The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
corresponds to, nucleotide by nucleotide
covalently connected 5prime to 3prime (transitive)
covalently connected 3prime to 5prime (transitive)
Pairwise interaction of the sugar edge with a phosphate unit. Only occurs with G.
3-(3-amino-3-carboxypropyl)uridine residue
5-carboxymethylaminomethyl-2-thiouridine residue
5-methoxycarbonylmethyl-2-thiouridine residue
A base pair consists of a pair of nucleotide residues that interact by nucleoside edge to nucleoside edge hydrogen bonds.
A ribose ring that does not have a hydroxy group at the 2prime position.
A family_1_base_pair is an RNAO_base_pair in which the two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
A family_2_base_pair is an RNAO_base_pair in which the two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
A family_3_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Hoogsteen edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
Forbidden pairings (Watson-Crick edge first); CA, UC, AC, AA, GC, GU.
A family_4_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Hoogsteen edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
Forbidden are the following pairings (Watson-Crick edge first); CU, UC, AC, AU, GC, GA.
A family_5_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
Forbidden is the pairing where G presents the Watson-Crick edge and A presents the sugar edge.
A family_6_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
A family_7_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
Forbidden pairings are: CC, CU, CA, UA, UC, UG, UU, AC, AU, AA and GU.
A family_8_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
A family_9_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
A family_10_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
A family_11_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Sugar edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other.
A family_12_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Sugar edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other.
Excluded are CA, CC, CU, CG, and UA, UC, UU, UG.
An RNAO_base_pair which has cis-Watson--Crick pairing and where the participating bases are AU, CG, GC or UA.
A nucleobase is an N-heterocyclic group that forms part of a nucleoside residue.
A phosphate group consists of a phosphorus atom doubly-bonded to two oxygen atoms and singly-bonded to two oxygen atoms, both of which have a free valence. Unlike the phosphate group in ChEBI (CHEBI:32958), the RNAO phosphate group has two free valences.
A ribonucleoside consists of a nitrogen heterocycle (a nucleobase) covalently bonded to a ribose ring, with free valences at the 3prime oxgen and 5prime oxygen atoms on the ring.
A ribonucleotide residue consists of a nitrogen heterocyclic group covalently bonded to the 1prime position of a ribose ring and a phosphate group covalently bonded the 5' oxygen of the ribose ring. There are free valances at the 3'-oxygen of the ribose and on the phosphorus atom of the phosphate group where the ribonucleotide is connected to two other ribonucleotides in the chain.
A ribose ring is a furanose ring with free valences at the 4prime position (to bond to the nucleobase), and the 3prime and 5prime positions.
A purine nucleobase is a heterocyclic group consisting of a five-membered aromatic ring ortho,para-fused to a six-membered aromatic ring and where the atoms at the 1-, 3-, 7- and 9- positions are nitrogen atoms.
A pyrimidine nucleobase is a heterocyclic group consisting of a six-membered ring where the atoms at the 1- and 3-positions are nitrogen atoms.
A cytosine nucleobase is a pyrimidine that contains a 4-amino group and a 2-oxo group and has a free valence at the 1-position.
A uracil nucleobase is a pyrimidine nucleobase that contains a 2-oxo group and a 4-oxo group and has a free valence at the 1-position.
An adenine nucleobase is a purine nucleobase that contains a 6-amino group and a free valence at the 9-position.
A guanine nucleobase is a purine nucleobase that contains a 2-amino group, a 6-oxo group and a free valence at the 9-position.
A nucleoside edge is either a Watson-Crick edge or a Hoogsteen edge or a sugar edge.
The Watson-Crick edge of a nucleobase is the preferred edge along which it undergoes hydrogen bonding with other nucleobases.
The Hoogsteen edge of a nucleobase is the edge of the nucleobase which is not adjacent to the 2prime-hydroxyl group on the ribose ring.
