| No | Rfam id | Description | # seeds | Source of secondary structure | Source of alignment | Comment |
| 1 | RF00001 | 5S ribosomal RNA | 602 | PMID:11283358 | PMID:11752286 Szymanski et al, 5S ribosomal database, |
NO 5S rRNA data is included from Gutell CRW database. |
| 2 | RF00002 | 5.8S ribosomal RNA | 63 | PMID:11125083 | PMID:11125083 Wuyts et al, European LSU rRNA database, |
NO Ribosomal RNAs have already been included from Gutell CRW database. |
| 3 | RF00003 | U1 spliceosomal RNA | 100 | PMID:2405391 | PMID:9016512 Zwieb C, The uRNA database, |
NO Interactions with other molecules. uRNADB not accessible. |
| 4 | RF00004 | U2 spliceosomal RNA | 77 | PMID:2339054 | PMID:9016512 The uRNA database, ; Griffiths-Jones SR |
NO Interactions with other molecules. uRNADB not accessible. |
| 5 | RF00005 | tRNA | 1088 | PMID:8256282 | Eddy SR | NO Sprinzl tRNA data is included instead. |
| 6 | RF00008 | Hammerhead ribozyme (type III) | 84 | PMID:7969422 | Bateman A | YES Crystal structure, but between 2 molecules: an RNA and a DNA. The hammerhead ribozyme is often a self-cleaving molecule though, so I included it as one molecule. |
| 7 | RF00009 | Nuclear RNase P | 59 | PMID:9847214 | PMID:9847214 Brown JW, The Ribonuclease P Database, |
NO RNase P RNA data is included instead from RNase P database. |
| 8 | RF00010 | Bacterial RNase P class A | 49 | PMID:9847214 | PMID:9847214 Brown JW, The Ribonuclease P Database, |
NO RNase P RNA data is included instead from RNase P database. |
| 9 | RF00011 | Bacterial RNase P class B | 31 | PMID:9847214 | Brown JW, The Ribonuclease P Database, 9847214 | NO RNase P RNA data is included instead from RNase P database. |
| 10 | RF00012 | Small nucleolar RNA U3 | 20 | PMID:10199569 | PMID:9016512 Zwieb C, The uRNA database, ; Jones T |
NO The secondary structure paper doesn't talk about U3! uRNADB not accessible. |
| 11 | RF00013 | 6S / SsrS RNA | 77 | PMID:15811922 | Barrick JE | NO Sequences are computationally identified. |
| 12 | RF00014 | DsrA RNA | 4 | PMID:9770508 | Bateman A | NO Pred. |
| 13 | RF00015 | U4 spliceosomal RNA | 30 | PMID:2339054 | PMID:9016512 Zwieb C, The uRNA database, |
NO U4 forms significant secondary structure with U6. uRNADB not accessible. |
| 14 | RF00017 | Eukaryotic type signal recognition particle RNA | 50 | PMID:12520023 | PMID:12520023 Rosenblad et al, SRPDB, |
NO Data from SRPDB is included instead. |
| 15 | RF00019 | Y RNA | 16 | PMID:10606662 | Griffiths-Jones SR | YES Phylogenetic analysis of 3 species (not sure if enough though) + chemical/enzymatic probing. |
| 16 | RF00020 | U5 spliceosomal RNA | 33 | PMID:2339054 | PMID:9016512 Zwieb C, The uRNA database, |
NO Interactions with other molecules uRNADB not accessible. |
| 17 | RF00021 | Spot 42 RNA | 6 | PMID:12101127 | Bateman A | NO Based only on structural probing and predictions, few structures (only 6). |
| 18 | RF00023 | tmRNA | 178 | PMID:8972778 | PMID:12520048 tmRDB, |
NO Data from tmRDB is included instead. |
| 19 | RF00024 | Vertebrate telomerase RNA | 37 | PMID:10721988 | Machado Lima A | YES Phylogenetic analysis using 32 RNA genes. |
| 20 | RF00025 | Ciliate telomerase RNA | 24 | PMID:7958872 | PMID:7739888 McCormick-Graham and Romero, ; Griffiths-Jones SR, Moxon SJ |
YES Phylogenetic analysis using 6 RNA genes. |
| 21 | RF00026 | U6 spliceosomal RNA | 53 | PMID:2339054 | Griffiths-Jones SR | NO U6 forms significant secondary structure with U4. |
