Family,Domain,Seed domains,Full region domains,Rfam ID,Description,RNA type
RF00001,Mixed/Eukaryota,"Bacteria (48.6%), Eukaryota (45.51%), Archaea (5.9%)","Eukaryota (95.39%), Bacteria (4.52%), Archaea (0.09%)",5S_rRNA,5S ribosomal RNA,Gene; rRNA;
RF00005,Mixed/Eukaryota,"Eukaryota (78.2%), Bacteria (17.3%), Archaea (3.46%), Viruses (1.05%)","Eukaryota (90.4%), Bacteria (9.16%), Archaea (0.25%), Viruses (0.19%)",tRNA,tRNA,Gene; tRNA;
RF01689,unclassified sequences/Bacteria,unclassified sequences (100.0%),"Bacteria (97.7%), Eukaryota (2.3%)",AdoCbl-II,AdoCbl-II (Cobalamin/B12) riboswitch aptamer,Cis-reg; riboswitch;
RF01706,unclassified sequences/Mixed,unclassified sequences (100.0%),"Bacteria (82.35%), Eukaryota (17.65%)",Gut-1,Gut-1 RNA,Gene; sRNA;
RF01712,unclassified sequences/Bacteria,"unclassified sequences (97.06%), Bacteria (2.94%)",Bacteria (100.0%),Methylobacterium-1,Methylobacterium-1 RNA,Gene; sRNA;
RF01714,unclassified sequences/Archaea,unclassified sequences (100.0%),Archaea (100.0%),Ocean-V,Ocean-V RNA,Gene; sRNA;
RF01717,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),PhotoRC-II,PhotoRC-II RNA,Cis-reg;
RF01718,unclassified sequences/Bacteria,"unclassified sequences (93.75%), Bacteria (6.25%)",Bacteria (100.0%),Polynucleobacter-1,Polynucleobacter-1 RNA,Gene; sRNA;
RF01725,unclassified sequences/Bacteria,"unclassified sequences (91.61%), Bacteria (7.91%), Other (0.48%)","Bacteria (98.94%), Eukaryota (1.06%)",SAM-I-IV,SAM-I/IV (S-adenosyl methionine) riboswitch aptamer,Cis-reg; riboswitch;
RF01729,unclassified sequences/Mixed,unclassified sequences (100.0%),"Bacteria (75.0%), Eukaryota (25.0%)",Termite-flg,Termite-flg RNA,Cis-reg;
RF01730,unclassified sequences/Mixed,unclassified sequences (100.0%),,Termite-leu,Termite-leu RNA,Cis-reg;
RF01739,unclassified sequences/Bacteria,"unclassified sequences (96.7%), Bacteria (3.19%), Viruses (0.11%)","Bacteria (96.9%), Viruses (1.72%), Eukaryota (1.38%)",Glutamine,Glutamine riboswitch aptamer (glnA leader),Cis-reg; riboswitch;
RF01745,unclassified sequences/Viruses,"unclassified sequences (98.79%), Bacteria (1.21%)","Viruses (95.0%), Bacteria (5.0%)",manA,manA RNA,Cis-reg;
RF01751,unclassified sequences/Eukaryota,unclassified sequences (100.0%),Eukaryota (100.0%),potC,potC RNA,Cis-reg;
RF01761,unclassified sequences/Mixed,"unclassified sequences (98.15%), Viruses (1.85%)","Viruses (58.57%), Eukaryota (41.43%)",wcaG,wcaG RNA,Cis-reg;
RF01762,unclassified sequences/Bacteria,unclassified sequences (100.0%),"Bacteria (94.03%), Eukaryota (5.97%)",whalefall-1,Whalefall-1 RNA,Gene; sRNA;
RF01810,unclassified sequences/Bacteria,"unclassified sequences (90.0%), Bacteria (10.0%)",Bacteria (100.0%),pntA,pntA sRNA,Gene; sRNA;
RF01815,unclassified sequences/Bacteria,unclassified sequences (100.0%),"Bacteria (97.96%), Eukaryota (2.04%)",rpsB,rpsB sRNA,Gene; sRNA;
RF01852,Mixed,"Bacteria (68.81%), Eukaryota (29.36%), Archaea (1.83%)","Bacteria (55.11%), Eukaryota (44.32%), Viruses (0.4%), Archaea (0.16%)",tRNA-Sec,Selenocysteine transfer RNA,Gene; tRNA;
RF02034,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),IMES-1,IMES-1 RNA motif,Gene;
RF02035,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),IMES-2,IMES-2 RNA motif,Gene;