The sugar edge of a nucleoside consists of the edge of the nucleobase adjacent ot the 2prime-hydroxyl group on the ribose ring and the 2prime-hydroxyl group on the ribose ring.
A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair.
A collection of one or more nucleotides that are not involved in base pairing.
A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair.
A contiguous sequence of nucleotide residues that directly links the two halves of an unbroken stem (but does not participate in the stem); this structure is also known as a "hairpin loop". Because a terminal loop may also participate in other inter-base interactions, (a) it is defined relative to a particular unbroken_stem, and (b) it is not implicitly defined as unpaired (or paired).
A collection of nucleotide residues that link two given unbroken_stems.
this term encompasses the concepts of "bulge" and "mismatch" as well. Again, this term is defined relative to two particular unbroken_stems and does not imply unpairedness (or pairedness).
A collection of nucleotide residues consisting of all and only the nucleotide regions that link more than two unbroken stems such that each region links exactly two unbroken stems. This term is defined relative to the particular unbroken_stems involved and, again, does not imply anything about the pairedness/unpairedness of the bases in this region. The degree of a junction is a property (e.g. 3-junction, 4-junction), so the different degrees do not get separate entries in the ontology.
A sequence_region bounded at one end by the 5prime or 3prime end of the molecule, and at the other by an unbroken_stem.
A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides.
The spatial arrangement of the atoms in a molecule or molecular part affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds.
A conformation that inheres in an RNA base pair. It may be cis- or trans- depending on the orientations of the ribose rings relative to the edge-edge interaction of the nucleobases.
PERSON: Colin Batchelor, based on the Leontis-Westhof classification.
A base pair conformation where the ribose rings are on the same side of a plane drawn through the middle of the edge-edge hydrogen bonds.
A base pair conformation where the ribose rings are on opposite sides of a plane drawn through the middle of the edge-edge hydrogen bonds.
A conformation that inheres in an nucleoside based on the rotation of the nucleobase about the glycosidic torsion angle χ with the furanose.
A syn nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented towards the ribose due to rotation about the glycosidic torsion angle χ. From χ = 0°, where the plane of the base is aligned with the O4’-C1’ bond in a direction towards the O4’ atom, the syn conformation covers the remaining rotations of ±90°: χ = [-90°, 90°].
A anti nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented away from the ribose due to rotation about the glycosidic torsion angle χ. From χ = 180°, where the plane of the base is aligned with the O4’-C1’ bond in a direction away from the O4’ atom, the anti conformation covers a rotations of ±90°: χ = [-180°, 90°].
An envelope conformation is a furan ring conformation in which only one of the five fruan atoms (C1’, C2’, C3’, C4’ or O4’) is out of the plane formed by the four others.
An envelope conformation is a furan ring conformation in which two atoms are in opposite sides of the plane formed by the remaining three.
A furan ring conformation is a conformation that inheres in a furan ring and is characterized by the values of torsion angles: θ0-4.
C2prime-endo pucker (2E conformation) is an envelope conformation in which the C2prime atom is above the plane formed by the other 4 atoms.
C3prime-endo pucker (An 3E conformation) is an envelope conformation in which the C3prime atom is above the plane formed by the other 4 atoms.
C4prime-exo pucker (E4 conformation) is an envelope conformation in which the C4prime atom is below the plane formed by the other 4 atoms.
C3prime-endo - C4prime exo pucker (3E4 conformation) is a twist conformation in which the C3prime atom is above the plane and the C4prime atom is below the plane.
C3prime-endo - C2prime exo pucker (3E2 conformation) is a twist conformation in which the C3prime atom is above the plane and the C2prime atom is below the plane.
A base stack consists of a pair of nucleotides that interact by London dispersion inter-molecular interactions between their nucleobases such that one base is stacked on top of the other.
An adjacent base stack is a base stack between a pair of sequence-adjacent nucleotides.
A non-adjacent base stack is a base stack between a pair of non sequence-adjacent nucleotides.