| 22 | RF00028 | Group I catalytic intron | 30 | PMID:2197983 | Eddy SR | NO Data from Gutell CRW is included instead. |
| 23 | RF00030 | RNase MRP | 27 | PMID:7678563 | Griffiths-Jones SR, reference [2], Daub J | YES Comparative sequence analysis on 6+ species, consistent with available chemical modification data. |
| 24 | RF00031 | Selenocysteine insertion sequence | 63 | PMID:12458087 | PMID:12458087 Gautheret D, |
NO They are fragments. The secondary structure was well characterized. The paper only shows 44 confirmed sequences, I don't know where the other ones come from. |
| 25 | RF00032 | Histone 3' UTR stem-loop | 64 | PMID:10571029 | Griffiths-Jones SR | NO Fragments |
| 26 | RF00035 | OxyS RNA | 5 | PMID:11804582 | Noncoding RNAs Database | NO Secondary structure predicted using Mfold. |
| 27 | RF00036 | HIV Rev response element | 65 | PMID:12177299 | Griffiths-Jones SR | NO The paper doesn't mention how the "conserved secondary structure" was determined. |
| 28 | RF00037 | Iron response element | 39 | PMID:8710843 | Griffiths-Jones SR | NO Structure is suggested, a bit different from what was proposed before (I think this is the one included in Rfam), and the papers gives 2 alternative structures. |
| 29 | RF00040 | RNase E 5' UTR element | 9 | PMID:10817759 | Griffiths-Jones SR, Moxon SJ | YES Secondary structure determined by phylogenetic analysis and chemical alkylation (5 sequences used). |
| 30 | RF00045 | Small nucleolar RNA SNORA73 family | 23 | PMID:11821910 | PMID:11821910 Griffiths-Jones SR; Cervelli et al, |
NO It's based on sequence comparison and thermodynamic prediction. |
| 31 | RF00048 | Enterovirus cis-acting replication element | 56 | PMID:11044080 | Bateman A | NO Secondary structure is predicted. |
| 32 | RF00050 | FMN riboswitch (RFN element) | 34 | PMID:12456892 | Vitreshchak A | NO Riboswitch - alternative structures in different contexts. |
| 33 | RF00059 | TPP riboswitch (THI element) | 174 | PMID:12376536 | Vitreshchak A | NO Riboswitch - alternative structures in different contexts. |
| 34 | RF00061 | Hepatitis C virus internal ribosome entry site | 821 | PMID:12212848 | Griffiths-Jones SR | NO Not exactly clear how the secondary structure was determined, although it looks like several studies exist about its structure. |
| 35 | RF00065 | Small nucleolar RNA snoR9 | 3 | PMID:12032319 | Bateman A | NO Secondary structure is predicted. |
| 36 | RF00094 | Hepatitis delta virus ribozyme | 15 | PMID:9783582 | Griffiths-Jones SR | YES Crystal structure. |
| 37 | RF00096 | U8 small nucleolar RNA | 6 | PMID:11675000 | Griffiths-Jones SR | NO The paper refines a "proposed secondary structure". |
| 38 | RF00100 | 7SK RNA | 6 | PMID:1646389 | Griffiths-Jones SR | YES Structure determined by chemical and enzymatic probing. |
| 39 | RF00102 | VA RNA | 54 | PMID:8809020 | Bateman A, Moxon SJ | NO Not sure. The secondary structure paper focuses on the central domain. The other parts of the structure are taken from previous publications, and have been determined by computational predictions, nuclease sensitivity analysis, mutagenesis, functional and PKR binding assays, phylogenetic comparisons, PKR protection, and footprinting techniques. |
| 40 | RF00106 | RNAI | 10 | PMID:7535193 | Griffiths-Jones SR | NO Pred. |
| 41 | RF00107 | FinP | 6 | PMID:9917389 | Griffiths-Jones SR | NO Pred. |
| 42 | RF00109 | Vimentin 3' UTR protein-binding region | 19 | PMID:9241253 | Griffiths-Jones SR | YES Phylogenetic analysis of 7 species, chemical and enzymatic probing. |