RF02036,unclassified sequences/Mixed,unclassified sequences (100.0%),,IMES-3,IMES-3 RNA motif,Gene;
RF02037,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),IMES-4,IMES-4 RNA motif,Gene;
RF02678,unclassified sequences/Viruses,"unclassified sequences (98.06%), Other (1.29%), Bacteria (0.65%)",Viruses (100.0%),Hatchet,Hatchet ribozyme,Gene; ribozyme;
RF02681,unclassified sequences/Mixed,"unclassified sequences (99.12%), Bacteria (0.88%)","Bacteria (88.24%), Archaea (5.88%), Eukaryota (5.88%)",Twister-sister,Twister_sister_ribozyme,Gene; ribozyme;
RF02684,unclassified sequences/Mixed,"unclassified sequences (98.14%), Bacteria (1.4%), Eukaryota (0.47%)","Bacteria (84.62%), Eukaryota (15.38%)",Twister-P5,Type-P5 twister ribozyme,Gene; ribozyme;
RF02686,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-6,RAGATH-6 RNA,Gene; ribozyme;
RF02687,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),RAGATH-8,RAGATH-8 RNA,Gene; sRNA;
RF02915,unclassified sequences/Mixed,"unclassified sequences (91.95%), Bacteria (8.05%)","Bacteria (74.29%), Eukaryota (22.86%), Viruses (2.86%)",DUF3800-VI,DUF3800-VI RNA,Cis-reg;
RF02918,unclassified sequences/Bacteria,"unclassified sequences (93.33%), Bacteria (6.67%)",Bacteria (100.0%),MDR-NUDIX,MDR-NUDIX RNA,Cis-reg;
RF02933,unclassified sequences/Bacteria,"unclassified sequences (94.29%), Bacteria (5.71%)",Bacteria (100.0%),ARRPOF,ARRPOF RNA,Gene; sRNA;
RF02939,unclassified sequences/Mixed,unclassified sequences (100.0%),,COG2908,COG2908 RNA,Cis-reg;
RF02941,unclassified sequences/Mixed,unclassified sequences (100.0%),,COG3943,COG3943 RNA,Gene; sRNA;
RF02946,unclassified sequences/Mixed,unclassified sequences (100.0%),,cow-rumen-1,cow-rumen-1 RNA,Gene; sRNA;
RF02947,unclassified sequences/Eukaryota,unclassified sequences (100.0%),Eukaryota (100.0%),cow-rumen-2,cow-rumen-2 RNA,Gene; sRNA;
RF02948,unclassified sequences/Mixed,unclassified sequences (100.0%),,cow-rumen-4,cow-rumen-4 RNA,Gene; sRNA;
RF02950,unclassified sequences/Mixed,unclassified sequences (100.0%),,D12-methyl,D12-methyl RNA,Gene; sRNA;
RF02953,unclassified sequences/Mixed,unclassified sequences (100.0%),,DUF1874,DUF1874 RNA,Cis-reg;
RF02954,unclassified sequences/Bacteria,"unclassified sequences (98.84%), Bacteria (1.16%)",Bacteria (100.0%),DUF3577,DUF3577 RNA,Cis-reg;
RF02956,unclassified sequences/Mixed,"unclassified sequences (98.41%), Bacteria (1.59%)",,DUF2693,DUF2693 RNA,Gene; sRNA;
RF02959,unclassified sequences/Bacteria,unclassified sequences (100.0%),"Bacteria (93.33%), Eukaryota (6.67%)",DUF3085,DUF3085 RNA,Cis-reg;
RF02960,unclassified sequences/Bacteria,"unclassified sequences (90.32%), Bacteria (9.68%)","Bacteria (95.0%), Eukaryota (5.0%)",DUF2800,DUF2800 RNA,Cis-reg;
RF02961,unclassified sequences/Mixed,unclassified sequences (100.0%),,DUF3800-II,DUF3800-II RNA,Gene; sRNA;
RF02962,unclassified sequences/Bacteria,"unclassified sequences (98.18%), Bacteria (1.82%)",Bacteria (100.0%),DUF3800-III,DUF3800-III RNA,Gene; sRNA;
RF02964,unclassified sequences/Mixed,"unclassified sequences (97.47%), Bacteria (2.53%)","Bacteria (75.0%), Eukaryota (25.0%)",DUF3800-V,DUF3800-V RNA,Gene; sRNA;
RF02966,unclassified sequences/Bacteria,"unclassified sequences (90.74%), Bacteria (9.26%)",Bacteria (100.0%),DUF3268,DUF3268 RNA,Gene; sRNA;