A base stack orientation is a conformation that inheres in a base stack by virtue of the orientation of the nucleobases relative to i) the alignment of base normals and ii) their sequence adjacency.
An base stack straight orientation is a base stack orientation in which the normals of both bases are aligned in the same direction.
A base stack reverse orientation is a base stack orientation in which the normals of both bases are aligned in the opposite directions.
A base stack base-normal orientation is a base stack orientation that depends on the relative orientation of the base normals.
A base stack above orientation is a base stack orientation in which the second base (B) is in the same direction as the normal to the first base (A).
A base stack below orientation is a base stack orientation in which the normal of the second base (B) is directed towards the first base (A).
A base stack sequence adjacency is a base stack orientation that depends on whether the stacked nucleobases are part of nucleotides that are sequence adjacent or not.
A base stack adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are sequence adjacent.
base stack non-adjacent base orientation
A base stack non-adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are not sequence adjacent.
A furanose ring is a ring that consists of four carbon and one oxygen atom and has free valences at each carbon position.
An upward base stack is a base stack that exhibits both an straight orientation and an above orientation.
A downward base stack is a base stack that exhibits both an straight orientation and a below orientation.
An inward base stack is a base stack that exhibits both a reverse orientation and an above orientation.
An outward base stack is a base stack that exhibits both a reverse orientation and a below orientation.
a submolecule is a part of a molecule that consists of covalently bonded sum of a collection of atoms.
a part of molecule is some part of a molecule.
A boundary is a region at which connections can be formed.
adenine nucleobase functional derivative
guanine nucleobase functional derivative
cytosine nucleobase functional derivative
adenosine ribonucleoside residue functional derivative
guanosine ribonucleoside residue functional derivative
cytidine ribonucleoside residue functional derivative
uridine ribonucleoside residue functional derivative
cytidylate residue functional derivative
pyrimidine nucleobase functional derivative
purine ribonucleoside residue functional derivative
pyrimidine ribonucleoside residue functional derivative
purine ribonucleotide functional derivative
pyrimidine ribonucleotide functional derivative
N6,N6,2prime-O-trimethyladenosine residue
N6,N6,2prime-O-trimethyladenylate residue
N4,N4,2prime-O-trimethylcytidine residue
N4,N4,2prime-O-trimethylcytidylate residue
N2,N2,2prime-O-trimethylguanosine residue
N2,N2,2prime-O-trimethylguanylate residue
2-methylthio-N6-methyladenine nucleobase
N4-acetyl-2prime-O-methylcytidine residue
N4-acetyl-2prime-O-methylcytidylate residue
5-formyl-2prime-O-methylcytidine residue
5-formyl-2prime-O-methylcytidylate residue
5-formyl-2prime-O-methyluridylate residue
5-carboxymethylaminomethyluracil nucleobase
5-carboxymethylaminomethyluridine residue
5-carboxymethylaminomethyluridylate residue
5-carboxymethylaminomethyl-2prime-O-methyluridine residue
5-carboxymethylaminomethyl-2prime-O-methyluridylate residue
5-carboxymethylaminomethyl-2-thiouracil nucleobase
5-carboxymethylaminomethyl-2-thiouridylate residue
5-carboxymethylaminomethyl-2-selenouracil nucleobase