| 43 | RF00114 | Ribosomal S15 leader | 47 | PMID:8955900 | Ji Y | NO The secondary structure paper has this sequence has 2 alternative structures: one contains 2 hairpins, and one contains a pseudoknot. |
| 44 | RF00140 | Alpha operon ribosome binding site | 15 | PMID:11504736 | Griffiths-Jones SR | NO Alternative structures. |
| 45 | RF00161 | Nanos 3' UTR translation control element | 3 | PMID:10882131 | Griffiths-Jones SR | NO Predicted by mfold. |
| 46 | RF00162 | SAM riboswitch (S box leader) | 48 | PMID:10094622 | PMID:10094622 Grundy F, Henkin T, |
NO Alternative structures. |
| 47 | RF00163 | Hammerhead ribozyme (type I) | 75 | PMID:9632772 | Bateman A | YES Chemical and enzymatic probing, crystal structures. Some of these contain 2 molecules, but the hammerhead ribozyme is also known to be a self-cleavage molecule. |
| 48 | RF00164 | Coronavirus 3' stem-loop II-like motif (s2m) | 38 | PMID:15630477 | PMID:9568965 ; Griffiths-Jones SR, Moxon SJ |
YES Crystal structure. |
| 49 | RF00165 | Coronavirus 3' UTR pseudoknot | 14 | PMID:10482585 | Griffiths-Jones SR | YES Phylogenetic analysis, enzymatic probing and thermodynamic predictions. (alternative structures are possible though) |
| 50 | RF00167 | Purine riboswitch | 22 | PMID:12787499 | Boese B, Barrick JE | NO Riboswitch - alternative structures in different contexts. |
| 51 | RF00168 | Lysine riboswitch | 43 | PMID:12787499 | Wickiser JK, Barrick JE | NO Riboswitch - alternative structures in different contexts. |
| 52 | RF00169 | Bacterial signal recognition particle RNA | 62 | PMID:12520023 | PMID:12520023 Rosenblad et al., SRPDB, |
NO Data from SRPDB is included instead. |
| 53 | RF00171 | Tombusvirus 5' UTR | 9 | PMID:11162089 | Griffiths-Jones SR | NO Predicted with mfold, plus chemical and enzymatic probing on only one structure. |
| 54 | RF00172 | ctgf/hcs24 CAESAR | 9 | PMID:11032028 | Griffiths-Jones SR | NO Predicted, I didn't find which program was used. |
| 55 | RF00173 | Hairpin ribozyme | 3 | PMID:7966321 | Griffiths-Jones SR | NO The hairpin ribozyme makes a complex with the substrate, so the 5' end is actually paired with the substrated, not unpaired. |
| 56 | RF00175 | Retroviral Psi packaging element | 173 | PMID:8627772 | Bateman A | NO Predicted with mfold, or Mfold-phylo. |
| 57 | RF00176 | Tombusvirus 3' UTR region IV | 18 | PMID:12954222 | Bateman A | NO Enzymatic probing, thermodynamic and phylogenetic analysis. I don't know where the pseudoknot comes from though. |
| 58 | RF00177 | Small subunit ribosomal RNA, 5' domain | 358 | PMID:11283358 | PMID:11752288 Wuyts et al., European SSU rRNA database, |
NO Ribosomal RNAs are already included from the Gutell CRW database. |
| 59 | RF00179 | GAIT element | 8 | PMID:12588972 | See reference [1] | NO Predicted with Mfold. |
| 60 | RF00180 | Renin stability regulatory element (REN-SRE) | 13 | PMID:12933794 | PMID:12933794 |
NO Predicted. |
| 61 | RF00181 | Small nucleolar RNA SNORD113/SNORD114 family | 59 | PMID:12045206 | PMID:12045206 |
NO Pred. |
| 62 | RF00182 | Coronavirus packaging signal | 15 | PMID:12791173 | PMID:12791173 |
NO Predicted with RNAstructure. |
| 63 | RF00183 | G-CSF factor stem-loop destabilising element (SLDE) | 6 | PMID:11865046 | PMID:11865046 |
NO Predicted with Mfold. |
| 64 | RF00184 | Potato virus X cis-acting regulatory element | 3 | PMID:12581634 | PMID:12581634 |