RF02968,unclassified sequences/Bacteria,"unclassified sequences (90.83%), Bacteria (9.17%)","Bacteria (94.29%), Eukaryota (5.71%)",DUF3800-IX,DUF3800-IX RNA,Gene; sRNA;
RF02970,unclassified sequences/Mixed,unclassified sequences (100.0%),,EGFOA-assoc-1,EGFOA-assoc-1 RNA,Gene; sRNA;
RF02974,unclassified sequences/Bacteria,"unclassified sequences (91.67%), Bacteria (8.33%)",Bacteria (100.0%),Fibro-purF,Fibro-purF RNA,Cis-reg;
RF02976,unclassified sequences/Mixed,"unclassified sequences (99.52%), Bacteria (0.48%)",,Flavobacterium-1,Flavobacterium-1 RNA,Gene; sRNA;
RF02979,unclassified sequences/Mixed,unclassified sequences (100.0%),,freshwater-1,freshwater-1 RNA,Gene; sRNA;
RF02980,unclassified sequences/Mixed,unclassified sequences (100.0%),,freshwater-2,freshwater-2 RNA,Cis-reg;
RF02981,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),FTHFS,FTHFS RNA,Cis-reg;
RF02984,unclassified sequences/Archaea,"unclassified sequences (92.05%), Archaea (7.95%)",Archaea (100.0%),DUF3800-X,DUF3800-X RNA,Gene; sRNA;
RF02985,unclassified sequences/Bacteria,"unclassified sequences (90.0%), Bacteria (10.0%)",Bacteria (100.0%),ftsZ-DE,ftsZ-DE RNA,Gene; sRNA;
RF02986,unclassified sequences/Bacteria,"unclassified sequences (97.06%), Bacteria (2.94%)",Bacteria (100.0%),FuFi-1,FuFi-1 RNA,Gene; sRNA;
RF02987,unclassified sequences/Bacteria,"unclassified sequences (98.54%), Bacteria (1.46%)","Bacteria (98.77%), Eukaryota (1.23%)",GA-cis,GA-cis RNA,Gene; sRNA;
RF02990,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),gut-2,gut-2 RNA,Gene; sRNA;
RF02991,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),GP20-a,GP20-a RNA,Cis-reg;
RF02994,unclassified sequences/Bacteria,"unclassified sequences (92.59%), Bacteria (7.41%)",Bacteria (100.0%),IMPDH,IMPDH RNA,Gene; sRNA;
RF02995,unclassified sequences/Mixed,unclassified sequences (100.0%),,IMES-5,IMES-5 RNA,Gene; sRNA;
RF02997,unclassified sequences/Mixed,unclassified sequences (100.0%),,HOLDH,HOLDH RNA,Gene; sRNA;
RF02998,unclassified sequences/Mixed,unclassified sequences (100.0%),,IS605-orfB-II,IS605-orfB-II RNA,Gene; sRNA;
RF03000,unclassified sequences/Bacteria,"unclassified sequences (98.1%), Bacteria (1.9%)",Bacteria (100.0%),LOOT,LOOT RNA,Gene; sRNA;
RF03005,unclassified sequences/Bacteria,"unclassified sequences (99.22%), Bacteria (0.78%)",Bacteria (100.0%),lysM-TM7,lysM-TM7 RNA,Cis-reg;
RF03009,unclassified sequences/Mixed,unclassified sequences (100.0%),,malK-III,malK-III RNA,Cis-reg;
RF03012,unclassified sequences/Mixed,unclassified sequences (100.0%),"Viruses (66.67%), Bacteria (33.33%)",Mu-gpT-DE,Mu-gpT-DE RNA,Gene; sRNA;
RF03013,unclassified sequences/Mixed,"unclassified sequences (91.94%), Bacteria (7.53%), Other (0.54%)","Bacteria (89.58%), Eukaryota (10.42%)",nadA,nadA riboswitch,Gene; sRNA;
RF03019,unclassified sequences/Archaea,"unclassified sequences (95.19%), Archaea (4.81%)",Archaea (100.0%),RT-16,RT-16 RNA,Gene; sRNA;
RF03021,unclassified sequences/Mixed,"unclassified sequences (93.62%), Bacteria (6.38%)","Bacteria (89.47%), Eukaryota (5.26%), Viruses (5.26%)",RT-18,RT-18 RNA,Gene; sRNA;