5-carboxymethylaminomethyl-2-selenouridine residue
5-carboxymethylaminomethyl-2-selenouridylate residue
5-methylaminomethyl-2-thiouracil nucleobase
5-methylaminomethyl-2-thiouridine residue
5-methylaminomethyl-2-thiouridylate residue
5-methylaminomethyl-2-selenouracil nucleobase
5-methylaminomethyl-2-selenouridine residue
5-methylaminomethyl-2-selenouridylate residue
5-carbamoylmethyl-2prime-O-methyluridine residue
5-carbamoylmethyl-2prime-O-methyluridylate residue
N6-methyl-N6-threonylcarbamoyladenine nucleobase
N6-methyl-N6-threonylcarbamoyladenosine residue
N6-methyl-N6-threonylcarbamoyladenylate residue
2-methylthio-N6-threonylcarbamoyladenine nucleobase
2-methylthio-N6-threonylcarbamoyladenosine residue
2-methylthio-N6-threonylcarbamoyladenosylate residue
2prime-O-ribosyladenylate phosphate residue
2prime-O-ribosyladenosine phosphate residue
2prime-O-ribosylguanosine phosphate residue
2prime-O-ribosylguanylate phosphate residue
2-methylthio-N6-isopentenyladenine nucleobase
2-methylthio-N6-isopentenyladenosine residue
5-methoxycarbonylmethyluracil nucleobase
5-methoxycarbonylmethyluridylate residue
5-methoxycarbonylmethyl-2-thiouracil nucleobase
5-methoxycarbonylmethyl-2-thiouridylate residue
5-methoxycarbonylmethyl-2prime-O-methyluridine residue
5-methoxycarbonylmethyl-2prime-O-methyluridylate residue
3-(3-amino-3-carboxypropyl)uridylate residue
3-(3-amino-3-carboxypropyl)methyluridine residue
3-(3-amino-3-carboxypropyl)methyluridylate residue
1-methyl-3-(3-amino-3-carboxypropyl)uracil nucleobase
1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine residue
1-methyl-3-(3-amino-3-carboxypropyl)pseudouridylate residue
5-(carboxyhydroxymethyl)uracil nucleobase
5-(carboxyhydroxymethyl)uridylate residue
uracil 5-oxyaceticacid methyl ester nucleobase
uridine 5-oxyacetic acid methyl ester residue
uridylate 5-oxyacetic acid methyl ester residue
5-(carboxyhydroxymethyl)uracil methyl ester nucleobase
5-(carboxyhydroxymethyl)uridine methyl ester residue
5-(carboxyhydroxymethyl)uridylate methyl ester residue
N6-(cis-hydroxyisopentenyl)adenine nucleobase
N6-(cis-hydroxyisopentenyl)adenosine residue
N6-(cis-hydroxyisopentenyl)adenylate residue
2-methylthio-N6-(cis-hydroxyisopentenyl)adenine nucleobase
2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine residue
2-methylthio-N6-(cis-hydroxyisopentenyl)adenylate residue
Not in ChEBI. It derives from 2-aminopentanoic acid (norvaline). There are two enantiomers.
N6-hydroxynorvalylcarbamoyladenine nucleobase
N6-hydroxynorvalylcarbamoyladenosine residue
N6-hydroxynorvalylcarbamoyladenylate residue
2-methylthio-N6-hydroxynorvalylcarbamoyladenine nucleobase
2-methylthio-N6-hydroxynorvalylcarbamoyladenosine residue
2-methylthio-N6-hydroxynorvalylcarbamoyladenylate residue
Not in ChEBI. It derives from agmatine (CHEBI:17431; N-(4-aminobutyl)guanidine).
N2,7,2prime-O-trimethylguanosine residue
N2,7,2prime-O-trimethylguanylate residue
5-isopentenylaminomethyluracil nucleobase
5-isopentenylaminomethyluridylate residue
5-isopentenylaminomethyl-2prime-O-methyluridine residue
5-isopentenylaminomethyl-2prime-O-methyluridylate residue
5-isopentenylaminomethyl-2-thiouracil nucleobase
5-isopentenylaminomethyl-2-thiouridine residue
5-isopentenylaminomethyl-2-thiouridylate residue
undermodified hydroxywybutosinylate residue
10-glutamyl-4-demethylwyosinylate residue
10-glutamylmethylesterwyosinylate residue
2,3-epoxycyclopenta-(4,5-diol)-1-yl group
N2,N2,7-trimethylguanosine cap structure
3-(3-amino-3-carboxypropyl)uracil nucleobase