NO Predicted with Mfold, plus chemical and enzymatic probing. |
| 65 | RF00185 | Flavivirus 3' UTR cis-acting replication element (CRE) | 84 | PMID:9696848 | Bateman A, Moxon SJ, Weinberg Z | NO Predicted using DNAsis. |
| 66 | RF00192 | Bovine leukaemia virus RNA packaging signal | 5 | PMID:12359429 | PMID:12359429 |
NO Predicted with FOLDRNA and Mfold. |
| 67 | RF00193 | Citrus tristeza virus replication signal | 9 | PMID:12202214 | PMID:12202214 |
NO Predicted with Mfold. |
| 68 | RF00194 | Rubella virus 3' cis-acting element | 25 | PMID:10074193 | PMID:10074193 |
NO Predicted with Mfold, also chemical modifications, and mutagenesis. Might be ok. |
| 69 | RF00196 | Alfalfa mosaic virus RNA 1 5' UTR stem-loop | 4 | PMID:14512577 | PMID:14512577 |
NO Predicted. |
| 70 | RF00197 | rbcL 5' UTR RNA stabilising element | 3 | PMID:14628153 | PMID:14628153 |
NO Predicted. |
| 71 | RF00198 | SL1 RNA | 32 | PMID:12949121 | Moxon SJ, Daub J | NO Not sure how the structure is determined. These molecules also bind to the Sm protein for splicing. |
| 72 | RF00199 | SL2 RNA | 32 | PMID:10958663 | Moxon SJ | NO Not sure how the structure is determined. These molecules also bind to the Sm protein for splicing. |
| 73 | RF00207 | K10 transport/localisation element (TLS) | 3 | PMID:8582290 | PMID:8582290 |
NO Predicted, I couldn't find easily how. |
| 74 | RF00209 | Pestivirus internal ribosome entry site (IRES) | 25 | PMID:11142379 | PMID:11142379 |
NO Secondary structure is cited from 2 papers. The first one (Brown et al 1992) uses phylogenetic analysis on only 4 species, and thermodynamic predictions. Subsequent papers add some more chemical and enzymatic probing. |
| 75 | RF00210 | Aphthovirus internal ribosome entry site (IRES) | 92 | PMID:14561883 | PMID:14561883 |
NO Predicted with Mfold, chemical probing and phylogenetic analysis only on 26 structures. |
| 76 | RF00214 | Retrovirus direct repeat 1 (dr1) | 26 | PMID:10438832 | PMID:10438832 |
NO Secondary structure predicted using Mfold. |
| 77 | RF00215 | Tombus virus defective interfering (DI) RNA region 3 | 28 | PMID:12477830 | PMID:12477830 |
NO Predicted with mfold, and some structure probing has been done, not very convincing though. |
| 78 | RF00216 | c-myc internal ribosome entry site (IRES) | 23 | PMID:11419940 | PMID:11419940 |
YES Predicted with mfold, structural probing, phylogenetic analysis of 9 species, mutagenesis. Interesting pseudoknot. |
| 79 | RF00220 | Human rhinovirus internal cis-acting regulatory element (CRE) | 12 | PMID:9848654 | PMID:9848654 |
NO Secondary structures predicted with Mfold. |
| 80 | RF00225 | Tobamovirus internal ribosome entry site (IRES) | 7 | PMID:9185586 | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | NO Secondary structure was "proposed", not clear how it was determined, probably predicted. |
| 81 | RF00230 | T-box leader | 103 | PMID:12770710 | PMID:12770710 Barrick JE, predicted; Vitreschak A, |
NO T-boxes were found using predictions by the RNApattern program. Might have alternative structures. |
| 82 | RF00231 | Small Cajal body specific RNA 13 | 3 | PMID:12409454 | PMID:12409454 |
NO Predicted with Mfold. |
| 83 | RF00232 | Spi-1 (PU.1) 5' UTR regulatory element | 5 | PMID:9207037 | PMID:9207037 |
NO Predicted with RNAdraw and MULFOLD. |
| 84 | RF00233 | Tymovirus/Pomovirus tRNA-like 3' UTR element | 28 | PMID:15033563 | PMID:15033563 |
NO Not sure. Not clear how the secondary structure was determined, although it seems to be a well-known structure. |
