation_date: 2016-10-25T14:11:49Z [Term] id: SO:0002145 name: H2AZK4_acetylation_site def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.ZK4ac" EXACT [] synonym: "H2AZK4 acetylation site" EXACT [] synonym: "H2AZK4ac" EXACT [] is_a: SO:0002144 ! histone_2AZ_acetylation_site created_by: nicole creation_date: 2016-10-25T14:19:43Z [Term] id: SO:0002146 name: H2AZK7_acetylation_site def: "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.ZK7ac" EXACT [] synonym: "H2AZK7 acetylation site" EXACT [] synonym: "H2AZK7ac" EXACT [] is_a: SO:0002144 ! histone_2AZ_acetylation_site created_by: nicole creation_date: 2016-10-25T14:23:11Z [Term] id: SO:0002147 name: H2AZK11_acetylation_site def: "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.ZK11ac" EXACT [] synonym: "H2AZK11 acetylation site" EXACT [] synonym: "H2AZK11ac" EXACT [] is_a: SO:0002144 ! histone_2AZ_acetylation_site created_by: nicole creation_date: 2016-10-25T14:23:31Z [Term] id: SO:0002148 name: H2AZK13_acetylation_site def: "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.ZK13ac" EXACT [] synonym: "H2AZK13 acetylation site" EXACT [] synonym: "H2AZK13ac" EXACT [] is_a: SO:0002144 ! histone_2AZ_acetylation_site created_by: nicole creation_date: 2016-10-25T14:23:50Z [Term] id: SO:0002149 name: H2AZK15_acetylation_site def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated." [PMID:19385636, PMID:24316985, PMID:27087541] synonym: "H2A.ZK15ac" EXACT [] synonym: "H2AZK15 acetylation site" EXACT [] synonym: "H2AZK15ac" EXACT [] is_a: SO:0002144 ! histone_2AZ_acetylation_site created_by: nicole creation_date: 2016-10-25T14:24:08Z [Term] id: SO:0002150 name: AUG_initiated_uORF def: "A uORF beginning with the canonical start codon AUG." [PMID:26684391, PMID:27313038] synonym: "AUG initiated uORF" EXACT [] is_a: SO:0002027 ! uORF created_by: nicole creation_date: 2016-10-26T09:37:11Z [Term] id: SO:0002151 name: non_AUG_initiated_uORF def: "A uORF beginning with a codon other than AUG." [PMID:26684391, PMID:27313038] synonym: "non AUG initiated uORF" EXACT [] is_a: SO:0002027 ! uORF created_by: nicole creation_date: 2016-10-26T09:37:45Z [Term] id: SO:0002152 name: genic_downstream_transcript_variant def: "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke] synonym: "genic 3 prime transcript variant" EXACT [] synonym: "genic 3' transcript variant" EXACT [] synonym: "genic downstream transcript variant" EXACT [] is_a: SO:0001564 ! gene_variant created_by: nicole creation_date: 2016-10-28T10:20:55Z [Term] id: SO:0002153 name: genic_upstream_transcript_variant def: "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms." [NCBI:dm, SO:ke] synonym: "genic 5 prime transcript variant" EXACT [] synonym: "genic 5' transcript variant" EXACT [] synonym: "genic upstream transcript variant" EXACT [] is_a: SO:0001564 ! gene_variant created_by: nicole creation_date: 2016-10-28T10:23:17Z [Term] id: SO:0002154 name: mitotic_recombination_region def: "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells." [NCBI:cf, SO:ke] synonym: "INSDC_feature:misc_recomb" BROAD [] synonym: "INSDC_qualifier:mitotic" EXACT [] synonym: "INSDC_qualifier:mitotic_recombination" EXACT [] synonym: "mitotic recombination region" EXACT [] is_a: SO:0000298 ! recombination_feature created_by: nicole creation_date: 2016-10-28T10:33:54Z [Term] id: SO:0002155 name: meiotic_recombination_region def: "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase." [NCBI:cf, SO:ke] synonym: "INSDC_feature:misc_recomb" BROAD [] synonym: "INSDC_qualifier:meiotic" EXACT [] synonym: "INSDC_qualifier:meiotic_recombination" EXACT [] synonym: "meiotic recombination region" EXACT [] is_a: SO:0000298 ! recombination_feature created_by: nicole creation_date: 2016-10-28T10:34:55Z [Term] id: SO:0002156 name: CArG_box def: "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'." [PMID:1748287, PMID:7623803] comment: Requested by Antonia Lock synonym: "CArG box" EXACT [] is_a: SO:0001659 ! promoter_element created_by: nicole creation_date: 2016-10-28T10:42:06Z [Term] id: SO:0002157 name: Mat2P def: "A gene cassette array containing H+ mating type specific information." [PMID:18354497] is_a: SO:0001984 ! silent_mating_type_cassette_array created_by: nicole creation_date: 2016-11-17T10:59:00Z [Term] id: SO:0002158 name: Mat3M def: "A gene cassette array containing H- mating type specific information." [PMID:18354497] is_a: SO:0001984 ! silent_mating_type_cassette_array created_by: nicole creation_date: 2016-11-17T11:02:27Z [Term] id: SO:0002159 name: SHP_box def: "A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG." [PMID:17083136, PMID:27655872] synonym: "SHP box" EXACT [] is_a: SO:0100017 ! polypeptide_conserved_motif created_by: nicole creation_date: 2016-12-15T09:48:38Z [Term] id: SO:0002160 name: sequence_length_variant def: "A sequence variant that changes the length of one or more sequence features." [] synonym: "sequence length variant" EXACT [] is_a: SO:0001537 ! structural_variant created_by: nicole creation_date: 2017-04-26T12:31:12Z [Term] id: SO:0002161 name: short_tandem_repeat_change def: "A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded." [] synonym: "short tandem repeat change" EXACT [] synonym: "str change" EXACT [] is_a: SO:0002160 ! sequence_length_variant created_by: nicole creation_date: 2017-04-26T12:50:55Z [Term] id: SO:0002162 name: short_tandem_repeat_expansion def: "A short tandem repeat variant containing more repeat units than the reference sequence." [] synonym: "short tandem repeat expansion" EXACT [] synonym: "str expansion" EXACT [] is_a: SO:0002161 ! short_tandem_repeat_change created_by: nicole creation_date: 2017-04-26T12:51:26Z [Term] id: SO:0002163 name: short_tandem_repeat_contraction def: "A short tandem repeat variant containing fewer repeat units than the reference sequence." [] synonym: "short tandem repeat contraction" EXACT [] synonym: "str contraction" EXACT [] is_a: SO:0002161 ! short_tandem_repeat_change created_by: nicole creation_date: 2017-04-26T12:52:33Z [Term] id: SO:0002164 name: H2BK5_acetylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated." [http://www.actrec.gov.in/histome/ptm_sp.php?ptm_sp=H2BK5ac, PMID:18552846] synonym: "H2BK5 acetylation site" EXACT [] synonym: "H2BK5ac" EXACT [] is_a: SO:0002143 ! histone_2B_acetylation_site created_by: nicole creation_date: 2017-05-17T15:22:58Z [Term] id: SO:0002165 name: trinucleotide_repeat_expansion def: "A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence." [] synonym: "trinucleotide repeat expansion" EXACT [] is_a: SO:0002162 ! short_tandem_repeat_expansion created_by: nicole creation_date: 2017-06-02T10:43:42Z [Term] id: SO:0002166 name: ref_miRNA def: "A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA." [PMID:26453491] synonym: "ref miRNA" EXACT [] synonym: "RefSeq miRNA" EXACT [] synonym: "RefSeq-miRNA" EXACT [] is_a: SO:0000276 ! miRNA created_by: nicole creation_date: 2017-06-22T11:05:49Z [Term] id: SO:0002167 name: isomiR def: "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA." [PMID:26453491] is_a: SO:0000276 ! miRNA created_by: nicole creation_date: 2017-06-22T11:09:42Z [Term] id: SO:0002168 name: RNA_thermometer def: "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression." [PMID:22421878] synonym: "RNA thermometer" EXACT [] synonym: "RNA thermoregulator" EXACT [] synonym: "RNAT" EXACT [] synonym: "thermoregulator" EXACT [] xref: https://en.wikipedia.org/wiki/RNA_thermometer "wiki" is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000234 ! mRNA created_by: nicole creation_date: 2017-07-17T10:07:45Z [Term] id: SO:0002169 name: splice_polypyrimidine_tract_variant def: "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)." [] synonym: "splice polypyrimidine tract variant" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: nicole creation_date: 2017-07-31T13:40:13Z [Term] id: SO:0002170 name: splice_donor_region_variant def: "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron)." [] synonym: "splice donor region variant" EXACT [] is_a: SO:0001630 ! splice_region_variant created_by: nicole creation_date: 2017-07-31T13:48:32Z [Term] id: SO:0002171 name: telomeric_D_loop def: "A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." [PMID:10338204, PMID:15071557, PMID:24012755] comment: This definition is from GO:0061820 telomeric D-loop disassembly. synonym: "telomeric D loop" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2017-08-01T13:12:11Z [Term] id: SO:0002172 name: sequence_alteration_artifact def: "A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process." [] synonym: "sequence alteration artifact" EXACT [] is_a: SO:0000413 ! sequence_difference created_by: nicole creation_date: 2017-08-18T13:43:26Z [Term] id: SO:0002173 name: indel_artifact def: "An indel that is the result of base-calling or assembly error." [] synonym: "indel artifact" EXACT [] is_a: SO:0002172 ! sequence_alteration_artifact created_by: nicole creation_date: 2017-08-18T15:16:20Z [Term] id: SO:0002174 name: deletion_artifact def: "A deletion that is the result of base-calling or assembly error." [] synonym: "deletion artifact" EXACT [] is_a: SO:0002172 ! sequence_alteration_artifact created_by: nicole creation_date: 2017-08-18T15:17:11Z [Term] id: SO:0002175 name: insertion_artifact def: "An insertion that is the result of base-calling or assembly error." [] synonym: "insertion artifact" EXACT [] is_a: SO:0002172 ! sequence_alteration_artifact created_by: nicole creation_date: 2017-08-18T15:17:42Z [Term] id: SO:0002176 name: substitution_artifact def: "A substitution that is the result of base-calling or assembly error." [] synonym: "substitution artifact" EXACT [] is_a: SO:0002172 ! sequence_alteration_artifact created_by: nicole creation_date: 2017-08-18T15:18:12Z [Term] id: SO:0002177 name: duplication_artifact def: "A duplication that is the result of base-calling or assembly error." [] synonym: "duplication artifact" EXACT [] is_a: SO:0002175 ! insertion_artifact created_by: nicole creation_date: 2017-08-18T15:26:00Z [Term] id: SO:0002178 name: SNV_artifact def: "An SNV that is the result of base-calling or assembly error." [] synonym: "SNV artifact" EXACT [] is_a: SO:0002176 ! substitution_artifact created_by: nicole creation_date: 2017-08-18T15:26:49Z [Term] id: SO:0002179 name: MNV_artifact def: "An MNV that is the result of base-calling or assembly error." [] synonym: "MNV artifact" EXACT [] is_a: SO:0002176 ! substitution_artifact created_by: nicole creation_date: 2017-08-18T15:27:21Z [Term] id: SO:0002180 name: enzymatic_RNA_gene def: "A gene that encodes an enzymatic RNA." [] synonym: "enzymatic RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: nicole creation_date: 2017-09-27T10:30:27Z [Term] id: SO:0002181 name: ribozyme_gene def: "A gene that encodes a ribozyme." [] synonym: "ribozyme gene" EXACT [] is_a: SO:0002180 ! enzymatic_RNA_gene created_by: nicole creation_date: 2017-09-27T10:31:09Z [Term] id: SO:0002182 name: antisense_lncRNA_gene def: "A gene that encodes an antisense long, non-coding RNA." [] synonym: "antisense lncRNA gene" EXACT [] is_a: SO:0002127 ! lncRNA_gene created_by: nicole creation_date: 2017-09-27T10:44:00Z [Term] id: SO:0002183 name: sense_overlap_lncRNA_gene def: "A gene that encodes a sense overlap long non-coding RNA." [] comment: Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579. synonym: "sense overlap lncRNA gene" EXACT [] synonym: "sense overlap ncRNA gene" EXACT [] synonym: "sense_overlap_lncRNA_gene" EXACT [] is_a: SO:0002127 ! lncRNA_gene created_by: nicole creation_date: 2017-09-27T10:48:05Z [Term] id: SO:0002184 name: sense_intronic_lncRNA_gene def: "A gene that encodes a sense intronic long non-coding RNA." [] comment: Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579. synonym: "sense intronic lncRNA gene" EXACT [] synonym: "sense intronic ncRNA gene" EXACT [] synonym: "sense_intronic_lncRNA_gene" EXACT [] is_a: SO:0002127 ! lncRNA_gene created_by: nicole creation_date: 2017-09-27T11:03:50Z [Term] id: SO:0002185 name: bidirectional_promoter_lncRNA_gene def: "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand." [https://www.gencodegenes.org/pages/biotypes.html] comment: This is a gencode term. See GitHub Issue #408. Synonyms "bidirectional promoter lncRNA gene" and "bidirectional_promoter_lncRNA_gene" added 23 April 2021 by David Sant. See GitHub Issue #506. synonym: "bidirectional promoter lncRNA" EXACT [] synonym: "bidirectional promoter lncRNA gene" EXACT [] synonym: "bidirectional_promoter_lncRNA_gene" EXACT [] is_a: SO:0002127 ! lncRNA_gene created_by: nicole creation_date: 2017-10-03T11:43:48Z [Term] id: SO:0002186 name: mutational_hotspot def: "A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance." [] synonym: "mutational hotspot" EXACT [] is_a: SO:0001411 ! biological_region created_by: nicole creation_date: 2017-11-07T12:27:51Z [Term] id: SO:0002187 name: HERV_insertion def: "An insertion of sequence from the HERV family of mobile elements with respect to a reference." [NCBI:th] synonym: "HERV insertion" EXACT [] is_a: SO:0001837 ! mobile_element_insertion relationship: derives_from SO:0002268 ! Endogenous_Retrovirus_LTR_retrotransposon created_by: nicole creation_date: 2017-11-20T11:52:51Z [Term] id: SO:0002188 name: functional_gene_region def: "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product." [Clingen:mb] comment: A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors. synonym: "functional gene region" EXACT [] is_a: SO:0000831 ! gene_member_region created_by: nicole creation_date: 2017-12-15T11:08:43Z [Term] id: SO:0002189 name: allelic_pseudogene def: "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." [] synonym: "allelic pseudogene" EXACT [] synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:allelic" EXACT [] is_a: SO:0001759 ! unitary_pseudogene created_by: nicole creation_date: 2018-01-03T15:47:32Z [Term] id: SO:0002190 name: enhancer_blocking_element def: "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator." [NCBI:cf] comment: Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf). synonym: "enhancer blocking element" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:enhancer_blocking_element" EXACT [] synonym: "insulator" RELATED [] is_a: SO:0000627 ! insulator created_by: nicole creation_date: 2018-01-04T17:28:52Z [Term] id: SO:0002191 name: imprinting_control_region def: "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs." [] comment: Moved from is_a regulatory_region (SO:0005836) to is_a epigenetically_modified_region (SO:0001720) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. synonym: "imprinting control region" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:imprinting_control_region" EXACT [] is_a: SO:0001720 ! epigenetically_modified_region created_by: nicole creation_date: 2018-01-04T17:35:34Z [Term] id: SO:0002192 name: flanking_repeat def: "A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites)." [] synonym: "flanking repeat" EXACT [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:flanking" EXACT [] is_a: SO:0000657 ! repeat_region created_by: nicole creation_date: 2018-01-05T16:27:21Z [Term] id: SO:0002193 name: processed_pseudogenic_rRNA def: "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail." [] synonym: "INSDC_feature:rRNA" BROAD [] synonym: "INSDC_qualifier:processed" EXACT [] synonym: "processed pseudogenic rRNA" EXACT [] is_a: SO:0000777 ! pseudogenic_rRNA created_by: nicole creation_date: 2018-01-08T11:43:58Z [Term] id: SO:0002194 name: unprocessed_pseudogenic_rRNA def: "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions." [] synonym: "INSDC_feature:rRNA" BROAD [] synonym: "INSDC_qualifier:unprocessed" EXACT [] synonym: "unprocessed pseudogenic rRNA" EXACT [] is_a: SO:0000777 ! pseudogenic_rRNA created_by: nicole creation_date: 2018-01-08T11:49:41Z [Term] id: SO:0002195 name: unitary_pseudogenic_rRNA def: "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain." [] synonym: "INSDC_feature:rRNA" BROAD [] synonym: "INSDC_qualifier:unitary" EXACT [] synonym: "unitary pseudogenic rRNA" EXACT [] is_a: SO:0000777 ! pseudogenic_rRNA created_by: nicole creation_date: 2018-01-08T11:51:59Z [Term] id: SO:0002196 name: allelic_pseudogenic_rRNA def: "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." [] synonym: "allelic pseudogenic rRNA" EXACT [] synonym: "INSDC_feature:rRNA" BROAD [] synonym: "INSDC_qualifier:allelic" EXACT [] is_a: SO:0000777 ! pseudogenic_rRNA created_by: nicole creation_date: 2018-01-08T11:53:13Z [Term] id: SO:0002197 name: processed_pseudogenic_tRNA def: "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail." [] synonym: "INSDC_feature:tRNA" BROAD [] synonym: "INSDC_qualifier:processed" EXACT [] synonym: "processed pseudogenic tRNA" EXACT [] is_a: SO:0000778 ! pseudogenic_tRNA created_by: nicole creation_date: 2018-01-08T12:10:10Z [Term] id: SO:0002198 name: unprocessed_pseudogenic_tRNA def: "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions." [] synonym: "INSDC_feature:tRNA" BROAD [] synonym: "INSDC_qualifier:unprocessed" EXACT [] synonym: "unprocessed pseudogenic tRNA" EXACT [] is_a: SO:0000778 ! pseudogenic_tRNA created_by: nicole creation_date: 2018-01-08T12:14:34Z [Term] id: SO:0002199 name: unitary_pseudogenic_tRNA def: "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain." [] synonym: "INSDC_feature:tRNA" BROAD [] synonym: "INSDC_qualifier:unitary" EXACT [] synonym: "unitary pseudogenic tRNA" EXACT [] is_a: SO:0000778 ! pseudogenic_tRNA created_by: nicole creation_date: 2018-01-08T12:16:59Z [Term] id: SO:0002200 name: allelic_pseudogenic_tRNA def: "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes." [] synonym: "allelic pseudogenic tRNA" EXACT [] synonym: "INSDC_feature:tRNA" EXACT [] synonym: "INSDC_qualifier:allelic" EXACT [] is_a: SO:0000778 ! pseudogenic_tRNA created_by: nicole creation_date: 2018-01-08T12:18:38Z [Term] id: SO:0002201 name: terminal_repeat def: "A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat." [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:terminal" EXACT [] synonym: "terminal repeat" EXACT [] is_a: SO:0000657 ! repeat_region created_by: nicole creation_date: 2018-01-08T13:00:59Z [Term] id: SO:0002202 name: repeat_instability_region def: "A repeat region that is prone to expansions and/or contractions." [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:repeat_instability_region" EXACT [] synonym: "repeat instability region" EXACT [] is_a: SO:0000705 ! tandem_repeat created_by: nicole creation_date: 2018-01-09T11:19:55Z [Term] id: SO:0002203 name: replication_start_site def: "A nucleotide site from which replication initiates." [NCBI:cf] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:replication_start_site" EXACT [] synonym: "replication start site" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2018-01-09T11:23:35Z [Term] id: SO:0002204 name: nucleotide_cleavage_site def: "A point in nucleic acid where a cleavage event occurs." [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:nucleotide_cleavage_site" EXACT [] synonym: "nucleotide cleavage site" EXACT [] is_a: SO:0000699 ! junction created_by: nicole creation_date: 2018-01-09T11:30:34Z [Term] id: SO:0002205 name: response_element def: "A regulatory element that acts in response to a stimulus, usually via transcription factor binding." [] comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:response_element" EXACT [] synonym: "response element" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: nicole creation_date: 2018-01-10T16:33:25Z [Term] id: SO:0002206 name: sequence_source def: "Identifies the biological source of the specified span of the sequence" [NCBI:tm] comment: Terms such as genomic_DNA or mRNA can be used to describe a sequence source. synonym: "INSDC_feature:source" EXACT [] synonym: "sequence source" EXACT [] is_a: SO:0000400 ! sequence_attribute created_by: nicole creation_date: 2018-01-26T09:50:58Z [Term] id: SO:0002207 name: UNAAAC_motif def: "A hexameric RNA motif consisting of nucleotides UNAAAC (where N can be any nucleotide) that targets the RNA for degradation." [PMID:22645662, PMID:28765164, PomBase:al] synonym: "UNAAAC motif" EXACT [] is_a: SO:0001979 ! RNA_stability_element created_by: nicole creation_date: 2018-02-06T12:23:24Z [Term] id: SO:0002208 name: long_terminal_repeat_transcript def: "An RNA that is transcribed from a long terminal repeat." [PMID:24256266, PomBase:mh] synonym: "long terminal repeat transcript" EXACT [] synonym: "LTR transcript" EXACT [] is_a: SO:0000673 ! transcript created_by: nicole creation_date: 2018-02-07T11:51:45Z [Term] id: SO:0002209 name: genomic_DNA_contig def: "A contig composed of genomic DNA derived sequences." [BCS:etrwz] comment: Requested by Bayer Crop Science, March 2018 synonym: "gDNA contig" EXACT [] synonym: "gDNA_contig" EXACT [] synonym: "genomic DNA contig" EXACT [] is_a: SO:0000149 ! contig created_by: nicole creation_date: 2018-03-21T12:25:14Z [Term] id: SO:0002210 name: presence_absence_variation def: "A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome." [BCS:bbean, PMID:19956538, PMID:25881062] comment: Requested by Bayer Crop Science, March 2018 synonym: "PAV" EXACT [] synonym: "presence absence variation" EXACT [] synonym: "presence-absence variation" EXACT [] synonym: "presence-absence_variation" EXACT [] synonym: "presence/absence variation" EXACT [] synonym: "presence/absence_variation" EXACT [] is_a: SO:0001019 ! copy_number_variation created_by: nicole creation_date: 2018-03-21T12:59:14Z [Term] id: SO:0002211 name: circular_plasmid def: "A self replicating circular nucleic acid molecule that is distinct from a chromosome in the organism." [PMID:21719542, SBOL:jb] synonym: "circular plasmid" EXACT [] is_a: SO:0000155 ! plasmid created_by: nicole creation_date: 2018-04-18T11:13:38Z [Term] id: SO:0002212 name: linear_plasmid def: "A self replicating linear nucleic acid molecule that is distinct from a chromosome in the organism. They are capped by terminal proteins covalently bound to the 5' ends of the DNA." [PMID:21719542, SBOL:jb] synonym: "linear plasmid" EXACT [] is_a: SO:0000155 ! plasmid created_by: nicole creation_date: 2018-04-18T11:14:04Z [Term] id: SO:0002213 name: transcription_termination_signal def: "Termination signal preferentially observed downstream of polyadenylation signal" [PMID:28367989] synonym: "(A(U)GUA) motif" EXACT [] synonym: "Nrd1 binding motif" EXACT [] synonym: "Nrd1-dependent terminator" EXACT [] synonym: "polyA site associated transcription termination signal" EXACT [] synonym: "polyA site downstream element" EXACT [] synonym: "transcription termination signal" EXACT [] synonym: "UCUUG motif" EXACT [] synonym: "UGUAA/G motif" EXACT [] is_a: SO:0000951 ! eukaryotic_terminator created_by: nicole creation_date: 2018-05-18T17:10:14Z [Term] id: SO:0002214 name: redundant_inserted_stop_gained def: "A sequence variant whereby at least one base of a codon is changed, resulting in a stop codon inserted next to an existing stop codon. This leads to a polypeptide of the same length." [] synonym: "redundant inserted stop gained" EXACT [] is_a: SO:0001992 ! nonsynonymous_variant created_by: nicole creation_date: 2018-06-13T09:53:31Z [Term] id: SO:0002215 name: Zas1_recognition_motif def: "A DNA motif to which the S. pombe Zas1 protein binds. The consensus sequence is 5'-(Y)CCCCAY-3'." [PMID:29735745, PomBase:vw] synonym: "Zas1 recognition motif" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: nicole creation_date: 2018-06-20T10:05:17Z [Term] id: SO:0002216 name: Pho7_binding_site def: "A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7." [PMID:28811350] synonym: "Pho7 binding site" EXACT [] is_a: SO:0001659 ! promoter_element created_by: nicole creation_date: 2018-09-12T12:26:50Z [Term] id: SO:0002217 name: unspecified_indel def: "A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category." [ZFIN:st] comment: This term is used when there is a change that is either an insertion or a deletion but it is unknown which event occurred. synonym: "insertion or deletion" EXACT [] synonym: "unspecified indel" EXACT [] is_a: SO:0001059 ! sequence_alteration created_by: nicoleruiz creation_date: 2019-02-24T18:26:05Z [Term] id: SO:0002218 name: functionally_abnormal def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [] comment: Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019. synonym: "function modified variant" EXACT [] synonym: "function_modified_variant" RELATED [] synonym: "functionally abnormal" RELATED [] is_a: SO:0001536 ! functional_effect_variant created_by: david creation_date: 2019-03-01T10:21:26Z [Term] id: SO:0002219 name: functionally_normal def: "A sequence variant in which the function of a gene product is retained with respect to a reference." [] comment: Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019. synonym: "function retained variant" EXACT [] synonym: "function_retained_variant" RELATED [] synonym: "functionally normal" RELATED [] is_a: SO:0001536 ! functional_effect_variant created_by: david creation_date: 2019-03-01T10:28:12Z [Term] id: SO:0002220 name: function_uncertain_variant def: "A sequence variant in which the function of a gene product is unknown with respect to a reference." [] comment: Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019. synonym: "function uncertain variant" EXACT [] synonym: "function_uncertain_variant" EXACT [] is_a: SO:0001536 ! functional_effect_variant created_by: david creation_date: 2019-03-01T10:29:01Z [Term] id: SO:0002221 name: eukaryotic_promoter def: "A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions." [] synonym: "Eukaryotic promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: david creation_date: 2019-07-31T14:01:20Z [Term] id: SO:0002222 name: prokaryotic_promoter def: "A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous." [PMID:32665585] synonym: "Prokaryotic promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: david creation_date: 2019-07-31T14:02:26Z [Term] id: SO:0002223 name: inert_DNA_spacer def: "Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes." [PMID:20843779, PMID:24933158, PMID:27034378, PMID:28422998] comment: Updated by Evan Christensen on May 27, 2021 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/494 synonym: "Inert DNA Spacer" RELATED [] xref: doi:10.1101/584664 "https://www.biorxiv.org/content/10.1101/584664v1" is_a: SO:0005836 ! regulatory_region created_by: david creation_date: 2019-09-06T19:05:52Z [Term] id: SO:0002224 name: 2A_self_cleaving_peptide_region def: "A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction." [PMID:22301656, PMID:28526819] comment: Added by Dave Sant on October 21, 2019 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/475 synonym: "2A polypeptide region" RELATED [] synonym: "2A self-cleaving polypeptide region" RELATED [] is_a: SO:0000839 ! polypeptide_region created_by: david creation_date: 2019-10-21T10:41:49Z [Term] id: SO:0002225 name: LOZ1_response_element def: "A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc." [] comment: Added on October 30, 2019 as per request of Val Wood request on GitHub Issue# 476 https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/476 synonym: "Loz1 response element" RELATED [] synonym: "LRE" RELATED [] synonym: "LRE element" RELATED [] is_a: SO:0002006 ! zinc_repressed_element created_by: david creation_date: 2019-10-30T11:19:52Z [Term] id: SO:0002226 name: group_IIC_intron def: "A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA." [PMID:20463000] synonym: "group IIB intron" EXACT [] is_a: SO:0000603 ! group_II_intron created_by: david creation_date: 2020-03-27T08:56:34Z [Term] id: SO:0002227 name: CDS_extension def: "A sequence variant extending the CDS, that causes elongation of the resulting polypeptide sequence." [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195] comment: Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480) synonym: "CDS Extension" EXACT [] synonym: "elongated CDS" EXACT [] synonym: "elongated_CDS" EXACT [] is_a: SO:0000316 ! CDS created_by: david creation_date: 2020-03-27T17:56:30Z [Term] id: SO:0002228 name: CDS_five_prime_extension def: "A sequence variant extending the CDS at the 5' end, that causes elongation of the resulting polypeptide sequence at the N terminus." [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195] comment: Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480) synonym: "CDS Extension 5 prime" EXACT [] synonym: "CDS Extension five prime" EXACT [] synonym: "elongated CDS five prime" EXACT [] synonym: "elongated_CDS_five_prime" EXACT [] is_a: SO:0002227 ! CDS_extension created_by: david creation_date: 2020-03-27T17:57:30Z [Term] id: SO:0002229 name: CDS_three_prime_extension def: "A sequence variant extending the CDS at the 3' end, that causes elongation of the resulting polypeptide sequence at the C terminus." [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195] comment: Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480) synonym: "CDS Extension 3 prime" EXACT [] synonym: "CDS Extension three prime" EXACT [] synonym: "elongated CDS three prime" EXACT [] synonym: "elongated_CDS_three_prime" EXACT [] is_a: SO:0002227 ! CDS_extension created_by: david creation_date: 2020-03-27T17:58:30Z [Term] id: SO:0002230 name: CAAX_box def: "A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E." [] comment: Added as per request by Val Wood GitHub issue #479 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/479) synonym: "CAAX box" EXACT [] is_a: SO:0100017 ! polypeptide_conserved_motif created_by: david creation_date: 2020-03-27T18:04:30Z [Term] id: SO:0002231 name: self_cleaving_ribozyme def: "An RNA that catalyzes its own cleavage." [] comment: Added as per request by John T. Sexton GitHub issue #470 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470) synonym: "self cleaving ribozyme" EXACT [] is_a: SO:0000374 ! ribozyme intersection_of: SO:0000374 ! ribozyme intersection_of: has_quality SO:0001977 ! ribonuclease_site relationship: has_quality SO:0001977 ! ribonuclease_site created_by: david creation_date: 2020-03-30T16:02:30Z [Term] id: SO:0002232 name: selection_marker def: "A genetic feature that encodes a trait used for artificial selection of a subpopulation." [] comment: Added as per request by Bryan Bartley GitHub issue #468 and #402 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/468) synonym: "selectable marker" EXACT [] synonym: "selectable_marker" EXACT [] synonym: "selection marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: david creation_date: 2020-04-01T10:04:30Z [Term] id: SO:0002233 name: homologous_chromosome_recognition_and_pairing_locus def: "A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I." [PMID:22582262, PMID:31811152] comment: Added as per request by Val Wood GitHub issue #483 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/483) synonym: "homologous chromosome recognition and pairing locus" EXACT [] is_a: SO:0000409 ! binding_site relationship: member_of SO:0000830 ! chromosome_part created_by: david creation_date: 2020-04-14T10:09:30Z [Term] id: SO:0002234 name: pumilio_response_element def: "A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA)." [PMID:30601114] comment: Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455) synonym: "PRE binding RNA" EXACT [] synonym: "pumilio response element" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR created_by: david creation_date: 2020-04-14T10:40:30Z [Term] id: SO:0002235 name: SUMO_interaction_motif def: "A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3." [PMID:15388847\,PMID\:16524884] comment: Added as per request GitHub issue #434 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/434) synonym: "SBM" EXACT [] synonym: "SIM" EXACT [] synonym: "SUMO binding motif" EXACT [] synonym: "SUMO interaction motif" EXACT [] is_a: SO:0001093 ! protein_protein_contact created_by: david creation_date: 2020-04-22T12:40:30Z [Term] id: SO:0002236 name: cytosolic_rRNA_18S_gene def: "A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "18S rRNA gene" EXACT [] synonym: "18S_rRNA_gene" EXACT [] is_a: SO:0002362 ! cytosolic_SSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002237 name: cytosolic_rRNA_16S_gene def: "A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "16S rRNA gene" EXACT [] synonym: "16S_rRNA_gene" EXACT [] is_a: SO:0002362 ! cytosolic_SSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002238 name: cytosolic_rRNA_5S_gene def: "A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "5S rRNA gene" EXACT [] synonym: "5S_rRNA_gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002239 name: cytosolic_rRNA_28S_gene def: "A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "28S rRNA gene" EXACT [] synonym: "28S_rRNA_gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002240 name: cytosolic_rRNA_5_8S_gene def: "A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "5.8S rRNA gene" EXACT [] synonym: "5_8S rRNA gene" EXACT [] synonym: "5_8S_rRNA_gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002241 name: rRNA_21S_gene def: "A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472) Removed relationship derives_from SO:0001171 on 10 June 2021 when SO:0001171 rRNA_21S was obsoleted into SO:0002345 mt_LSU_rRNA. See GitHub Issue #493. OBSOLETED on 12 September 2022, merged into SO:0002364 mt_LSU_rRNA_gene see GitHub Issue #513. synonym: "21S rRNA gene" EXACT [] synonym: "21S_rRNA_gene" EXACT [] is_obsolete: true replaced_by: SO:0002364 created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002242 name: cytosolic_rRNA_25S_gene def: "A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "25S rRNA gene" EXACT [] synonym: "25S_rRNA_gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002243 name: cytosolic_rRNA_23S_gene def: "A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes." [] comment: Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "23S rRNA gene" EXACT [] synonym: "23S_rRNA_gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2020-05-07T16:12:30Z [Term] id: SO:0002244 name: partially_duplicated_transcript def: "A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional." [] comment: Added as per request from the Illumina group synonym: "partially duplicated transcript" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: david creation_date: 2020-05-13T09:07:30Z [Term] id: SO:0002245 name: five_prime_duplicated_transcript def: "A partially_duplicated_transcript where the 5' end of the transcript is duplicated." [] comment: Added as per request from the Illumina group synonym: "5' duplicated transcript" EXACT [] synonym: "five prime duplicated transcript" EXACT [] synonym: "five prime partially duplicated transcript" EXACT [] is_a: SO:0002244 ! partially_duplicated_transcript created_by: david creation_date: 2020-05-13T09:07:30Z [Term] id: SO:0002246 name: three_prime_duplicated_transcript def: "A partially_duplicated_transcript where the 3' end of the transcript is duplicated." [] comment: Added as per request from the Illumina group synonym: "3' duplicated transcript" EXACT [] synonym: "three prime duplicated transcript" EXACT [] synonym: "three prime partially duplicated transcript" EXACT [] is_a: SO:0002244 ! partially_duplicated_transcript created_by: david creation_date: 2020-05-13T09:07:30Z [Term] id: SO:0002247 name: sncRNA def: "A non-coding RNA less than 200 nucleotides in length." [PMID:30069443] comment: Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485) synonym: "Small noncoding RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: david creation_date: 2020-05-13T11:07:30Z [Term] id: SO:0002248 name: spurious_protein def: "A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature." [PMID:21771858] comment: Added as per request from GitHub Issue #478 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/478) synonym: "spurious protein" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: david creation_date: 2020-05-13T11:40:30Z [Term] id: SO:0002249 name: mature_protein_region_of_CDS def: "A CDS region corresponding to a mature protein region of a polypeptide." [] comment: Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) synonym: "INSDC_feature:mat_peptide" EXACT [] synonym: "mature protein region of CDS" EXACT [] is_a: SO:0000851 ! CDS_region created_by: david creation_date: 2020-05-13T13:40:30Z [Term] id: SO:0002250 name: propeptide_region_of_CDS def: "A CDS region corresponding to a propeptide of a polypeptide." [] comment: Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) synonym: "INSDC_feature:propeptide" EXACT [] synonym: "propeptide region of CDS" EXACT [] is_a: SO:0000851 ! CDS_region created_by: david creation_date: 2020-05-13T13:40:30Z [Term] id: SO:0002251 name: signal_peptide_region_of_CDS def: "A CDS region corresponding to a signal peptide of a polypeptide." [] comment: Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) synonym: "INSDC_feature:sig_peptide" EXACT [] synonym: "Signal peptide region of CDS" EXACT [] is_a: SO:0000851 ! CDS_region created_by: david creation_date: 2020-05-13T13:40:30Z [Term] id: SO:0002252 name: transit_peptide_region_of_CDS def: "CDS region corresponding to a transit peptide region of a polypeptide." [] comment: Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) synonym: "INSDC_feature:transit_peptide" EXACT [] synonym: "transit peptide region of CDS" EXACT [] is_a: SO:0000851 ! CDS_region created_by: david creation_date: 2020-05-13T13:40:30Z [Term] id: SO:0002253 name: stem_loop_region def: "A portion of a stem loop secondary structure in RNA." [] comment: Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451) synonym: "stem loop region" EXACT [] is_a: SO:0000122 ! RNA_sequence_secondary_structure relationship: part_of SO:0000313 ! stem_loop created_by: david creation_date: 2020-05-13T11:40:30Z [Term] id: SO:0002254 name: loop def: "The loop portion of a stem loop, which is not folded back upon itself. " [] comment: Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451) synonym: "loop portion of stem loop" EXACT [] is_a: SO:0002253 ! stem_loop_region created_by: david creation_date: 2020-05-13T11:40:30Z [Term] id: SO:0002255 name: stem def: "The portion of a stem loop where the RNA is folded back upon