RF03022,unclassified sequences/Mixed,"unclassified sequences (97.37%), Bacteria (1.75%), Other (0.88%)","Bacteria (66.67%), Viruses (33.33%)",Phage_DGR,Bacteriophage Diversity-Generating Retroelement RNA,Gene; sRNA;
RF03025,unclassified sequences/Mixed,"unclassified sequences (91.49%), Bacteria (8.51%)","Bacteria (80.0%), Viruses (20.0%)",RT-4,RT-4 RNA,Gene; sRNA;
RF03026,unclassified sequences/Bacteria,"unclassified sequences (98.59%), Bacteria (1.41%)",Bacteria (100.0%),RT-5,RT-5 RNA,Gene; sRNA;
RF03040,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),PGK,PGK RNA,Cis-reg;
RF03041,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),poplar-1,poplar-1 RNA,Gene; sRNA;
RF03047,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-16,RAGATH-16 RNA,Gene; sRNA;
RF03048,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-20,RAGATH-20 RNA,Gene; sRNA;
RF03049,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-24,RAGATH-24 RNA,Gene; sRNA;
RF03051,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-26,RAGATH-26 RNA,Gene; sRNA;
RF03053,unclassified sequences/Mixed,unclassified sequences (100.0%),,OTKONC,OTKONC RNA,Gene; sRNA;
RF03055,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-30,RAGATH-30 RNA,Gene; sRNA;
RF03062,unclassified sequences/Bacteria,"unclassified sequences (95.83%), Bacteria (4.17%)",Bacteria (100.0%),xerDC,xerDC RNA,Cis-reg;
RF03065,unclassified sequences/Bacteria,"unclassified sequences (99.61%), Bacteria (0.39%)",Bacteria (100.0%),IS605-orfB-I,IS605-orfB-I RNA,Gene; sRNA;
RF03069,unclassified sequences/Bacteria,"unclassified sequences (92.86%), Bacteria (7.14%)",Bacteria (100.0%),malK-I,malK-I RNA,Cis-reg;
RF03070,unclassified sequences/Bacteria,"unclassified sequences (92.31%), Bacteria (7.69%)",Bacteria (100.0%),ssNA-helicase,ssNA-helicase RNA,Gene; sRNA;
RF03077,unclassified sequences/Mixed,"unclassified sequences (95.9%), Bacteria (4.1%)","Bacteria (88.46%), Viruses (7.69%), Eukaryota (3.85%)",RT-2,RT-2 RNA,Gene; sRNA;
RF03079,unclassified sequences/Mixed,"unclassified sequences (97.73%), Bacteria (2.27%)","Bacteria (88.89%), Eukaryota (11.11%)",MISL,MISL RNA,Gene; sRNA;
RF03083,unclassified sequences/Mixed,unclassified sequences (100.0%),,cow-rumen-3,cow-rumen-3 RNA,Gene; sRNA;
RF03084,unclassified sequences/Mixed,unclassified sequences (100.0%),,DUF2815,DUF2815 RNA,Gene; sRNA;
RF03087,unclassified sequences/Mixed,"unclassified sequences (96.55%), Bacteria (3.45%)","Bacteria (51.28%), Viruses (46.15%), Eukaryota (2.56%)",ROOL,ROOL RNA,Gene; sRNA;
RF03089,unclassified sequences/Mixed,unclassified sequences (100.0%),,cold-seep-1,cold-seep-1 RNA,Gene; sRNA;
RF03092,unclassified sequences/Mixed,unclassified sequences (100.0%),,Ocean-VII,Ocean-VII RNA,Gene; sRNA;
RF03093,unclassified sequences/Mixed,unclassified sequences (100.0%),"Bacteria (66.67%), Eukaryota (33.33%)",queA,queA RNA,Gene; sRNA;
RF03094,unclassified sequences/Archaea,"unclassified sequences (92.0%), Archaea (8.0%)",Archaea (100.0%),LAGLIDADG-2,LAGLIDADG-2 RNA,Gene; sRNA;
RF03095,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-17,RAGATH-17 RNA,Gene; sRNA;
RF03096,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-19,RAGATH-19 RNA,Gene; sRNA;
RF03098,unclassified sequences/Viruses,"unclassified sequences (94.44%), Bacteria (5.56%)",Viruses (100.0%),RAGATH-22,RAGATH-22 RNA,Gene; sRNA;