| 85 | RF00234 | glmS glucosamine-6-phosphate activated ribozyme | 11 | PMID:00000000 | Barrick JE, Breaker RR | NO Not clear how the structure was determined (in the first cited Nature paper). No paper is cited from the web site (pmid is 0000000). |
| 86 | RF00236 | ctRNA | 15 | PMID:12670963 | PMID:12670963 |
NO Secondary structure is predicted. |
| 87 | RF00242 | ctRNA | 16 | PMID:2478296 | PMID:2478296 |
NO I couldn't access the paper, but the abstract doesn't talk about structure determination. |
| 88 | RF00250 | Trans-activation response element (TAR) | 426 | PMID:12882959 | PMID:12882959 |
NO Structure might be ok. Fragments. |
| 89 | RF00252 | Alfalfa mosaic virus coat protein binding (CPB) RNA | 18 | PMID:14718638 | PMID:14718638 |
NO They don't mention how the secondary structure was obtained. |
| 90 | RF00259 | Interferon gamma 5' UTR regulatory element | 5 | PMID:11832212 | PMID:11832212 |
NO They concentrate on the pseudoknot, not clear how the other parts of the structure were determined. |
| 91 | RF00260 | Hepatitis C virus (HCV) cis-acting replication element (CRE) | 52 | PMID:14722290 | PMID:14722290 |
NO Prediction with Mfold, phynogenetic analysis, and some structure probing. |
| 92 | RF00261 | L-myc internal ribosome entry site (IRES) | 3 | PMID:14730027 | PMID: 14730027 | NO Predicted with Mfold, plus chemical and enzymatic probing. |
| 93 | RF00264 | Small nucleolar RNA SNORA64/SNORA10 family | 9 | PMID:10487763 | PMID:10487763 , Daub J |
NO Predicted, I couldn't find which program was used. |
| 94 | RF00286 | Small Cajal body specific RNA 8 | 3 | PMID:12032087 | Moxon SJ | NO Predicted. |
| 95 | RF00290 | Bamboo mosaic potexvirus (BaMV) cis-regulatory element | 4 | PMID:14585345 | PMID:14585345 |
NO Not clear how the secondary structure was determined, but is probably predicted. |
| 96 | RF00362 | Pospiviroid RY motif stem loop | 16 | PMID:14500815 | PMID:14500815 |
NO Secondary structures predicted with Mfold. |
| 97 | RF00363 | mir-BART1 microRNA precursor family | 3 | PMID:15118162 | PMID:15118162 |
NO Predicted. |
| 98 | RF00364 | mir-BART2 microRNA precursor family | 8 | PMID:15118162 | PMID:15118162 |
NO Predicted. |
| 99 | RF00365 | mir-BHRF1-1 microRNA precursor family | 3 | PMID:15118162 | PMID:15118162 |
NO Predicted. |
| 100 | RF00366 | mir-BHRF1-2 microRNA precursor family | 4 | PMID:15118162 | PMID:15118162 |
NO Predicted. |
| 101 | RF00367 | mir-BHRF1-3 microRNA precursor family | 3 | PMID:15118162 | PMID:15118162 |
NO Predicted. |
| 102 | RF00373 | Archaeal RNase P | 34 | PMID:9847214 | PMID:9847214 Brown JW, The Ribonuclease P Database, |
NO Already included from the RNaseP database. |
| 103 | RF00374 | Gammaretrovirus core encapsidation signal | 23 | PMID:15003457 | PMID:15003457 |
YES Tertiary structure determined by NMR. |
| 104 | RF00378 | Qrr RNA | 6 | PMID:15242645 | PMID:15242645 |
NO Predicted. |
| 105 | RF00381 | Antizyme RNA frameshifting stimulation element | 13 | PMID:15147837 | PMID:15147837 |
NO The secondary structure paper doesn't make it clear how the secondary structure was determined. |
| 106 | RF00382 | DnaX ribosomal frameshifting element | 3 | PMID:9300054 | PMID:9300054 |
NO Used enzymatic probing, but I don't think they used phylogeny. |
| 107 | RF00383 | Insertion sequence IS1222 ribosomal frameshifting element | 6 | PMID:15126494 | PMID:15126494 |
NO Predicted. |