itself. " [] comment: Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451) synonym: "stem portion of stem loop" EXACT [] is_a: SO:0002253 ! stem_loop_region created_by: david creation_date: 2020-05-13T11:40:30Z [Term] id: SO:0002256 name: non_complimentary_stem def: "A region of a stem in a stem loop structure where the sequences are non-complimentary." [] comment: Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451) synonym: "non-complimentary stem" EXACT [] synonym: "noncomplimentary stem" EXACT [] is_a: SO:0002255 ! stem created_by: david creation_date: 2020-05-13T11:40:30Z [Term] id: SO:0002257 name: knob def: "Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons." [PMID:6439888] comment: Added as per request from GitHub Issue #487 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/487) synonym: "Heterochromatin Knob" EXACT [] is_a: SO:0000657 ! repeat_region created_by: david creation_date: 2020-05-27T10:45:30Z [Term] id: SO:0002258 name: teb1_recognition_motif def: "A binding motif with the consensus sequence TTAGGG to which Teb1 binds." [PMID:23314747, PMID:27901072] comment: Requested by Antonia Locke, (Pombe) as per GitHub Issue Request #439 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/439) synonym: "teb1 recognition motif" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: david creation_date: 2020-05-27T11:03:30Z [Term] id: SO:0002259 name: polyA_site_cluster def: "A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal." [PMID:17202160, PMID:24072873, PMID:25906188] comment: Added as per GitHub Issue Request #450 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/450) synonym: "polyA cluster" EXACT [] synonym: "polyA site cluster" EXACT [] synonym: "polyA_cluster" EXACT [] is_a: SO:0001411 ! biological_region relationship: has_part SO:0000553 ! polyA_site relationship: part_of SO:0000205 ! three_prime_UTR created_by: david creation_date: 2020-05-27T14:17:30Z [Term] id: SO:0002260 name: LARD def: "Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins." [PMID:15082561] comment: Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429) synonym: "Large Retrotransposon Derivative" EXACT [] synonym: "large_retrotransposon_derivative" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-05-27T15:47:30Z [Term] id: SO:0002261 name: TRIM def: "TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100–300 bp. TRIMs lack coding domains and thus do not encode proteins." [PMID:11717436] comment: Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429) synonym: "terminal-repeat retrotransposons in miniature" EXACT [] synonym: "terminal-repeat_retrotransposons_in_miniature" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-05-27T15:47:30Z [Term] id: SO:0002262 name: Watson_strand def: "An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym." [PMID:21303550] comment: Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419) synonym: "Forward strand" EXACT [] synonym: "Plus strand" BROAD [] synonym: "Top strand" EXACT [] synonym: "Watson strand" EXACT [] is_a: SO:0000830 ! chromosome_part created_by: david creation_date: 2020-05-28T10:33:30Z [Term] id: SO:0002263 name: Crick_strand def: "An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym." [PMID:21303550] comment: Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419) synonym: "Bottom strand" EXACT [] synonym: "Crick strand" EXACT [] synonym: "Minus strand" BROAD [] synonym: "Reverse strand" EXACT [] is_a: SO:0000830 ! chromosome_part created_by: david creation_date: 2020-05-28T10:33:30Z [Term] id: SO:0002264 name: Copia_LTR_retrotransposon def: "LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Copia LTR retrotransposon" EXACT [] synonym: "RLC retrotransposon" EXACT [] synonym: "Ty1 retrotransposon" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002265 name: Gypsy_LTR_retrotransposon def: "LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Gypsy LTR retrotransposon" EXACT [] synonym: "RLG retrotransposon" EXACT [] synonym: "Ty3 retrotransposon" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002266 name: Bel_Pao_LTR_retrotransposon def: "LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Bel Pao LTR retrotransposon" EXACT [] synonym: "Bel-Pao LTR retrotransposon" EXACT [] synonym: "RLB retrotransposon" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002267 name: Retrovirus_LTR_retrotransposon def: "LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Retrovirus LTR retrotransposon" EXACT [] synonym: "RLR retrotransposon" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002268 name: Endogenous_Retrovirus_LTR_retrotransposon def: "Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Endogenous Retrovirus LTR retrotransposon" EXACT [] synonym: "HERV" EXACT [] synonym: "RLE retrotransposon" EXACT [] is_a: SO:0000186 ! LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002269 name: R2_LINE_retrotransposon def: "R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes." [PMID:21734471] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "R2 LINE retrotransposon" EXACT [] synonym: "R2 retrotransposon" EXACT [] synonym: "RIR retrotransposon" EXACT [] is_a: SO:0000194 ! LINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002270 name: RTE_LINE_retrotransposon def: "RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain." [PMID:9729877] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "RIT retrotransposon" EXACT [] synonym: "RTE LINE retrotransposon" EXACT [] synonym: "RTE retrotransposon" EXACT [] is_a: SO:0000194 ! LINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002271 name: Jockey_LINE_retrotransposon def: "Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT)." [PMID:31709017] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Jockey LINE retrotransposon" EXACT [] synonym: "LINE Jockey element" EXACT [] synonym: "RIJ retrotransposon" EXACT [] is_a: SO:0000194 ! LINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002272 name: L1_LINE_retrotransposon def: "Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs." [PMID:31709017] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "L1 element" EXACT [] synonym: "L1 LINE retrotransposon" EXACT [] synonym: "LINE 1 element" EXACT [] synonym: "LINE-1 element" EXACT [] is_a: SO:0000194 ! LINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002273 name: I_LINE_retrotransposon def: "Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain." [] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "I LINE retrotransposon" EXACT [] synonym: "LINE I element" EXACT [] synonym: "RII retrotransposon" EXACT [] xref: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element is_a: SO:0000194 ! LINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002274 name: tRNA_SINE_retrotransposon def: "Short interspersed elements that originated from tRNAs." [PMID:21673742] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "RST retrotransposon" EXACT [] synonym: "tRNA SINE element" EXACT [] synonym: "tRNA SINE retrotransposon" EXACT [] is_a: SO:0000206 ! SINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002275 name: 7SL_SINE_retrotransposon def: "Short interspersed elements that originated from 7SL RNAs." [PMID:21673742] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "7SL SINE element" EXACT [] synonym: "7SL SINE retrotransposon" EXACT [] synonym: "RSL retrotransposon" EXACT [] is_a: SO:0000206 ! SINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002276 name: 5S_SINE_retrotransposon def: "Short interspersed elements that originated from 5S rRNAs." [PMID:21673742] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "5S SINE element" EXACT [] synonym: "5S SINE retrotransposon" EXACT [] synonym: "RSS retrotransposon" EXACT [] is_a: SO:0000206 ! SINE_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002277 name: Crypton_YR_transposon def: "Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules." [PMID:22011512] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Crypton transposon" EXACT [] synonym: "Crypton YR transposon" EXACT [] synonym: "DYC transposon" EXACT [] is_a: SO:0000182 ! DNA_transposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002278 name: Tc1_Mariner_TIR_transposon def: "Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp." [PMID:17984973, PMID:8556864] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTT transposon" EXACT [] synonym: "Mariner" EXACT [] synonym: "Stowaway" EXACT [] synonym: "Tc1 Mariner TIR transposon" EXACT [] synonym: "Tc1 transposon" EXACT [] synonym: "TcMar-Stowaway transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002279 name: hAT_TIR_transposon def: "The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb." [PMID:11454746] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Ac transposon" EXACT [] synonym: "Ac/Ds transposon" EXACT [] synonym: "Ds transposon" EXACT [] synonym: "DTA transposon" EXACT [] synonym: "hAT TIR transposon" EXACT [] synonym: "hAT transposon" EXACT [] synonym: "hAT-Ac transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002280 name: Mutator_TIR_transposon def: "Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal G…C nucleotides, or with the G…C nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTM transposon" EXACT [] synonym: "MLE transposon" EXACT [] synonym: "Mu transposon" EXACT [] synonym: "MuDR" EXACT [] synonym: "MULE" EXACT [] synonym: "Mutator TIR transposon" EXACT [] synonym: "Mutator transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002281 name: Merlin_TIR_transposon def: "Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD)." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTE transposon" EXACT [] synonym: "Merlin TIR transposon" EXACT [] synonym: "Merlin transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002282 name: Transib_TIR_transposon def: "Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTR transposon" EXACT [] synonym: "Transib TIR transposon" EXACT [] synonym: "transib transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002283 name: piggyBac_TIR_transposon def: "Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA." [PMID:17984973] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTB transposon" EXACT [] synonym: "piggyBac TIR transposon" EXACT [] synonym: "PiggyBac transposable element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002284 name: PIF_Harbinger_TIR_transposon def: "Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCC…GGC/GCC' or 'GA/GGCA…TGCC/TC'." [PMID:26709091] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DTH transposon" EXACT [] synonym: "Harbinger transposon" EXACT [] synonym: "PIF Harbinger TIR transposon" EXACT [] synonym: "PIF transposon" EXACT [] synonym: "Tourist transposon element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002285 name: CACTA_TIR_transposon def: "This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/G…C/TAGTG'." [PMID:26709091] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "CACTA TIR transposon" EXACT [] synonym: "CACTA transposon element" EXACT [] synonym: "CACTC transposon" EXACT [] synonym: "CMC-EnSpm transposon" EXACT [] synonym: "dSpm transposon" EXACT [] synonym: "DTC transposon" EXACT [] synonym: "En transposon" EXACT [] synonym: "En-Spm transposon" EXACT [] synonym: "EnSpm transposon" EXACT [] synonym: "Spm transposon" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002286 name: YR_retrotransposon def: "Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs)." [PMID:24086727] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "tyrosine kinase retrotransposon" EXACT [] synonym: "YR retrotransposon" EXACT [] is_a: SO:0000189 ! non_LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002287 name: DIRS_YR_retrotransposon def: "Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase." [PMID:24086727] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "DIRS retrotransposon" EXACT [] synonym: "DIRS YR retrotransposon" EXACT [] synonym: "RYD retrotransposon" EXACT [] is_a: SO:0002286 ! YR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002288 name: Ngaro_YR_retrotransposon def: "Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs." [PMID:24086727] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Ngaro retrotransposon" EXACT [] synonym: "Ngaro YR retrotransposon" EXACT [] synonym: "RYN retrotransposon" EXACT [] is_a: SO:0002286 ! YR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002289 name: Viper_YR_retrotransposon def: "VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes." [PMID:16297462] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "RYV retrotransposon" EXACT [] synonym: "Viper retrotransposon" EXACT [] synonym: "Viper YR retrotransposon" EXACT [] is_a: SO:0002286 ! YR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002290 name: Penelope_retrotransposon def: "Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease." [PMID:23914310] comment: Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488) synonym: "Penelope retrotransposon" EXACT [] synonym: "RPP retrotransposon" EXACT [] is_a: SO:0000189 ! non_LTR_retrotransposon created_by: david creation_date: 2020-06-25T14:00:30Z [Term] id: SO:0002291 name: circular_ncRNA def: "A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail." [PMID:29086764, PMID:29182528, PMID:29230098, PMID:29576969, PMID:29626935] comment: Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391) synonym: "circRNA" BROAD [] synonym: "circular ncRNA" EXACT [] synonym: "noncoding circRNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: david creation_date: 2020-07-01T11:49:30Z [Term] id: SO:0002292 name: circular_mRNA def: "An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail." [PMID:29086764, PMID:29182528, PMID:29576969] comment: Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391) synonym: "circular mRNA" EXACT [] synonym: "coding circRNA" EXACT [] is_a: SO:0000234 ! mRNA created_by: david creation_date: 2020-07-01T11:49:30Z [Term] id: SO:0002293 name: mitochondrial_control_region def: "The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis." [PMID: 19407924, PMID:10968878] comment: Added as per GitHub Issue Request #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) from INSDC synonym: "Mitochondrial A+T region" EXACT [] synonym: "Mitochondrial DNA control region" EXACT [] synonym: "Mitochondrial NCR" EXACT [] synonym: "Mitochondrial noncoding region" EXACT [] synonym: "MtDNA control region" EXACT [] synonym: "MtDNA_control_region" EXACT [] xref: https://en.wikipedia.org/wiki/MtDNA_control_region "wiki" is_a: SO:0000296 ! origin_of_replication relationship: has_origin SO:0000737 ! mitochondrial_sequence created_by: david creation_date: 2020-07-01T16:40:30Z [Term] id: SO:0002294 name: mitochondrial_D_loop def: "Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region." [http://www.insdc.org/files/feature_table.html] comment: Added as per request by Terence Murphy (INSDC) for GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) synonym: "Mitochondrial D loop" EXACT [] synonym: "Mitochondrial displacement loop" EXACT [] xref: http://en.wikipedia.org/wiki/D_loop "wiki" is_a: SO:0000297 ! D_loop is_a: SO:0002293 ! mitochondrial_control_region created_by: david creation_date: 2020-07-08T11:49:30Z [Term] id: SO:0002295 name: transcription_factor_regulatory_site def: "A TF_binding_site that is involved in regulation of expression." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "TFRS" EXACT [] synonym: "transcription factor regulatory site" EXACT [] is_a: SO:0000235 ! TF_binding_site created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002296 name: TFRS_module def: "The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. " [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "TFRS module" EXACT [] synonym: "TFRS phrase" EXACT [] synonym: "transcription factor regulatory site module" EXACT [] synonym: "transcription factor regulatory site phrase" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region relationship: has_part SO:0002295 ! transcription_factor_regulatory_site created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002297 name: TFRS_collection def: "The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. synonym: "TFRS collection" EXACT [] synonym: "transcription factor regulatory site collection" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region relationship: has_part SO:0002295 ! transcription_factor_regulatory_site created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002298 name: simple_operon def: "An operon whose transcription is coordinated on a single transcription unit." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "simple operon" EXACT [] is_a: SO:0000178 ! operon created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002299 name: complex_operon def: "An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "complex operon" EXACT [] is_a: SO:0000178 ! operon created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002300 name: unit_of_gene_expression def: "Transcription units or transcribed coding sequences." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "unit of gene expression" EXACT [] is_a: SO:0001411 ! biological_region created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002301 name: transcription_unit def: "DNA regions delimited by different nonspurious TSS-TTS pairs." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "transcription unit" EXACT [] is_a: SO:0002300 ! unit_of_gene_expression created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002302 name: simple_regulon def: "A regulon defined by considering one regulatory gene product." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "simple regulon" EXACT [] is_a: SO:1001284 ! regulon created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002303 name: complex_regulon def: "A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products." [Bacterial_regulation_working_group:CMA, PMID:32665585] comment: Added as per Mejia-Almonte et.al PMID:32665585 synonym: "simple regulon" EXACT [] is_a: SO:1001284 ! regulon created_by: david creation_date: 2020-08-05T11:49:30Z [Term] id: SO:0002304 name: topologically_associated_domain def: "An instance of a self-interacting DNA region flanked by left and right TAD boundaries." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "TAD" EXACT [] synonym: "topologically associated domain" EXACT [] is_a: SO:0001412 ! topologically_defined_region created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002305 name: topologically_associated_domain_boundary def: "A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "TAD boundary" EXACT [] synonym: "TAD_boundary" EXACT [] synonym: "topologically associated domain boundary" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0002304 ! topologically_associated_domain created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002306 name: chromatin_regulatory_region def: "A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "chromatin regulatory region" EXACT [] is_a: SO:0000830 ! chromosome_part created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002307 name: DNA_loop def: "A region of DNA between two loop anchor positions that are held in close physical proximity." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534. synonym: "DNA loop" EXACT [] is_a: SO:0000830 ! chromosome_part relationship: overlaps SO:0002304 ! topologically_associated_domain created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002308 name: DNA_loop_anchor def: "The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534. synonym: "DNA loop anchor" EXACT [] is_a: SO:0000727 ! cis_regulatory_module relationship: part_of SO:0002307 ! DNA_loop created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002309 name: core_promoter_element def: "An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements." [GREEKC:rl] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "core promoter element" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000167 ! promoter created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002310 name: cryptic_promoter def: "The promoter of a cryptic gene." [GREEKC:cl] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "cryptic promoter" EXACT [] is_a: SO:0000167 ! promoter relationship: part_of SO:0001431 ! cryptic_gene created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002311 name: viral_promoter def: "A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses." [GREEKC:cl] synonym: "viral promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002312 name: core_prokaryotic_promoter_element def: "An element that always exists within the promoter region of a prokaryotic gene." [GREEKC:rl] synonym: "core prokaryotic promoter element" EXACT [] synonym: "general transcription factor binding site" RELATED [] is_a: SO:0002309 ! core_promoter_element relationship: part_of SO:0002222 ! prokaryotic_promoter created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002313 name: core_viral_promoter_element def: "An element that always exists within the promoter region of a viral gene." [GREEKC:rl] synonym: "core viral promoter element" EXACT [] synonym: "general transcription factor binding site" RELATED [] is_a: SO:0002309 ! core_promoter_element relationship: part_of SO:0002311 ! viral_promoter created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002314 name: altered_gene_product_level def: "A sequence variant that alters the level or amount of gene product produced. This high level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612. synonym: "altered gene product level" EXACT [] synonym: "altered transcription level" EXACT [] synonym: "altered_transcription_level" EXACT [] is_a: SO:0001536 ! functional_effect_variant created_by: david creation_date: 2020-12-18T22:35:30Z [Term] id: SO:0002315 name: increased_gene_product_level def: "A variant that increases the level or amount of gene product produced." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612. synonym: "increased gene product level" EXACT [] synonym: "increased transcription level" EXACT [] synonym: "increased_transcription_level" EXACT [] is_a: SO:0002314 ! altered_gene_product_level created_by: david creation_date: 2020-12-18T22:35:30Z [Term] id: SO:0002316 name: decreased_gene_product_level def: "A sequence variant that decreases the level or amount of gene product produced." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612. synonym: "decreased gene product level" EXACT [] synonym: "decreased transcription level" EXACT [] synonym: "decreased_transcription_level" EXACT [] synonym: "reduced gene product level" EXACT [] synonym: "reduced transcription level" EXACT [] synonym: "reduced_gene_product_level" EXACT [] synonym: "reduced_transcription_level" EXACT [] is_a: SO:0002314 ! altered_gene_product_level created_by: david creation_date: 2020-12-18T22:35:30Z [Term] id: SO:0002317 name: absent_gene_product def: "A sequence variant that results in no gene product." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612. synonym: "absent gene product" EXACT [] is_a: SO:0002055 ! null_mutation is_a: SO:0002316 ! decreased_gene_product_level created_by: david creation_date: 2020-12-18T22:35:30Z [Term] id: SO:0002318 name: altered_gene_product_sequence def: "A sequence variant that alters the sequence of a gene product." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501) synonym: "altered gene product structure" EXACT [] is_a: SO:0001536 ! functional_effect_variant created_by: david creation_date: 2020-12-18T22:35:30Z [Term] id: SO:0002319 name: NMD_triggering_variant def: "A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "NMD triggering variant" EXACT [] synonym: "nonsense-mediated decay triggering variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002320 name: NMD_escaping_variant def: "A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "NMD escaping variant" EXACT [] synonym: "nonsense-mediated decay escaping variant" EXACT [] is_a: SO:0002218 ! functionally_abnormal created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002321 name: stop_gained_NMD_triggering def: "A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "stop gained variant-nonsense-mediated decay triggering" EXACT [] synonym: "stop gained-NMD triggering" EXACT [] is_a: SO:0001587 ! stop_gained is_a: SO:0002319 ! NMD_triggering_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002322 name: stop_gained_NMD_escaping def: "A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "stop gained variant-nonsense-mediated decay escaping" EXACT [] synonym: "stop gained-NMD escaping" EXACT [] is_a: SO:0001587 ! stop_gained is_a: SO:0002320 ! NMD_escaping_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002323 name: frameshift_variant_NMD_triggering def: "A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "frameshift variant-NMD triggering" EXACT [] synonym: "frameshift variant-nonsense-mediated decay triggering" EXACT [] is_a: SO:0001589 ! frameshift_variant is_a: SO:0002319 ! NMD_triggering_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002324 name: frameshift_variant_NMD_escaping def: "A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "frameshift variant-NMD escaping" EXACT [] synonym: "frameshift variant-nonsense-mediated decay escaping" EXACT [] is_a: SO:0001589 ! frameshift_variant is_a: SO:0002320 ! NMD_escaping_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002325 name: splice_donor_variant_NMD_triggering def: "A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "splice donor variant-NMD triggering" EXACT [] synonym: "splice donor variant-nonsense-mediated decay triggering" EXACT [] is_a: SO:0001575 ! splice_donor_variant is_a: SO:0002319 ! NMD_triggering_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002326 name: splice_donor_variant_NMD_escaping def: "A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "splice donor variant-NMD escaping" EXACT [] synonym: "splice donor variant-nonsense-mediated decay escaping" EXACT [] is_a: SO:0001575 ! splice_donor_variant is_a: SO:0002320 ! NMD_escaping_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002327 name: splice_acceptor_variant_NMD_triggering def: "A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "splice acceptor variant-NMD triggering" EXACT [] synonym: "splice acceptor variant-nonsense-mediated decay triggering" EXACT [] is_a: SO:0001574 ! splice_acceptor_variant is_a: SO:0002319 ! NMD_triggering_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002328 name: splice_acceptor_variant_NMD_escaping def: "A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD)." [GenCC:AR] comment: Added as per request from Ang Roberts as part of GenCC November 2020. synonym: "splice acceptor variant-NMD escaping" EXACT [] synonym: "splice acceptor variant-nonsense-mediated decay escaping" EXACT [] is_a: SO:0001574 ! splice_acceptor_variant is_a: SO:0002320 ! NMD_escaping_variant created_by: david creation_date: 2020-12-30T17:12:30Z [Term] id: SO:0002329 name: minus_1_translational_frameshift def: "The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ds] comment: Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522. synonym: "minus 1 ribosomal frameshift" EXACT [] synonym: "minus 1 ribosomal slippage" EXACT [] synonym: "minus 1 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift created_by: david creation_date: 2021-02-03T20:33:30Z [Term] id: SO:0002330 name: minus_2_translational_frameshift def: "The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ds] comment: Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522. synonym: "minus 2 ribosomal frameshift" EXACT [] synonym: "minus 2 ribosomal slippage" EXACT [] synonym: "minus 2 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift created_by: david creation_date: 2021-02-03T20:33:30Z [Term] id: SO:0002331 name: accessible_DNA_region def: "A region of DNA that is depleted of nucleosomes and accessible to DNA-binding proteins including transcription factors and nucleases." [PMID:25903461, SO:ds] comment: Added as part of GREEKC terms. See GitHub Issues #531 & #534. synonym: "accessible DNA region" EXACT [] is_a: SO:0001411 ! biological_region relationship: overlaps SO:0001720 ! epigenetically_modified_region created_by: david creation_date: 2021-02-11T16:41:30Z [Term] id: SO:0002332 name: epigenomically_modified_region def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ds] comment: Added as part of GREEKC terms to differentiate between inherited and not inherited epigenetic changes. See GitHub Issue #532. synonym: "epigenomically modified region" EXACT [] xref: https://epi.grants.cancer.gov/epigen/#\:~\:text=mail.nih.gov-\,Overview\,a%20cell%20or%20entire%20organism. is_a: SO:0001720 ! epigenetically_modified_region relationship: has_quality SO:0000133 ! epigenetically_modified created_by: david creation_date: 2021-02-11T21:16:30Z [Term] id: SO:0002333 name: amber_stop_codon def: "A stop codon with the DNA sequence TAG." [https://en.wikipedia.org/wiki/Stop_codon] comment: Added as per GitHub request #537. synonym: "Amber stop codon" EXACT [] is_a: SO:0000319 ! stop_codon created_by: david creation_date: 2021-04-21T21:16:30Z [Term] id: SO:0002334 name: ochre_stop_codon def: "A stop codon with the DNA sequence TAA." [https://en.wikipedia.org/wiki/Stop_codon] comment: Added as per GitHub request #537. synonym: "Ochre stop codon" EXACT [] is_a: SO:0000319 ! stop_codon created_by: david creation_date: 2021-04-21T21:16:30Z [Term] id: SO:0002335 name: opal_stop_codon def: "A stop codon with the DNA sequence TGA." [https://en.wikipedia.org/wiki/Stop_codon] comment: Added as per GitHub request #537. synonym: "Opal stop codon" EXACT [] is_a: SO:0000319 ! stop_codon created_by: david creation_date: 2021-04-21T21:16:30Z [Term] id: SO:0002336 name: cytosolic_rRNA_2S_gene def: "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488] comment: Added as a request from FlyBase. See GitHub Issue #507. Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "2S rRNA gene" EXACT [] synonym: "rRNA 2S gene" EXACT [] is_a: SO:0002361 ! cytosolic_LSU_rRNA_gene created_by: david creation_date: 2021-04-23T22:59:30Z [Term] id: SO:0002337 name: cytosolic_2S_rRNA def: "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488] comment: Added as a request from FlyBase. See GitHub Issue #507. Renamed from rRNA_2S to cytosolic_2S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. synonym: "cytosolic 2S rRNA" EXACT [] synonym: "cytosolic rRNA 2S" EXACT [] is_a: SO:0000651 ! cytosolic_LSU_rRNA relationship: derives_from SO:0002336 ! cytosolic_rRNA_2S_gene created_by: david creation_date: 2021-04-23T22:59:30Z [Term] id: SO:0002338 name: U7_snRNA def: "A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing." [PMID:15526162] comment: Added as a request from FlyBase. See GitHub Issue #508 synonym: "small nuclear RNA U7" EXACT [] synonym: "snRNA U7" EXACT [] synonym: "U7 small nuclear RNA" EXACT [] synonym: "U7 snRNA" EXACT [] is_a: SO:0000274 ! snRNA created_by: david creation_date: 2021-04-24T16:59:30Z [Term] id: SO:0002339 name: scaRNA_gene def: "A gene that encodes for a scaRNA (small Cajal body-specific RNA)." [PMID:27775477, PMID:28869095] comment: Added as a request from FlyBase. See GitHub Issue #510 synonym: "scaRNA gene" EXACT [] synonym: "Small Cajal body-specific RNA gene" EXACT [] is_a: SO:0001267 ! snoRNA_gene created_by: david creation_date: 2021-04-24T16:59:30Z [Term] id: SO:0002340 name: RNA_7SK def: "An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length." [PMID:19246988, PMID:21853533, PMID:27369380] comment: Added as a request from FlyBase. See GitHub Issue #512 synonym: "7SK RNA" EXACT [] synonym: "RNA 7SK" EXACT [] is_a: SO:0000655 ! ncRNA created_by: david creation_date: 2021-04-27T14:50:30Z [Term] id: SO:0002341 name: RNA_7SK_gene def: "A gene encoding a 7SK RNA (SO:0002340)." [PMID:19246988, PMID:21853533, PMID:27369380] comment: Added as a request from FlyBase. See GitHub Issue #512 synonym: "7SK RNA gene" EXACT [] synonym: "RNA 7SK gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: david creation_date: 2021-04-27T14:50:30Z [Term] id: SO:0002342 name: sncRNA_gene def: "A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length." [PMID:28449079, PMID:30069443, PMID:30937442] comment: Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514 synonym: "small non-coding RNA gene" EXACT [] synonym: "sncRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: david creation_date: 2021-04-27T14:50:30Z [Term] id: SO:0002343 name: cytosolic_rRNA def: "Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes." [PMID:3044395] comment: Added as a request from EBI. See GitHub Issue #493 synonym: "cytosolic ribosomal RNA" EXACT [] synonym: "cytosolic rRNA" EXACT [] is_a: SO:0000252 ! rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002344 name: mt_SSU_rRNA def: "Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes." [PMID: 24572720, PMID:3044395] comment: Added as a request from EMBL. See GitHub Issue #493 synonym: "mitochondrial small subunit rRNA" EXACT [] synonym: "mitochondrial SSU rRNA" EXACT [] synonym: "MT SSU rRNA" EXACT [] is_a: SO:0002128 ! mt_rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002345 name: mt_LSU_rRNA def: "Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes." [PMID: 24572720, PMID:3044395] comment: Added as a request from EMBL. See GitHub Issue #493 synonym: "mitochondrial large subunit rRNA" EXACT [] synonym: "mitochondrial LSU rRNA" EXACT [] synonym: "MT LSU rRNA" EXACT [] is_a: SO:0002128 ! mt_rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002346 name: plastid_rRNA def: "Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395] comment: Added as a request from EMBL. See GitHub Issue #493 synonym: "plastid rRNA" EXACT [] is_a: SO:0000252 ! rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002347 name: plastid_SSU_rRNA def: "Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395] comment: Added as a request from EMBL. See GitHub Issue #493 synonym: "plastid small subunit rRNA" EXACT [] synonym: "plastid SSU rRNA" EXACT [] is_a: SO:0002346 ! plastid_rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002348 name: plastid_LSU_rRNA def: "Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395] comment: Added as a request from EMBL. See GitHub Issue #493 synonym: "plastid large subunit rRNA" EXACT [] synonym: "plastid LSU rRNA" EXACT [] is_a: SO:0002346 ! plastid_rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0002349 name: fragile_site def: "A heritable locus on a chromosome that is prone to DNA breakage." [] comment: See GitHub Issue #301. is_a: SO:0001021 ! chromosome_breakpoint created_by: evan creation_date: 2021-09-30T19:29:24Z [Term] id: SO:0002350 name: common_fragile_site def: "A fragile site considered part of the normal chromosomal structure." [PMID: 16236432, PMID: 17608616] comment: See GitHub Issue #301. is_a: SO:0002349 ! fragile_site created_by: evan creation_date: 2021-09-30T19:33:59Z [Term] id: SO:0002351 name: rare_fragile_site def: "A fragile site found in the chromosomes of less than five percent of the human population." [PMID:16236432, PMID:17608616] comment: See GitHub Issue #301. is_a: SO:0002349 ! fragile_site created_by: evan creation_date: 2021-09-30T19:34:13Z [Term] id: SO:0002352 name: sisRNA def: "A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails." [PMID:27147469, PMID:29397203, PMID:30391089] comment: See GitHub Issue #515. synonym: "Stable intronic sequence RNA" EXACT [] synonym: "stable_intronic_sequence_RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: evan creation_date: 2021-09-30T21:07:18Z [Term] id: SO:0002353 name: sbRNA_gene def: "A gene encoding a stem-bulge RNA." [PMID:25908866, PMID:30666901] comment: See GitHub Issue #516. synonym: "Stem-bulge RNA gene" EXACT [] synonym: "stem_bulge_RNA_gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: evan creation_date: 2021-09-30T21:25:37Z [Term] id: SO:0002354 name: sbRNA def: "A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA." [PMID:25908866, PMID:30666901] comment: See GitHub Issue #516. synonym: "Stem-bulge RNA" EXACT [] synonym: "stem_bulge_RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: evan creation_date: 2021-09-30T21:29:19Z [Term] id: SO:0002355 name: hpRNA_gene def: "A gene encoding a hpRNA." [PMID:18463630, PMID:18719707, PMID:25544562] comment: See GitHub Issue #518. synonym: "Hairpin RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: evan creation_date: 2021-10-07T17:09:18Z [Term] id: SO:0002356 name: hpRNA def: "An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs)." [PMID:18463630, PMID:18719707, PMID:25544562] comment: See GitHub Issue #518. synonym: "Hairpin RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: evan creation_date: 2021-10-07T17:35:56Z [Term] id: SO:0002357 name: biosynthetic_gene_cluster def: "A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants)." [PMID:26284661] comment: See GitHub Issue #558. synonym: "Metabolic gene cluster" EXACT [] is_a: SO:0001411 ! biological_region created_by: evan creation_date: 2021-10-07T18:20:34Z [Term] id: SO:0002358 name: vault_RNA_gene def: "A gene that encodes a vault RNA." [PMID:19298825, PMID:19491402, PMID:22058117, PMID:22926522, PMID:30773316, PMID:9535882] comment: As of 11 November 2021 the HNGC lists 4 genes as RNA, vault. These are HGNC IDs: 12654, 12655, 12656, 37054. is_a: SO:0001263 ! ncRNA_gene created_by: evan creation_date: 2021-11-11T23:25:13Z [Term] id: SO:0002359 name: Y_RNA_gene def: "A gene that encodes a Y RNA." [PMID:1698620, PMID:6187471, PMID:6816230, PMID:7520568, PMID:7539809, PMID:8836182] comment: There are four genes from HGNC that are annotated this way. HGNC IDs: 10242, 10243, 10244, and 10248. is_a: SO:0001263 ! ncRNA_gene created_by: evan creation_date: 2021-11-11T23:52:21Z [Term] id: SO:0002360 name: cytosolic_rRNA_gene def: "A gene that codes for cytosolic rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). is_a: SO:0001637 ! rRNA_gene created_by: evan creation_date: 2021-11-19T04:30:40Z [Term] id: SO:0002361 name: cytosolic_LSU_rRNA_gene def: "A gene that codes for cytosolic LSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "cytosolic large subunit rRNA gene" EXACT [] is_a: SO:0002360 ! cytosolic_rRNA_gene created_by: evan creation_date: 2021-11-19T04:32:20Z [Term] id: SO:0002362 name: cytosolic_SSU_rRNA_gene def: "A gene that codes for cytosolic SSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "cytosolic small subunit rRNA gene" EXACT [] is_a: SO:0002360 ! cytosolic_rRNA_gene created_by: evan creation_date: 2021-11-19T04:37:02Z [Term] id: SO:0002363 name: mt_rRNA_gene def: "A gene that codes for mitochondrial rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "mitochondrial rRNA gene" EXACT [] is_a: SO:0000088 ! mt_gene is_a: SO:0001637 ! rRNA_gene created_by: evan creation_date: 2021-11-19T04:55:58Z [Term] id: SO:0002364 name: mt_LSU_rRNA_gene def: "A gene that codes for mitochondrial LSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). Obsoleted term rRNA_21S_gene (SO:0002241) merged into this term on 12 Sept 2022, see GitHub Issue #513. synonym: "mitochondrial large subunit rRNA gene" EXACT [] synonym: "rRNA 21S gene" EXACT [] synonym: "rRNA_21S_gene" EXACT [] is_a: SO:0002363 ! mt_rRNA_gene created_by: evan creation_date: 2021-11-19T04:57:49Z [Term] id: SO:0002365 name: mt_SSU_rRNA_gene def: "A gene that codes for mitochondrial SSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "mitochondrial small subunit rRNA gene" EXACT [] is_a: SO:0002363 ! mt_rRNA_gene created_by: evan creation_date: 2021-11-19T04:58:07Z [Term] id: SO:0002366 name: plastid_rRNA_gene def: "A gene that codes for plastid rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). is_a: SO:0000090 ! plastid_gene is_a: SO:0001637 ! rRNA_gene created_by: evan creation_date: 2021-11-19T05:00:08Z [Term] id: SO:0002367 name: plastid_LSU_rRNA_gene def: "A gene that codes for plastid LSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "plastid large subunit rRNA gene" EXACT [] is_a: SO:0002366 ! plastid_rRNA_gene created_by: evan creation_date: 2021-11-19T05:00:49Z [Term] id: SO:0002368 name: plastid_SSU_rRNA_gene def: "A gene that codes for plastid SSU rRNA." [] comment: Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). synonym: "plastid small subunit rRNA gene" EXACT [] is_a: SO:0002366 ! plastid_rRNA_gene created_by: evan creation_date: 2021-11-19T05:01:03Z [Term] id: SO:0002369 name: C_D_box_scaRNA def: "A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "C/D scaRNA" EXACT [] is_a: SO:0002095 ! scaRNA created_by: evan creation_date: 2021-11-19T05:34:44Z [Term] id: SO:0002370 name: H_ACA_box_scaRNA def: "A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "H/ACA scaRNA" EXACT [] is_a: SO:0002095 ! scaRNA created_by: evan creation_date: 2021-11-19T05:35:04Z [Term] id: SO:0002371 name: C-D_H_ACA_box_scaRNA def: "A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "C/D-H/ACA scaRNA" EXACT [] is_a: SO:0002095 ! scaRNA created_by: evan creation_date: 2021-11-19T05:35:23Z [Term] id: SO:0002372 name: C_D_box_scaRNA_gene def: "A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "C/D scaRNA gene" EXACT [] is_a: SO:0002339 ! scaRNA_gene created_by: evan creation_date: 2021-11-19T05:40:46Z [Term] id: SO:0002373 name: H_ACA_box_scaRNA_gene def: "A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "H/ACA scaRNA gene" EXACT [] is_a: SO:0002339 ! scaRNA_gene created_by: evan creation_date: 2021-11-19T05:40:58Z [Term] id: SO:0002374 name: C-D_H_ACA_box_scaRNA_gene def: "A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs." [PMID:17099227, PMID:24659245] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "C/D-H/ACA scaRNA gene" EXACT [] is_a: SO:0002339 ! scaRNA_gene created_by: evan creation_date: 2021-11-19T05:41:06Z [Term] id: SO:0002375 name: C_D_box_snoRNA_gene def: "A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [PMID:12457565, PMID:22065625] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565. synonym: "box C/D snoRNA gene, C D box snoRNA gene, C/D box snoRNA gene" EXACT [] is_a: SO:0001267 ! snoRNA_gene created_by: evan creation_date: 2021-11-19T05:49:55Z [Term] id: SO:0002376 name: H_ACA_box_snoRNA_gene def: "A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [PMID:12457565, PMID:22065625] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565. synonym: "box H/ACA snoRNA gene, H ACA box snoRNA gene, H/ACA box snoRNA gene" EXACT [] is_a: SO:0001267 ! snoRNA_gene created_by: evan creation_date: 2021-11-19T05:50:14Z [Term] id: SO:0002377 name: U14_snoRNA_gene def: "A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "small nucleolar RNA U14 gene, snoRNA U14 gene, U14 small nucleolar RNA gene, U14 snoRNA gene" EXACT [] is_a: SO:0002375 ! C_D_box_snoRNA_gene created_by: evan creation_date: 2021-11-19T05:50:43Z [Term] id: SO:0002378 name: U3_snoRNA_gene def: "A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "small nucleolar RNA U3 gene, snoRNA U3 gene, U3 small nucleolar RNA gene, U3 snoRNA gene" EXACT [] is_a: SO:0002375 ! C_D_box_snoRNA_gene created_by: evan creation_date: 2021-11-19T05:50:57Z [Term] id: SO:0002379 name: methylation_guide_snoRNA_gene def: "A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [PMID:12457565] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "methylation guide snoRNA gene" EXACT [] is_a: SO:0002375 ! C_D_box_snoRNA_gene created_by: evan creation_date: 2021-11-19T05:51:12Z [Term] id: SO:0002380 name: pseudouridylation_guide_snoRNA_gene def: "A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [PMID:12457565] comment: Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). synonym: "pseudouridylation guide snoRNA gene" EXACT [] is_a: SO:0002376 ! H_ACA_box_snoRNA_gene created_by: evan creation_date: 2021-11-19T05:51:40Z [Term] id: SO:0002381 name: bidirectional_promoter_lncRNA def: "A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction." [PMID:30175284, PMID:34956340] {comment="PMID:26578749"} comment: Created new term "bidirectional_promoter_lncRNA" (SO:0002381). See GitHub Issue #579. synonym: "bidirectional lncRNA" EXACT [] synonym: "bidirectional promoter lncRNA" EXACT [] synonym: "bidirectional promoter long non-coding RNA" EXACT [] synonym: "bidirectional_lncRNA" EXACT [] synonym: "bidirectional_promoter_long_non-coding_RNA" EXACT [] is_a: SO:0001877 ! lncRNA created_by: evan creation_date: 2022-10-28T19:05:35Z [Term] id: SO:0005836 name: regulatory_region def: "A region of sequence that is involved in the control of a biological process." [SO:ke] subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:other" EXACT [] synonym: "regulatory region" EXACT [] xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0005837 name: U14_snoRNA_primary_transcript def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119] synonym: "4.5S snRNA primary transcript" EXACT [] synonym: "U14 snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0005841 name: methylation_guide_snoRNA def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561). synonym: "methylation guide snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript [Term] id: SO:0005843 name: rRNA_cleavage_RNA def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc] synonym: "rRNA cleavage RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript [Term] id: SO:0005845 name: exon_of_single_exon_gene def: "An exon that is the only exon in a gene." [RSC:cb] synonym: "exon of single exon gene" EXACT [] synonym: "single_exon" RELATED [] synonym: "singleton exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0005847 name: cassette_array_member def: "A gene that is a member of a gene cassette, which is a mobile genetic element." [] synonym: "cassette array member" EXACT [] is_a: SO:0005848 ! gene_cassette_member [Term] id: SO:0005848 name: gene_cassette_member def: "A gene that is a member of a gene cassette, which is a mobile genetic element." [] synonym: "gene cassette member" EXACT [] is_a: SO:0000081 ! gene_array_member [Term] id: SO:0005849 name: gene_subarray_member def: "A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together." [] synonym: "gene subarray member" EXACT [] is_a: SO:0000081 ! gene_array_member [Term] id: SO:0005850 name: primer_binding_site def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.insdc.org/files/feature_table.html] synonym: "INSDC_feature:primer_bind" EXACT [] synonym: "primer binding site" EXACT [] xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki" is_a: SO:0001655 ! nucleotide_binding_site relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0005851 name: gene_array def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma] comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays. synonym: "gene array" EXACT [] is_a: SO:0005855 ! gene_group [Term] id: SO:0005852 name: gene_subarray def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma] comment: This would include, for example, a cluster of genes encoding different histones. synonym: "gene subarray" EXACT [] is_a: SO:0005855 ! gene_group [Term] id: SO:0005853 name: gene_cassette def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid. synonym: "gene cassette" EXACT [] xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0005854 name: gene_cassette_array def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma] comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes. synonym: "gene cassette array" EXACT [] is_a: SO:0005855 ! gene_group relationship: has_part SO:0005853 ! gene_cassette [Term] id: SO:0005855 name: gene_group def: "A collection of related genes." [SO:ma] subset: SOFA synonym: "gene group" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0005856 name: selenocysteine_tRNA_primary_transcript def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] synonym: "selenocysteine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0005857 name: selenocysteinyl_tRNA def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke] synonym: "selenocysteinyl tRNA" EXACT [] synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT [] synonym: "selenocysteinyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript [Term] id: SO:0005858 name: syntenic_region def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml] synonym: "syntenic region" EXACT [] is_a: SO:0000330 ! conserved_region intersection_of: SO:0000330 ! conserved_region intersection_of: has_quality SO:0000860 ! syntenic relationship: has_quality SO:0000860 ! syntenic [Term] id: SO:0100001 name: biochemical_region_of_peptide def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "biochemical motif" EXACT [] synonym: "biochemical region of peptide" EXACT [] synonym: "biochemical_region" RELATED [] is_a: SO:0001067 ! polypeptide_motif [Term] id: SO:0100002 name: molecular_contact_region def: "A region that is involved a contact with another molecule." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "molecular contact region" RELATED [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0100003 name: intrinsically_unstructured_polypeptide_region def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR] subset: biosapiens synonym: "disordered region" RELATED BS [] synonym: "intrinsically unstructured polypeptide region" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0100004 name: catmat_left_handed_three def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "catmat-3l" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100005 name: catmat_left_handed_four def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "catmat-4l" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100006 name: catmat_right_handed_three def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "catmat-3r" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100007 name: catmat_right_handed_four def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "catmat-4r" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100008 name: alpha_beta_motif def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "alpha beta motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100009 name: lipoprotein_signal_peptide def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR] subset: biosapiens synonym: "lipoprotein signal peptide" EXACT [] synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0100010 name: no_output def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR] subset: biosapiens synonym: "no output" EXACT BS [] is_a: SO:0000703 ! experimental_result_region [Term] id: SO:0100011 name: cleaved_peptide_region def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "cleaved peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0100012 name: peptide_coil def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR] subset: biosapiens synonym: "coil" RELATED BS [] synonym: "peptide coil" EXACT [] synonym: "random coil" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0100013 name: hydrophobic_region_of_peptide def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "hydropathic" RELATED [] synonym: "hydrophobic region of peptide" RELATED [] synonym: "hydrophobic_region" EXACT [] synonym: "hydrophobicity" RELATED [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0100014 name: n_terminal_region def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR] subset: biosapiens synonym: "N-region" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0000418 ! signal_peptide [Term] id: SO:0100015 name: c_terminal_region def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR] subset: biosapiens synonym: "C-region" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0000418 ! signal_peptide [Term] id: SO:0100016 name: central_hydrophobic_region_of_signal_peptide def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR] subset: biosapiens synonym: "central hydrophobic region of signal peptide" EXACT [] synonym: "central_hydrophobic_region" RELATED [] synonym: "H-region" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0000418 ! signal_peptide [Term] id: SO:0100017 name: polypeptide_conserved_motif def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] subset: biosapiens synonym: "motif" RELATED [] is_a: SO:0001067 ! polypeptide_motif [Term] id: SO:0100018 name: polypeptide_binding_motif def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR] subset: biosapiens synonym: "binding" RELATED [uniprot:feature_type] synonym: "polypeptide binding motif" EXACT [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0100019 name: polypeptide_catalytic_motif def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR] subset: biosapiens synonym: "catalytic_motif" RELATED [] synonym: "polypeptide catalytic motif" EXACT [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0100020 name: polypeptide_DNA_contact def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke] subset: biosapiens synonym: "DNA_bind" EXACT BS [uniprot:feature] synonym: "polypeptide DNA contact" EXACT [] is_a: SO:0001429 ! DNA_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0100021 name: polypeptide_conserved_region def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide conserved region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:1000002 name: substitution def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] subset: SOFA xref: loinc:LA6690-7 "Substitution" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1000005 name: complex_substitution def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA synonym: "complex substitution" EXACT [] is_a: SO:1000002 ! substitution [Term] id: SO:1000008 name: point_mutation def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] subset: SOFA synonym: "point mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" is_a: SO:0001483 ! SNV [Term] id: SO:1000009 name: transition def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:0001483 ! SNV [Term] id: SO:1000010 name: pyrimidine_transition def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke] synonym: "pyrimidine transition" EXACT [] is_a: SO:1000009 ! transition [Term] id: SO:1000011 name: C_to_T_transition def: "A transition of a cytidine to a thymine." [SO:ke] synonym: "C to T transition" EXACT [] is_a: SO:1000010 ! pyrimidine_transition [Term] id: SO:1000012 name: C_to_T_transition_at_pCpG_site def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "C to T transition at pCpG site" EXACT [] is_a: SO:1000011 ! C_to_T_transition [Term] id: SO:1000013 name: T_to_C_transition def: "A transition of a thymine to a cytidine." [] synonym: "T to C transition" EXACT [] is_a: SO:1000010 ! pyrimidine_transition [Term] id: SO:1000014 name: purine_transition def: "A substitution of a purine, A or G, for another purine." [SO:ke] synonym: "purine transition" EXACT [] is_a: SO:1000009 ! transition [Term] id: SO:1000015 name: A_to_G_transition def: "A transition of an adenine to a guanine." [SO:ke] synonym: "A to G transition" EXACT [] is_a: SO:1000014 ! purine_transition [Term] id: SO:1000016 name: G_to_A_transition def: "A transition of a guanine to an adenine." [SO:ke] synonym: "G to A transition" EXACT [] is_a: SO:1000014 ! purine_transition [Term] id: SO:1000017 name: transversion def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] xref: http://en.wikipedia.org/wiki/Transversion "wiki" is_a: SO:0001483 ! SNV [Term] id: SO:1000018 name: pyrimidine_to_purine_transversion def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] synonym: "pyrimidine to purine transversion" EXACT [] is_a: SO:1000017 ! transversion [Term] id: SO:1000019 name: C_to_A_transversion def: "A transversion from cytidine to adenine." [SO:ke] synonym: "C to A transversion" EXACT [] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000020 name: C_to_G_transversion def: "A transversion of a cytidine to a guanine." [] synonym: "C to G transversion" EXACT [] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000021 name: T_to_A_transversion def: "A transversion from T to A." [SO:ke] synonym: "T to A transversion" EXACT [] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000022 name: T_to_G_transversion def: "A transversion from T to G." [SO:ke] synonym: "T to G transversion" EXACT [] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000023 name: purine_to_pyrimidine_transversion def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke] synonym: "purine to pyrimidine transversion" EXACT [] is_a: SO:1000017 ! transversion [Term] id: SO:1000024 name: A_to_C_transversion def: "A transversion from adenine to cytidine." [SO:ke] synonym: "A to C transversion" EXACT [] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000025 name: A_to_T_transversion def: "A transversion from adenine to thymine." [SO:ke] synonym: "A to T transversion" EXACT [] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000026 name: G_to_C_transversion def: "A transversion from guanine to cytidine." [SO:ke] synonym: "G to C transversion" EXACT [] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000027 name: G_to_T_transversion def: "A transversion from guanine to thymine." [SO:ke] synonym: "G to T transversion" EXACT [] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000028 name: intrachromosomal_mutation def: "A chromosomal structure variation within a single chromosome." [SO:ke] synonym: "intrachromosomal mutation" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation intersection_of: SO:1000183 ! chromosome_structure_variation intersection_of: has_quality SO:0001510 ! intrachromosomal relationship: has_quality