RF03099,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-23,RAGATH-23 RNA,Gene; sRNA;
RF03101,unclassified sequences/Bacteria,"unclassified sequences (96.15%), Bacteria (3.85%)",Bacteria (100.0%),RAGATH-31,RAGATH-31 RNA,Gene; sRNA;
RF03102,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-33,RAGATH-33 RNA,Gene; sRNA;
RF03103,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-34,RAGATH-34 RNA,Gene; sRNA;
RF03104,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-36,RAGATH-36 RNA,Gene; sRNA;
RF03105,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-7-assoc,RAGATH-7-assoc RNA,Gene; sRNA;
RF03106,unclassified sequences/Mixed,unclassified sequences (100.0%),,RT-11,RT-11 RNA,Gene; sRNA;
RF03107,unclassified sequences/Mixed,unclassified sequences (100.0%),,saliva-tongue-1,saliva-tongue-1 RNA,Gene; sRNA;
RF03110,unclassified sequences/Mixed,unclassified sequences (100.0%),,throat-1,throat-1 RNA,Gene; sRNA;
RF03112,unclassified sequences/Mixed,"unclassified sequences (95.24%), Bacteria (4.76%)",,Staphylococcus-1,Staphylococcus-1 RNA,Gene; sRNA;
RF03145,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-14,RAGATH-14 RNA,Gene; sRNA;
RF03146,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-9,RAGATH-9 RNA,Gene; sRNA;
RF03147,unclassified sequences/Bacteria,unclassified sequences (100.0%),Bacteria (100.0%),RAGATH-10,RAGATH-10 RNA,Gene; sRNA;
RF03148,unclassified sequences/Eukaryota,unclassified sequences (100.0%),Eukaryota (100.0%),RAGATH-11,RAGATH-11 RNA,Gene; sRNA;
RF03149,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-12,RAGATH-12 RNA,Gene; sRNA;
RF03150,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-15,RAGATH-15 RNA,Gene; sRNA;
RF03152,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-1-hammerhead,RAGATH-1 hammerhead ribozyme,Gene; ribozyme;
RF03153,unclassified sequences/Mixed,unclassified sequences (100.0%),,RAGATH-4,RAGATH-4 RNA,Gene; sRNA;
RF03154,unclassified sequences/Eukaryota,unclassified sequences (100.0%),Eukaryota (100.0%),twister-P3,type-P3 twister ribozyme,Gene; ribozyme;
RF03159,unclassified sequences/Viruses,unclassified sequences (100.0%),Viruses (100.0%),RAGATH-7,RAGATH-7 RNA,Gene; sRNA;
RF03165,unclassified sequences/Bacteria,"unclassified sequences (96.67%), Bacteria (3.33%)",Bacteria (100.0%),2dG-II,2dG-II purine riboswitch aptamer,Cis-reg; riboswitch;
RF03167,unclassified sequences/Bacteria,"unclassified sequences (92.5%), Bacteria (7.5%)","Bacteria (99.61%), Eukaryota (0.39%)",c-di-GMP-I-GGC,c-di-GMP-I-GGC riboswitch aptamer,Cis-reg; riboswitch;
RF03169,unclassified sequences/Bacteria,"unclassified sequences (90.47%), Bacteria (9.53%)",Bacteria (100.0%),c-di-GMP-II-GAG,c-di-GMP-II-GAG riboswitch aptamer,Cis-reg; riboswitch;
RF04190,unclassified sequences/Mixed,unclassified sequences (100.0%),,Hairpin-meta1,Hairpin ribozyme 1 from viruses-like metatranscriptomes,Gene; ribozyme;
RF04191,unclassified sequences/Mixed,unclassified sequences (100.0%),,Hairpin-meta2,Hairpin ribozyme 2 from viruses-like metatranscriptomes,Gene; ribozyme;
RF04325,unclassified sequences/Mixed,unclassified sequences (100.0%),,Pestivirus-3UTR-SLIII-scrofae,Pestivirus 3' UTR SLIII P. scrofae Atypical porcine pestivirus,Gene; sRNA;