| 108 | RF00384 | Poxvirus AX element late mRNA cis-regulatory element | 7 | PMID:10049834 | PMID:10049834 |
NO predicted using Zuker's RNA FOLD program. |
| 109 | RF00385 | Infectious bronchitis virus D-RNA | 10 | PMID:11119581 | PMID:11119581 |
NO Structure predicted using the software package RNAdraw. |
| 110 | RF00386 | Enterovirus 5' cloverleaf cis-acting replication element | 160 | PMID:11250909 | PMID:11250909 |
NO Not clear in the paper how the secondary structure was determined. |
| 111 | RF00387 | FGF-1 internal ribosome entry site (IRES) | 6 | PMID:15314170 | PMID:15314170 |
NO Predicted with Mfold. |
| 112 | RF00388 | Qa RNA | 5 | PMID:14651627 | PMID:14651627 |
NO Predicted with Mfold. |
| 113 | RF00389 | Bamboo mosaic virus satellite RNA cis-regulatory element | 42 | PMID:12832220 | PMID:12832220 |
NO Structure predicted with Mfold. Part of the structure has been confirmed by chemical modification, but not all of it. |
| 114 | RF00390 | UPSK RNA | 4 | PMID:9223489 | PMID:9223489 |
NO Pred. |
| 115 | RF00391 | RtT RNA | 16 | PMID:1840671 | PMID:1840671 |
NO Secondary structures were predicted using RNAFOLD by Zuker and Abraham. |
| 116 | RF00433 | Hsp90 cis-regulatory element | 4 | PMID:15347681 | PMID:15347681 |
NO Secondary structures were predicted with Mfold. |
| 117 | RF00434 | Luteovirus cap-independent translation element (BTE) | 17 | PMID:15351207 | PMID:15351207 |
NO Not clear how the secondary structure was determined. |
| 118 | RF00435 | Repression of heat shock gene expression (ROSE) element | 13 | PMID:11726689 | PMID:11726689 |
NO Secondary structure predicted with Mfold. |
| 119 | RF00436 | UnaL2 LINE 3' element | 30 | PMID:15273327 | Bateman A | NO Solution structure was determined by NMR only for the 17nt hairpin, not for the longer molecule. |
| 120 | RF00437 | Hairy RNA localisation element (HLE) | 4 | PMID:12743042 | PMID:12743042 |
NO Predictions using ConStruct. |
| 121 | RF00444 | PrrF RNA | 5 | PMID:15210934 | PMID:15210934 |
NO Predicted. |
| 122 | RF00453 | Cardiovirus cis-acting replication element (CRE) | 12 | PMID:10500216 | PMID:10500216 |
NO Structures were predicted using Palmenberg and Sgro. |
| 123 | RF00458 | Cripavirus internal ribosome entry site (IRES) | 7 | PMID:11233983 | Published; 11233983 | NO Uses Mfold predictions, alignment of seven related viruses, and mutation analysis. Interesting pseudoknots though. |
| 124 | RF00460 | U1A polyadenylation inhibition element (PIE) | 8 | PMID:11233983 | PMID:15491147 |
NO Predicted. |
| 125 | RF00461 | Vascular endothelial growth factor (VEGF) IRES A | 7 | PMID:9774635 | PMID:9774635 Published; |
NO Predicted by the ESSA folding algorithms. |
| 126 | RF00462 | APC internal ribosome entry site (IRES) | 6 | PMID:12034871 | Published; 12034871 | NO Predicted with Mfold. |
| 127 | RF00463 | Apolipoprotein B (apoB) 5' UTR cis-regulatory element | 3 | PMID:15157107 | PMID:15157107 |
NO Predicted with Mfold. |
| 128 | RF00465 | Japanese encephalitis virus (JEV) hairpin structure | 20 | PMID:15113895 | PMID:15113895 |
NO Secondary structures predicted with Mfold. |
| 129 | RF00467 | Rous sarcoma virus (RSV) primer binding site (PBS) | 23 | PMID:15153244 | PMID:15153244 |
NO Secondary structure heavily interact with another RNA. |
| 130 | RF00478 | Small Cajal body specific RNA 6 | 4 | PMID:12032087 | Moxon SJ | NO Secondary structures were computationally predicted. |
| 131 | RF00480 | HIV Ribosomal frameshift signal | 853 | PMID:14747573 | PMID:14747573 |