SO:0001510 ! intrachromosomal [Term] id: SO:1000029 name: chromosomal_deletion def: "An incomplete chromosome." [SO:ke] synonym: "(bacteria)&Dgr;" RELATED [] synonym: "(Drosophila)Df" RELATED [] synonym: "(fungi)D" RELATED [] synonym: "chromosomal deletion" EXACT [] synonym: "deficiency" EXACT [] xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki" is_a: SO:1000028 ! intrachromosomal_mutation intersection_of: SO:1000028 ! intrachromosomal_mutation intersection_of: has_part SO:0000159 ! deletion relationship: has_part SO:0000159 ! deletion [Term] id: SO:1000030 name: chromosomal_inversion def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke] synonym: "(bacteria)IN" RELATED [] synonym: "(Drosophila)In" RELATED [] synonym: "(fungi)In" RELATED [] synonym: "chromosomal inversion" EXACT [] xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki" is_a: SO:1000028 ! intrachromosomal_mutation intersection_of: SO:1000028 ! intrachromosomal_mutation intersection_of: has_part SO:1000036 ! inversion relationship: has_part SO:1000036 ! inversion [Term] id: SO:1000031 name: interchromosomal_mutation def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke] synonym: "interchromosomal mutation" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation intersection_of: SO:1000183 ! chromosome_structure_variation intersection_of: has_quality SO:0001511 ! interchromosomal relationship: has_quality SO:0001511 ! interchromosomal [Term] id: SO:1000032 name: delins def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [http://varnomen.hgvs.org/recommendations/DNA/variant/delins/] comment: Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. synonym: "deletion-insertion" EXACT [] synonym: "indel" EXACT [] xref: http://en.wikipedia.org/wiki/Indel "wiki" xref: loinc:LA9659-9 "Insertion and Deletion" is_a: SO:0001059 ! sequence_alteration [Term] id: SO:1000035 name: duplication def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th] synonym: "nucleotide duplication" EXACT [] synonym: "nucleotide_duplication" RELATED [] xref: loinc:LA6686-5 "Duplication" is_a: SO:0000667 ! insertion [Term] id: SO:1000036 name: inversion def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: DBVAR subset: SOFA synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] xref: loinc:LA6689-9 "Inversion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1000037 name: chromosomal_duplication def: "An extra chromosome." [SO:ke] synonym: "(Drosophila)Dp" RELATED [] synonym: "(fungi)Dp" RELATED [] synonym: "chromosomal duplication" EXACT [] xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki" is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000038 name: intrachromosomal_duplication def: "A duplication that occurred within a chromosome." [SO:ke] synonym: "intrachromosomal duplication" EXACT [] is_a: SO:1000028 ! intrachromosomal_mutation is_a: SO:1000037 ! chromosomal_duplication intersection_of: SO:1000028 ! intrachromosomal_mutation intersection_of: has_part SO:1000035 ! duplication relationship: has_part SO:1000035 ! duplication [Term] id: SO:1000039 name: direct_tandem_duplication def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke] synonym: "direct tandem duplication" EXACT [] is_a: SO:1000173 ! tandem_duplication [Term] id: SO:1000040 name: inverted_tandem_duplication def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke] synonym: "inverted tandem duplication" EXACT [] synonym: "mirror duplication" RELATED [] is_a: SO:1000173 ! tandem_duplication [Term] id: SO:1000041 name: intrachromosomal_transposition def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke] synonym: "(Drosophila)Tp" RELATED [] synonym: "intrachromosomal transposition" EXACT [] is_a: SO:0000453 ! chromosomal_transposition is_a: SO:1000038 ! intrachromosomal_duplication intersection_of: SO:1000028 ! intrachromosomal_mutation intersection_of: has_part SO:0000199 ! translocation intersection_of: has_part SO:1000035 ! duplication relationship: has_part SO:0000199 ! translocation relationship: has_part SO:1000035 ! duplication [Term] id: SO:1000042 name: compound_chromosome def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke] synonym: "compound chromosome" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000043 name: Robertsonian_fusion def: "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation] synonym: "centric-fusion translocations" EXACT [] synonym: "Robertsonian fusion" EXACT [] synonym: "whole-arm translocations" EXACT [] xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki" is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000044 name: chromosomal_translocation def: "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual] synonym: "(Drosophila)T" RELATED [] synonym: "(fungi)T" RELATED [] synonym: "chromosomal translocation" EXACT [] xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki" is_a: SO:0000199 ! translocation is_a: SO:1000031 ! interchromosomal_mutation [Term] id: SO:1000045 name: ring_chromosome def: "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome] synonym: "(Drosophila)R" RELATED [] synonym: "(fungi)C" RELATED [] synonym: "ring chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki" is_a: SO:1000028 ! intrachromosomal_mutation intersection_of: SO:1000028 ! intrachromosomal_mutation intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:1000046 name: pericentric_inversion def: "A chromosomal inversion that includes the centromere." [FB:reference_manual] synonym: "pericentric inversion" EXACT [] is_a: SO:1000030 ! chromosomal_inversion intersection_of: SO:1000030 ! chromosomal_inversion intersection_of: has_quality SO:0001518 ! pericentric relationship: has_quality SO:0001518 ! pericentric [Term] id: SO:1000047 name: paracentric_inversion def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual] synonym: "paracentric inversion" EXACT [] is_a: SO:1000030 ! chromosomal_inversion intersection_of: SO:1000030 ! chromosomal_inversion intersection_of: has_quality SO:0001519 ! paracentric relationship: has_quality SO:0001519 ! paracentric [Term] id: SO:1000048 name: reciprocal_chromosomal_translocation def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual] synonym: "reciprocal chromosomal translocation" EXACT [] is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000049 name: sequence_variation_affecting_transcript alt_id: SO:1000177 alt_id: SO:1000179 def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcript" EXACT [] synonym: "mutation causing partially characterised change in transcript" RELATED [] synonym: "mutation causing uncharacterised change in transcript" RELATED [] synonym: "sequence variant causing partially characterised change in transcript" EXACT [] synonym: "sequence variant causing uncharacterised change in transcript" EXACT [] synonym: "sequence variation affecting transcript" EXACT [] synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT [] synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT [] is_obsolete: true replaced_by: SO:0001576 [Term] id: SO:1000050 name: sequence_variant_causing_no_change_in_transcript def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term. synonym: "mutation causing no change in transcript" RELATED [] synonym: "sequence variant causing no change in transcript" EXACT [] is_obsolete: true [Term] id: SO:1000054 name: sequence_variation_affecting_coding_sequence def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting coding sequence" EXACT [] synonym: "sequence variation affecting coding sequence" RELATED [] is_obsolete: true replaced_by: SO:0001580 [Term] id: SO:1000055 name: sequence_variant_causing_initiator_codon_change_in_transcript def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing initiator codon change in transcript" RELATED [] synonym: "sequence variant causing initiator codon change in transcript" EXACT [] is_obsolete: true replaced_by: SO:0001582 [Term] id: SO:1000056 name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutaton causing amino acid coding codon change in transcript" RELATED [] synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001606 [Term] id: SO:1000057 name: sequence_variant_causing_synonymous_codon_change_in_transcript def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing synonymous codon change in transcript" RELATED [] synonym: "sequence variant causing synonymous codon change in transcript" EXACT [] is_obsolete: true replaced_by: SO:0001819 [Term] id: SO:1000058 name: sequence_variant_causing_non_synonymous_codon_change_in_transcript def: "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing non synonymous codon change in transcript" RELATED [] synonym: "non-synonymous codon change in transcript" EXACT [] synonym: "sequence variant causing non synonymous codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001583 [Term] id: SO:1000059 name: sequence_variant_causing_missense_codon_change_in_transcript def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing missense codon change in transcript" RELATED [] synonym: "sequence variant causing missense codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001583 [Term] id: SO:1000060 name: sequence_variant_causing_conservative_missense_codon_change_in_transcript def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. synonym: "mutation causing conservative missense codon change in transcript" RELATED [] synonym: "sequence variant causing conservative missense codon change in transcript" EXACT [] is_obsolete: true replaced_by: SO:0001585 [Term] id: SO:1000061 name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. synonym: "mutation causing nonconservative missense codon change in transcript" RELATED [] synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001586 [Term] id: SO:1000062 name: sequence_variant_causing_nonsense_codon_change_in_transcript def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing nonsense codon change in transcript" RELATED [] synonym: "sequence variant causing nonsense codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001587 [Term] id: SO:1000063 name: sequence_variant_causing_terminator_codon_change_in_transcript def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing terminator codon change in transcript" RELATED [] synonym: "sequence variant causing terminator codon change in transcript" EXACT [] is_obsolete: true consider: SO:0001590 [Term] id: SO:1000064 name: sequence_variation_affecting_reading_frame def: "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting reading frame" EXACT [] synonym: "sequence variation affecting reading frame" RELATED [] is_obsolete: true [Term] id: SO:1000065 name: frameshift_sequence_variation def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] synonym: "frameshift mutation" EXACT [] synonym: "frameshift sequence variation" RELATED [] synonym: "out of frame mutation" RELATED [] xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki" is_obsolete: true [Term] id: SO:1000066 name: sequence_variant_causing_plus_1_frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "plus 1 frameshift mutation" EXACT [] synonym: "sequence variant causing plus 1 frameshift mutation" EXACT [] is_obsolete: true replaced_by: SO:0001594 [Term] id: SO:1000067 name: sequence_variant_causing_minus_1_frameshift def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "minus 1 frameshift mutation" EXACT [] synonym: "sequence variant causing minus 1 frameshift" EXACT [] is_obsolete: true replaced_by: SO:0001592 [Term] id: SO:1000068 name: sequence_variant_causing_plus_2_frameshift def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "plus 2 frameshift mutation" EXACT [] synonym: "sequence variant causing plus 2 frameshift" EXACT [] is_obsolete: true replaced_by: SO:0001595 [Term] id: SO:1000069 name: sequence_variant_causing_minus_2_frameshift def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "minus 2 frameshift mutation" EXACT [] synonym: "sequence variant causing minus 2 frameshift" EXACT [] is_obsolete: true replaced_by: SO:0001593 [Term] id: SO:1000070 name: sequence_variant_affecting_transcript_processing def: "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcript processing" RELATED [] synonym: "sequence variant affecting transcript processing" EXACT [] is_obsolete: true replaced_by: SO:0001543 [Term] id: SO:1000071 name: sequence_variant_affecting_splicing def: "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting splicing" RELATED [] synonym: "sequence variant affecting splicing" EXACT [] is_obsolete: true replaced_by: SO:0001568 [Term] id: SO:1000072 name: sequence_variant_affecting_splice_donor def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting splice donor" RELATED [] synonym: "sequence variant affecting splice donor" RELATED [] synonym: "splice donor mutation" EXACT [] is_obsolete: true replaced_by: SO:0001575 [Term] id: SO:1000073 name: sequence_variant_affecting_splice_acceptor def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting splicing" RELATED [] synonym: "sequence variant affecting splice acceptor" RELATED [] synonym: "splice acceptor mutation" EXACT [] is_obsolete: true replaced_by: SO:0001574 [Term] id: SO:1000074 name: sequence_variant_causing_cryptic_splice_activation def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration. synonym: "cryptic splice activator sequence variant" EXACT [] synonym: "mutation causing cryptic splice activator" RELATED [] synonym: "sequence variant causing cryptic splice activator" EXACT [] is_obsolete: true replaced_by: SO:0001569 [Term] id: SO:1000075 name: sequence_variant_affecting_editing def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting editing" RELATED [] synonym: "sequence variant affecting editing" EXACT [] is_obsolete: true replaced_by: SO:0001544 [Term] id: SO:1000076 name: sequence_variant_affecting_transcription def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcription" RELATED [] synonym: "sequence variant affecting transcription" EXACT [] is_obsolete: true replaced_by: SO:0001549 [Term] id: SO:1000078 name: sequence_variant_decreasing_rate_of_transcription def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation decreasing rate of transcription" RELATED [] synonym: "sequence variation decreasing rate of transcription" EXACT [] is_obsolete: true [Term] id: SO:1000079 name: sequence_variation_affecting_transcript_sequence comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcript sequence" EXACT [] synonym: "sequence variation affecting transcript sequence" EXACT [] is_obsolete: true [Term] id: SO:1000080 name: sequence_variant_increasing_rate_of_transcription comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation increasing rate of transcription" RELATED [] synonym: "sequence variation increasing rate of transcription" EXACT [] is_obsolete: true [Term] id: SO:1000081 name: sequence_variant_affecting_rate_of_transcription def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting rate of transcription" RELATED [] synonym: "sequence variant affecting rate of transcription" EXACT [] is_obsolete: true replaced_by: SO:0001550 [Term] id: SO:1000082 name: sequence variant_affecting_transcript_stability def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcript stability" RELATED [] synonym: "sequence variant affecting transcript stability" EXACT [] is_obsolete: true replaced_by: SO:0001546 [Term] id: SO:1000083 name: sequence_variant_increasing_transcript_stability def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation increasing transcript stability" RELATED [] synonym: "sequence variant increasing transcript stability" EXACT [] is_obsolete: true [Term] id: SO:1000084 name: sequence_variant_decreasing_transcript_stability def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation decreasing transcript stability" RELATED [] synonym: "sequence variant decreasing transcript stability" EXACT [] is_obsolete: true [Term] id: SO:1000085 name: sequence_variation_affecting_level_of_transcript def: "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting level of transcript" RELATED [] synonym: "sequence variation affecting level of transcript" EXACT [] is_obsolete: true replaced_by: SO:0001540 [Term] id: SO:1000086 name: sequence_variation_decreasing_level_of_transcript def: "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation decreasing level of transcript" EXACT [] synonym: "sequence variation decreasing level of transcript" RELATED [] is_obsolete: true [Term] id: SO:1000087 name: sequence_variation_increasing_level_of_transcript def: "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation increasing level of transcript" EXACT [] synonym: "sequence variation increasing level of transcript" EXACT [] is_obsolete: true [Term] id: SO:1000088 name: sequence_variant_affecting_translational_product alt_id: SO:1000090 alt_id: SO:1000091 def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting translational product" RELATED [] synonym: "mutation causing partially characterised change of translational product" RELATED [] synonym: "mutation causing uncharacterised change of translational product" RELATED [] synonym: "sequence variant affecting translational product" EXACT [] synonym: "sequence variant causing partially characterised change of translational product" EXACT [] synonym: "sequence variant causing uncharacterised change of translational product" EXACT [] synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT [] synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT [] is_obsolete: true replaced_by: SO:0001553 [Term] id: SO:1000089 name: sequence_variant_causing_no_change_of_translational_product def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term. synonym: "mutation causing no change of translational product" RELATED [] synonym: "sequence variant causing no change of translational product" EXACT [] is_obsolete: true [Term] id: SO:1000092 name: sequence_variant_causing_complex_change_of_translational_product def: "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing complex change of translational product" RELATED [] synonym: "sequence variant causing complex change of translational product" EXACT [] is_obsolete: true consider: SO:0001539 [Term] id: SO:1000093 name: sequence_variant_causing_amino_acid_substitution def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing amino acid substitution" RELATED [] synonym: "sequence variant causing amino acid substitution" EXACT [] is_obsolete: true replaced_by: SO:0001606 [Term] id: SO:1000094 name: sequence_variant_causing_conservative_amino_acid_substitution comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing conservative amino acid substitution" RELATED [] synonym: "sequence variant causing conservative amino acid substitution" EXACT [] is_obsolete: true replaced_by: SO:0001607 [Term] id: SO:1000095 name: sequence_variant_causing_nonconservative_amino_acid_substitution comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing nonconservative amino acid substitution" RELATED [] synonym: "sequence variant causing nonconservative amino acid substitution" EXACT [] is_obsolete: true replaced_by: SO:0001607 [Term] id: SO:1000096 name: sequence_variant_causing_amino_acid_insertion def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing amino acid insertion" RELATED [] synonym: "sequence variant causing amino acid insertion" EXACT [] is_obsolete: true replaced_by: SO:0001605 [Term] id: SO:1000097 name: sequence_variant_causing_amino_acid_deletion def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing amino acid deletion" RELATED [] synonym: "sequence variant causing amino acid deletion" EXACT [] is_obsolete: true consider: SO:0001825 [Term] id: SO:1000098 name: sequence_variant_causing_polypeptide_truncation def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide truncation" RELATED [] synonym: "sequence variant causing polypeptide truncation" EXACT [] is_obsolete: true replaced_by: SO:0001587 [Term] id: SO:1000099 name: sequence_variant_causing_polypeptide_elongation def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide elongation" RELATED [] synonym: "sequence variant causing polypeptide elongation" EXACT [] is_obsolete: true replaced_by: SO:0001609 [Term] id: SO:1000100 name: mutation_causing_polypeptide_N_terminal_elongation def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide N terminal elongation" EXACT [] synonym: "polypeptide N-terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001611 [Term] id: SO:1000101 name: mutation_causing_polypeptide_C_terminal_elongation def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide C terminal elongation" EXACT [] synonym: "polypeptide C-terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001610 [Term] id: SO:1000102 name: sequence_variant_affecting_level_of_translational_product comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting level of translational product" RELATED [] synonym: "sequence variant affecting level of translational product" EXACT [] is_obsolete: true replaced_by: SO:0001553 [Term] id: SO:1000103 name: sequence_variant_decreasing_level_of_translation_product comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutationdecreasing level of translation product" RELATED [] synonym: "sequence variant decreasing level of translation product" EXACT [] is_obsolete: true replaced_by: SO:0001555 [Term] id: SO:1000104 name: sequence_variant_increasing_level_of_translation_product comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutationt increasing level of translation product" RELATED [] synonym: "sequence variant increasing level of translation product" EXACT [] is_obsolete: true [Term] id: SO:1000105 name: sequence_variant_affecting_polypeptide_amino_acid_sequence comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting polypeptide amino acid sequence" RELATED [] synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT [] is_obsolete: true replaced_by: SO:0001603 [Term] id: SO:1000106 name: mutation_causing_inframe_polypeptide_N_terminal_elongation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "inframe polypeptide N-terminal elongation" EXACT [] synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001614 [Term] id: SO:1000107 name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT [] synonym: "out of frame polypeptide N-terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001615 [Term] id: SO:1000108 name: mutaton_causing_inframe_polypeptide_C_terminal_elongation synonym: "inframe_polypeptide C-terminal elongation" EXACT [] synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001612 [Term] id: SO:1000109 name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT [] synonym: "out of frame polypeptide C-terminal elongation" EXACT [] is_obsolete: true replaced_by: SO:0001613 [Term] id: SO:1000110 name: frame_restoring_sequence_variant def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] synonym: "frame restoring mutation" EXACT [] synonym: "frame restoring sequence variant" EXACT [] is_obsolete: true [Term] id: SO:1000111 name: sequence_variant_affecting_3D_structure_of_polypeptide alt_id: SO:1000113 alt_id: SO:1000114 def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting 3D structure of polypeptide" RELATED [] synonym: "mutation causing partially characterised 3D structural change" RELATED [] synonym: "mutation causing uncharacterised 3D structural change" RELATED [] synonym: "sequence variant affecting 3D structure of polypeptide" EXACT [] synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT [] synonym: "sequence variant causing partially characterised 3D structural change" EXACT [] synonym: "sequence variant causing uncharacterised 3D structural change" EXACT [] synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT [] synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT [] is_obsolete: true replaced_by: SO:0001599 [Term] id: SO:1000112 name: sequence_variant_causing_no_3D_structural_change comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term. synonym: "mutation causing no 3D structural change" RELATED [] synonym: "sequence variant causing no 3D structural change" EXACT [] is_obsolete: true [Term] id: SO:1000115 name: sequence_variant_causing_complex_3D_structural_change comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing complex 3D structural change" RELATED [] synonym: "sequence variant causing complex 3D structural change" EXACT [] is_obsolete: true replaced_by: SO:0001600 [Term] id: SO:1000116 name: sequence_variant_causing_conformational_change comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing conformational change" RELATED [] synonym: "sequence variant causing conformational change" EXACT [] is_obsolete: true replaced_by: SO:0001601 [Term] id: SO:1000117 name: sequence_variant_affecting_polypeptide_function comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting polypeptide function" RELATED [] synonym: "sequence variant affecting polypeptide function" EXACT [] is_obsolete: true replaced_by: SO:0001554 [Term] id: SO:1000118 name: sequence_variant_causing_loss_of_function_of_polypeptide comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "loss of function of polypeptide" RELATED [] synonym: "mutation causing loss of function of polypeptide" RELATED [] synonym: "sequence variant causing loss of function of polypeptide" EXACT [] is_obsolete: true replaced_by: SO:0001559 [Term] id: SO:1000119 name: sequence_variant_causing_inactive_ligand_binding_site comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing inactive ligand binding site" RELATED [] synonym: "sequence variant causing inactive ligand binding site" EXACT [] is_obsolete: true replaced_by: SO:0001560 [Term] id: SO:1000120 name: sequence_variant_causing_inactive_catalytic_site comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing inactive catalytic site" RELATED [] synonym: "sequence variant causing inactive catalytic site" EXACT [] is_obsolete: true replaced_by: SO:0001618 [Term] id: SO:1000121 name: sequence_variant_causing_polypeptide_localization_change comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide localization change" RELATED [] synonym: "sequence variant causing polypeptide localization change" EXACT [] is_obsolete: true replaced_by: SO:0001558 [Term] id: SO:1000122 name: sequence_variant_causing_polypeptide_post_translational_processing_change comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide post translational processing change" RELATED [] synonym: "polypeptide post-translational processing affected" EXACT [] synonym: "sequence variant causing polypeptide post translational processing change" EXACT [] is_obsolete: true replaced_by: SO:0001562 [Term] id: SO:1000123 name: polypeptide_post_translational_processing_affected synonym: "polypeptide_post-translational_processing_affected" RELATED [] is_obsolete: true [Term] id: SO:1000124 name: sequence_variant_causing_partial_loss_of_function_of_polypeptide comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing partial loss of function of polypeptide" RELATED [] synonym: "partial loss of function of polypeptide" EXACT [] synonym: "sequence variant causing partial loss of function of polypeptide" EXACT [] is_obsolete: true replaced_by: SO:0001561 [Term] id: SO:1000125 name: sequence_variant_causing_gain_of_function_of_polypeptide comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "gain of function of polypeptide" EXACT [] synonym: "mutation causing gain of function of polypeptide" RELATED [] synonym: "sequence variant causing gain of function of polypeptide" EXACT [] is_obsolete: true replaced_by: SO:0001557 [Term] id: SO:1000126 name: sequence_variant_affecting_transcript_secondary_structure def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting transcript secondary structure" RELATED [] synonym: "sequence variant affecting transcript secondary structure" EXACT [] is_obsolete: true replaced_by: SO:0001596 [Term] id: SO:1000127 name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED [] synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT [] is_obsolete: true replaced_by: SO:0001597 [Term] id: SO:1000132 name: sequence_variant_effect def: "The effect of a change in nucleotide sequence." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09. synonym: "sequence variant effect" RELATED [] is_obsolete: true [Term] id: SO:1000134 name: sequence_variant_causing_polypeptide_fusion comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing polypeptide fusion" RELATED [] synonym: "sequence variant causing polypeptide fusion" EXACT [] is_obsolete: true replaced_by: SO:0001616 [Term] id: SO:1000136 name: autosynaptic_chromosome def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304] synonym: "(Drosophila)A" RELATED [] synonym: "autosynaptic chromosome" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000138 name: homo_compound_chromosome def: "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke] synonym: "homo compound chromosome" EXACT [] synonym: "homo-compound chromosome" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:1000140 name: hetero_compound_chromosome def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke] synonym: "hetero compound chromosome" EXACT [] synonym: "hetero-compound chromosome" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:1000141 name: chromosome_fission def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke] synonym: "chromosome fission" EXACT [] is_a: SO:1000028 ! intrachromosomal_mutation [Term] id: SO:1000142 name: dextrosynaptic_chromosome def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual] comment: Corrected spelling from dexstrosynaptic_chromosome to dextrosynaptic_chromosome on April 14, 2020 in response to GitHub request #447 synonym: "dextrosynaptic chromosome" EXACT [] is_a: SO:1000136 ! autosynaptic_chromosome [Term] id: SO:1000143 name: laevosynaptic_chromosome def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual] synonym: "laevosynaptic chromosome" EXACT [] is_a: SO:1000136 ! autosynaptic_chromosome [Term] id: SO:1000144 name: free_duplication def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual] synonym: "free duplication" EXACT [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:1000145 name: free_ring_duplication def: "A ring chromosome which is a copy of another chromosome." [SO:ke] synonym: "(Drosophila)R" RELATED [] synonym: "free ring duplication" EXACT [] is_a: SO:1000045 ! ring_chromosome is_a: SO:1000144 ! free_duplication intersection_of: SO:1000045 ! ring_chromosome intersection_of: has_quality SO:0001516 ! free relationship: has_quality SO:0001516 ! free [Term] id: SO:1000147 name: deficient_translocation def: "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] synonym: "(Drosophila)Df" RELATED [] synonym: "(Drosophila)DfT" RELATED [] synonym: "deficient translocation" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000044 ! chromosomal_translocation relationship: has_part SO:0000159 ! deletion [Term] id: SO:1000148 name: inversion_cum_translocation def: "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual] synonym: "(Drosophila)InT" RELATED [] synonym: "(Drosophila)T" RELATED [] synonym: "inversion cum translocation" EXACT [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000044 ! chromosomal_translocation relationship: has_part SO:1000036 ! inversion [Term] id: SO:1000149 name: bipartite_duplication def: "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual] synonym: "(Drosophila)bDp" RELATED [] synonym: "bipartite duplication" EXACT [] is_a: SO:1000031 ! interchromosomal_mutation is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:1000150 name: cyclic_translocation def: "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual] synonym: "cyclic translocation" EXACT [] is_a: SO:0002060 ! interchromosomal_translocation [Term] id: SO:1000151 name: bipartite_inversion def: "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual] synonym: "(Drosophila)bIn" RELATED [] synonym: "bipartite inversion" EXACT [] is_a: SO:1000030 ! chromosomal_inversion [Term] id: SO:1000152 name: uninverted_insertional_duplication def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] synonym: "(Drosophila)eDp" RELATED [] synonym: "uninverted insertional duplication" EXACT [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000153 name: inverted_insertional_duplication def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] synonym: "(Drosophila)iDp" RELATED [] synonym: "inverted insertional duplication" EXACT [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000154 name: insertional_duplication def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke] synonym: "(Drosophila)Dpp" RELATED [] synonym: "insertional duplication" EXACT [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:1000155 name: interchromosomal_transposition def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke] synonym: "(Drosophila)Tp" RELATED [] synonym: "interchromosomal transposition" EXACT [] is_a: SO:0000453 ! chromosomal_transposition is_a: SO:1000031 ! interchromosomal_mutation [Term] id: SO:1000156 name: inverted_interchromosomal_transposition def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual] synonym: "(Drosophila)iTp" RELATED [] synonym: "inverted interchromosomal transposition" EXACT [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000157 name: uninverted_interchromosomal_transposition def: "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] synonym: "(Drosophila)eTp" RELATED [] synonym: "uninverted interchromosomal transposition" EXACT [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000158 name: inverted_intrachromosomal_transposition def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] synonym: "(Drosophila)iTp" RELATED [] synonym: "inverted intrachromosomal transposition" EXACT [] is_a: SO:1000148 ! inversion_cum_translocation relationship: has_part SO:1000036 ! inversion [Term] id: SO:1000159 name: uninverted_intrachromosomal_transposition def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] synonym: "(Drosophila)eTp" RELATED [] synonym: "uninverted intrachromosomal transposition" EXACT [] is_a: SO:1000041 ! intrachromosomal_transposition intersection_of: SO:1000041 ! intrachromosomal_transposition intersection_of: has_part SO:0001514 ! direct relationship: has_part SO:0001514 ! direct [Term] id: SO:1000160 name: unoriented_insertional_duplication def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] comment: Flag - unknown in the definition. synonym: "(Drosophila)uDp" RELATED [] synonym: "unoriented insertional duplication" EXACT [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000161 name: unoriented_interchromosomal_transposition def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] comment: FLAG - term describes an unknown. synonym: "(Drosophila)uTp" RELATED [] synonym: "unorientated interchromosomal transposition" EXACT [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000162 name: unoriented_intrachromosomal_transposition def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] comment: FLAG - definition describes an unknown. synonym: "(Drosophila)uTp" RELATED [] synonym: "unorientated intrachromosomal transposition" EXACT [] is_a: SO:1000041 ! intrachromosomal_transposition [Term] id: SO:1000170 name: uncharacterized_chromosomal_mutation def: "A chromosome structure variant that has not been characterized." [] synonym: "uncharacterized chromosomal mutation" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000171 name: deficient_inversion def: "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke] synonym: "(Drosophila)Df" RELATED [] synonym: "(Drosophila)DfIn" RELATED [] synonym: "deficient inversion" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000030 ! chromosomal_inversion relationship: has_part SO:0000159 ! deletion relationship: has_part SO:1000036 ! inversion [Term] id: SO:1000173 name: tandem_duplication def: "A duplication consisting of 2 identical adjacent regions." [SO:ke] subset: DBVAR synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "tandem duplication" EXACT [] is_a: SO:1000035 ! duplication [Term] id: SO:1000175 name: partially_characterized_chromosomal_mutation def: "A chromosome structure variant that has not been characterized fully." [] synonym: "partially characterized chromosomal mutation" EXACT [] is_a: SO:1000170 ! uncharacterized_chromosomal_mutation [Term] id: SO:1000180 name: sequence_variant_affecting_gene_structure def: "A sequence_variant_effect that changes the gene structure." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting gene structure" RELATED [] synonym: "sequence variant affecting gene structure" EXACT [] is_obsolete: true replaced_by: SO:0001564 [Term] id: SO:1000181 name: sequence_variant_causing_gene_fusion def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causing gene fusion" RELATED [] synonym: "sequence variant causing gene fusion" EXACT [] is_obsolete: true replaced_by: SO:0001565 [Term] id: SO:1000182 name: chromosome_number_variation def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] synonym: "chromosome number variation" EXACT [] synonym: "Jannovar:chromosome_number_variation" EXACT VAR [http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html] is_a: SO:0000240 ! chromosome_variation [Term] id: SO:1000183 name: chromosome_structure_variation def: "An alteration of the genome that leads to a change in the structure or number of one or more chromosomes." [] synonym: "chromosome structure variation" EXACT [] synonym: "snpEff:CHROMOSOME_LARGE_DELETION" EXACT VAR [] xref: http://snpeff.sourceforge.net/SnpEff_manual.html is_a: SO:0000240 ! chromosome_variation [Term] id: SO:1000184 name: sequence_variant_causes_exon_loss def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causes exon loss" RELATED [] synonym: "sequence variant causes exon loss" EXACT [] is_obsolete: true [Term] id: SO:1000185 name: sequence_variant_causes_intron_gain def: "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation causes intron gain" RELATED [] synonym: "sequence variant causes intron gain" EXACT [] is_obsolete: true [Term] id: SO:1000186 name: sequence_variant_causing_cryptic_splice_donor_activation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "sequence variant causing cryptic splice donor activation" EXACT [] is_obsolete: true replaced_by: SO:0001571 [Term] id: SO:1001186 name: sequence_variant_causing_cryptic_splice_acceptor_activation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "sequence variant causing cryptic splice acceptor activation" EXACT [] is_obsolete: true replaced_by: SO:0001570 [Term] id: SO:1001187 name: alternatively_spliced_transcript def: "A transcript that is alternatively spliced." [SO:xp] synonym: "alternatively spliced transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000877 ! alternatively_spliced relationship: has_quality SO:0000877 ! alternatively_spliced [Term] id: SO:1001188 name: encodes_1_polypeptide def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke] synonym: "encodes 1 polypeptide" EXACT [] is_a: SO:0000463 ! encodes_alternately_spliced_transcripts [Term] id: SO:1001189 name: encodes_greater_than_1_polypeptide def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke] synonym: "encodes greater than 1 polypeptide" EXACT [] is_a: SO:0000463 ! encodes_alternately_spliced_transcripts [Term] id: SO:1001190 name: encodes_different_polypeptides_different_stop def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke] synonym: "encodes different polypeptides different stop" EXACT [] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001191 name: encodes_overlapping_peptides_different_start def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke] synonym: "encodes overlapping peptides different start" EXACT [] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001192 name: encodes_disjoint_polypeptides def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke] synonym: "encodes disjoint polypeptides" EXACT [] is_a: SO:1001189 ! encodes_greater_than_1_polypeptide [Term] id: SO:1001193 name: encodes_overlapping_polypeptides_different_start_and_stop def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke] synonym: "encodes overlapping polypeptides different start and stop" EXACT [] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001194 name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping is_obsolete: true [Term] id: SO:1001195 name: encodes_overlapping_peptides def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke] synonym: "encodes overlapping peptides" EXACT [] is_a: SO:1001189 ! encodes_greater_than_1_polypeptide [Term] id: SO:1001196 name: cryptogene def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma] is_a: SO:0000654 ! maxicircle_gene is_a: SO:0001431 ! cryptic_gene intersection_of: SO:0000654 ! maxicircle_gene intersection_of: has_quality SO:0000976 ! cryptic relationship: has_quality SO:0000976 ! cryptic [Term] id: SO:1001197 name: dicistronic_primary_transcript def: "A primary transcript that has the quality dicistronic." [SO:xp] synonym: "dicistronic primary transcript" EXACT [] is_a: SO:0000079 ! dicistronic_transcript is_a: SO:0000631 ! polycistronic_primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:1001217 name: member_of_regulon def: "A gene that is a member of a group of genes that are either regulated or transcribed together." [] synonym: "member of regulon" EXACT [] is_a: SO:0000081 ! gene_array_member [Term] id: SO:1001244 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED [] is_obsolete: true [Term] id: SO:1001246 name: CDS_independently_known def: "A CDS with the evidence status of being independently known." [SO:xp] synonym: "CDS independently known" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000906 ! independently_known relationship: has_quality SO:0000906 ! independently_known [Term] id: SO:1001247 name: orphan_CDS def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma] synonym: "orphan CDS" EXACT [] is_a: SO:1001254 ! CDS_predicted intersection_of: SO:1001254 ! CDS_predicted intersection_of: has_origin SO:0000910 ! orphan relationship: has_origin SO:0000910 ! orphan [Term] id: SO:1001249 name: CDS_supported_by_domain_match_data def: "A CDS that is supported by domain similarity." [SO:xp] synonym: "CDS supported by domain match data" EXACT [] is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: has_quality SO:0000908 ! supported_by_domain_match relationship: has_quality SO:0000908 ! supported_by_domain_match [Term] id: SO:1001251 name: CDS_supported_by_sequence_similarity_data def: "A CDS that is supported by sequence similarity data." [SO:xp] synonym: "CDS supported by sequence similarity data" EXACT [] is_a: SO:1001254 ! CDS_predicted intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000907 ! supported_by_sequence_similarity relationship: has_quality SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:1001254 name: CDS_predicted def: "A CDS that is predicted." [SO:ke] synonym: "CDS predicted" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000732 ! predicted relationship: has_quality SO:0000732 ! predicted [Term] id: SO:1001255 name: status_of_coding_sequence is_obsolete: true [Term] id: SO:1001259 name: CDS_supported_by_EST_or_cDNA_data def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp] synonym: "CDS supported by EST or cDNA data" EXACT [] is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: has_quality SO:0000909 ! supported_by_EST_or_cDNA relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA [Term] id: SO:1001260 name: internal_Shine_Dalgarno_sequence def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke] synonym: "internal Shine Dalgarno sequence" EXACT [] synonym: "internal Shine-Dalgarno sequence" EXACT [] is_a: SO:0000243 ! internal_ribosome_entry_site is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001261 name: recoded_mRNA def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] synonym: "recoded mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000881 ! recoded relationship: has_quality SO:0000881 ! recoded [Term] id: SO:1001262 name: minus_1_translationally_frameshifted def: "An attribute describing a translational frameshift of -1." [SO:ke] synonym: "minus 1 translationally frameshifted" EXACT [] is_a: SO:0000887 ! translationally_frameshifted [Term] id: SO:1001263 name: plus_1_translationally_frameshifted def: "An attribute describing a translational frameshift of +1." [SO:ke] synonym: "plus 1 translationally frameshifted" EXACT [] is_a: SO:0000887 ! translationally_frameshifted [Term] id: SO:1001264 name: mRNA_recoded_by_translational_bypass def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] synonym: "mRNA recoded by translational bypass" EXACT [] is_a: SO:1001261 ! recoded_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass relationship: has_quality SO:0000886 ! recoded_by_translational_bypass [Term] id: SO:1001265 name: mRNA_recoded_by_codon_redefinition def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma] synonym: "mRNA recoded by codon redefinition" EXACT [] is_a: SO:1001261 ! recoded_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000882 ! codon_redefined relationship: has_quality SO:0000882 ! codon_redefined [Term] id: SO:1001266 name: stop_codon_redefinition_as_selenocysteine is_obsolete: true [Term] id: SO:1001267 name: stop_codon_readthrough is_obsolete: true [Term] id: SO:1001268 name: recoding_stimulatory_region def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:recoding_stimulatory_region" EXACT [] synonym: "recoding stimulatory region" EXACT [] synonym: "recoding stimulatory signal" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:1001269 name: four_bp_start_codon def: "A non-canonical start codon with 4 base pairs." [SO:ke] synonym: "4bp start codon" EXACT [] synonym: "four bp start codon" EXACT [] is_a: SO:0000680 ! non_canonical_start_codon [Term] id: SO:1001270 name: stop_codon_redefinition_as_pyrrolysine is_obsolete: true [Term] id: SO:1001271 name: archaeal_intron def: "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma] comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism. synonym: "archaeal intron" EXACT [] is_a: SO:0001216 ! endonuclease_spliced_intron [Term] id: SO:1001272 name: tRNA_intron def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] comment: Could be a cross product with Gene ontology, GO:0006388. synonym: "pre-tRNA intron" EXACT [] synonym: "tRNA intron" EXACT [] is_a: SO:0001216 ! endonuclease_spliced_intron [Term] id: SO:1001273 name: CTG_start_codon def: "A non-canonical start codon of sequence CTG." [SO:ke] synonym: "CTG start codon" EXACT [] is_a: SO:0000680 ! non_canonical_start_codon [Term] id: SO:1001274 name: SECIS_element def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031] synonym: "SECIS element" EXACT [] xref: http://en.wikipedia.org/wiki/SECIS_element "wiki" is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001275 name: retron def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma] is_a: SO:0001411 ! biological_region [Term] id: SO:1001277 name: three_prime_recoding_site def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke] synonym: "three prime recoding site" EXACT [] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001279 name: three_prime_stem_loop_structure def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke] synonym: "three prime stem loop structure" EXACT [] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001280 name: five_prime_recoding_site def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke] synonym: "five prime recoding site" EXACT [] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001281 name: flanking_three_prime_quadruplet_recoding_signal def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke] synonym: "flanking three prime quadruplet recoding signal" EXACT [] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001282 name: UAG_stop_codon_signal def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke] synonym: "UAG stop codon signal" EXACT [] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001283 name: UAA_stop_codon_signal def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke] synonym: "UAA stop codon signal" EXACT [] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001284 name: regulon def: "A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products." [ISBN:0198506732, PMID:32665585] comment: Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300 subset: SOFA xref: http://en.wikipedia.org/wiki/Regulon "wiki" is_a: SO:0005855 ! gene_group relationship: has_part SO:0002300 ! unit_of_gene_expression [Term] id: SO:1001285 name: UGA_stop_codon_signal def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke] synonym: "UGA stop codon signal" EXACT [] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001286 name: three_prime_repeat_recoding_signal def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke] synonym: "three prime repeat recoding signal" EXACT [] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001287 name: distant_three_prime_recoding_signal def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract] synonym: "distant three prime recoding signal" EXACT [] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001288 name: stop_codon_signal def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke] comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal. synonym: "stop codon signal" EXACT [] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:2000061 name: databank_entry def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke] subset: SOFA synonym: "accession" RELATED [] synonym: "databank entry" EXACT [] is_a: SO:0000695 ! reagent [Term] id: SO:3000000 name: gene_segment def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add] comment: Requested by tracker 2021594, July 2008, by Alex. synonym: "gene segment" EXACT [] is_a: SO:0000842 ! gene_component_region [Typedef] id: adjacent_to name: adjacent_to def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke] subset: SOFA [Typedef] id: associated_with name: associated_with comment: This relationship is vague and up for discussion. [Typedef] id: complete_evidence_for_feature name: complete_evidence_for_feature def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke] comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: connects_on name: connects_on def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267] comment: Example: A splice_junction connects_on exon, exon, mature_transcript. created_by: kareneilbeck creation_date: 2010-10-14T01:38:51Z [Typedef] id: contained_by name: contained_by def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267] comment: The inverse is contains. Example: intein contained_by immature_peptide_region. is_transitive: true created_by: kareneilbeck creation_date: 2010-10-14T01:26:16Z [Typedef] id: contains name: contains def: "The inverse of contained_by." [PMID:20226267] comment: Example: pre_miRNA contains miRNA_loop. is_transitive: true created_by: kareneilbeck creation_date: 2010-10-14T01:32:15Z [Typedef] id: derives_from name: derives_from subset: SOFA is_transitive: true [Typedef] id: disconnected_from name: disconnected_from def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267] created_by: kareneilbeck creation_date: 2010-10-14T01:42:10Z [Typedef] id: edited_from name: edited_from created_by: kareneilbeck creation_date: 2009-08-19T02:19:45Z [Typedef] id: edited_to name: edited_to created_by: kareneilbeck creation_date: 2009-08-19T02:19:11Z [Typedef] id: evidence_for_feature name: evidence_for_feature def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true [Typedef] id: exemplar_of name: exemplar_of def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke] comment: Tracker id: 2594157. [Typedef] id: finished_by name: finished_by def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267] comment: Example CDS finished_by stop_codon. created_by: kareneilbeck creation_date: 2010-10-14T01:45:45Z [Typedef] id: finishes name: finishes def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267] comment: Example: stop_codon finishes CDS. created_by: kareneilbeck creation_date: 2010-10-14T02:17:53Z [Typedef] id: gained name: gained def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke] comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence. created_by: kareneilbeck creation_date: 2011-06-28T12:51:10Z [Typedef] id: genome_of name: genome_of [Typedef] id: guided_by name: guided_by created_by: kareneilbeck creation_date: 2009-08-19T02:27:04Z [Typedef] id: guides name: guides created_by: kareneilbeck creation_date: 2009-08-19T02:27:24Z [Typedef] id: has_integral_part name: has_integral_part def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: mRNA has_integral_part CDS. is_a: has_part ! has_part created_by: kareneilbeck creation_date: 2009-08-19T12:01:46Z [Typedef] id: has_origin name: has_origin [Typedef] id: has_part name: has_part def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: operon has_part gene. [Typedef] id: has_quality name: has_quality comment: The relationship between a feature and an attribute. [Typedef] id: homologous_to name: homologous_to subset: SOFA is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: integral_part_of name: integral_part_of def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: exon integral_part_of transcript. is_a: part_of ! part_of created_by: kareneilbeck creation_date: 2009-08-19T12:03:28Z [Typedef] id: is_consecutive_sequence_of name: is_consecutive_sequence_of def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267] comment: Example: region is consecutive_sequence of base. created_by: kareneilbeck creation_date: 2010-10-14T02:19:48Z [Typedef] id: lost name: lost def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke] comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence. created_by: kareneilbeck creation_date: 2011-06-28T12:53:16Z [Typedef] id: maximally_overlaps name: maximally_overlaps def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267] comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR. created_by: kareneilbeck creation_date: 2010-10-14T01:34:48Z [Typedef] id: member_of name: member_of comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. subset: SOFA is_transitive: true is_a: part_of ! part_of [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] subset: SOFA is_a: homologous_to ! homologous_to [Typedef] id: orthologous_to name: orthologous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: overlaps name: overlaps def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267] comment: Example: coding_exon overlaps CDS. created_by: kareneilbeck creation_date: 2010-10-14T01:33:15Z [Typedef] id: paralogous_to name: paralogous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: part_of name: part_of def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: amino_acid part_of polypeptide. subset: SOFA is_transitive: true [Typedef] id: partial_evidence_for_feature name: partial_evidence_for_feature def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: position_of name: position_of [Typedef] id: processed_from name: processed_from def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA processed_from miRNA_primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:14:00Z [Typedef] id: processed_into name: processed_into def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA_primary_transcript processed into miRNA. created_by: kareneilbeck creation_date: 2009-08-19T12:15:02Z [Typedef] id: recombined_from name: recombined_from created_by: kareneilbeck creation_date: 2009-08-19T02:21:03Z [Typedef] id: recombined_to name: recombined_to created_by: kareneilbeck creation_date: 2009-08-19T02:20:07Z [Typedef] id: sequence_of name: sequence_of [Typedef] id: similar_to name: similar_to subset: SOFA is_symmetric: true [Typedef] id: started_by name: started_by def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267] comment: Example: CDS started_by start_codon. created_by: kareneilbeck creation_date: 2010-10-14T01:43:55Z [Typedef] id: starts name: starts def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267] comment: Example: start_codon starts CDS. created_by: kareneilbeck creation_date: 2010-10-14T01:47:53Z [Typedef] id: trans_spliced_from name: trans_spliced_from created_by: kareneilbeck creation_date: 2009-08-19T02:22:14Z [Typedef] id: trans_spliced_to name: trans_spliced_to created_by: kareneilbeck creation_date: 2009-08-19T02:22:00Z [Typedef] id: transcribed_from name: transcribed_from def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: primary_transcript transcribed_from gene. created_by: kareneilbeck creation_date: 2009-08-19T12:05:39Z [Typedef] id: transcribed_to name: transcribed_to def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1] comment: Example: gene transcribed_to primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:08:24Z [Typedef] id: translates_to name: translates_to def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: codon translates_to amino_acid. created_by: kareneilbeck creation_date: 2009-08-19T12:11:53Z [Typedef] id: translation_of name: translation_of def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: Polypeptide translation_of CDS. created_by: kareneilbeck creation_date: 2009-08-19T12:09:59Z [Typedef] id: variant_of name: variant_of def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.