NO Secondary structure is putative. |
| 132 | RF00481 | Hepatitis C virus 3'X element | 22 | PMID:15452207 | PMID:15452207 |
NO Secondary structures are predicted with Mfold. Also, they are fragments. |
| 133 | RF00483 | Insulin-like growth factor II IRES | 9 | PMID:11903044 | Moxon SJ | NO "Putative" secondary structure - some phylogenetic analysis, some chemical probing. |
| 134 | RF00484 | Connexin-32 internal ribosome entry site (IRES) | 6 | PMID:10931843 | Moxon SJ | NO Secondary structure predicted with Mfold. |
| 135 | RF00485 | Potassium channel RNA editing signal | 85 | PMID:15361858 | PMID:15361858 |
NO Predicted with mfold. |
| 136 | RF00487 | Connexin-43 internal ribosome entry site (IRES) | 14 | PMID:10618489 | Moxon SJ | NO Secondary structures are predicted with Mfold. |
| 137 | RF00488 | Yeast U1 spliceosomal RNA | 5 | PMID:2405391 | PMID:9016512 Zwieb C, The uRNA database, |
NO Interactions with other molecules, not enough sequences (only 5). uRNADB not accessible. |
| 138 | RF00489 | ctRNA | 14 | PMID:15554980 | PMID:15554980 |
NO Secondary structures are predicted. |
| 139 | RF00490 | S-element | 12 | PMID:15554980 | PMID:15554980 |
NO Secondary structures are predicted. |
| 140 | RF00491 | Simian virus 40 late polyadenylation signal (SVLPA) | 6 | PMID:15024068 | PMID:15024068 |
NO Alternative structures. There are at least three structures that exist in equilibrium. |
| 141 | RF00492 | small Cajal body-specific RNA 17 | 6 | PMID:15556860 | Moxon SJ | NO Secondary structures are predicted. |
| 142 | RF00493 | Small nucleolar RNA U2-30 | 3 | PMID:15556860 | Moxon SJ | NO Secondary structures are predicted. |
| 143 | RF00494 | Small nucleolar RNA U2-19 | 4 | PMID:15556860 | Moxon SJ | NO Secondary structures are predicted. |
| 144 | RF00496 | Coronavirus SL-III cis-acting replication element (CRE) | 5 | PMID:12767992 | PMID:12767992 |
NO Structures are predicted, although there is some chemical and enzymatic probing. |
| 145 | RF00498 | Equine arteritis virus leader TRS hairpin (LTH) | 4 | PMID:14970388 | PMID:14970388 |
NO Not sure how the structures of the mutants (Fig 5) was determined. These molecules are very short anyway. |
| 146 | RF00499 | Human parechovirus 1 (HPeV1) cis regulatory element (CRE) | 5 | PMID:12438643 | PMID:12438643 |
NO Structures are predicted. |
| 147 | RF00500 | Turnip crinkle virus (TCV) repressor of minus strand synthesis H5 | 3 | PMID:15220455 | PMID:15220455 |
NO Structures were determined by Mfold + some phylogenetic analysis on some larger structures. The Rfam family contains fragments of this. |
| 148 | RF00502 | Turnip crinkle virus (TCV) core promoter hairpin (Pr) | 4 | PMID:15220455 | PMID:15220455 |
NO Structures were determined by Mfold + some phylogenetic analysis on some larger structures. The Rfam family contains fragments of this. |
| 149 | RF00503 | RNAIII | 12 | PMID:10836788 | PMID:10836788 |
YES Structure determined by extensive chemical and enzymatic probing, and computer simulations. |
| 150 | RF00505 | RydC RNA | 2 | PMID:15618228 | PMID:15618228 |
YES Determined by structural probing and sequence alignment. |
| 151 | RF00506 | Threonine operon leader | 24 | PMID:6186194 | Bateman A | NO Cannot access the paper, but it's a review paper from 1982, I doubt it determines the secondary structure. |
| 152 | RF00507 | Coronavirus frameshifting stimulation element | 23 | PMID:15680415 | PMID:15680415 |
NO Secondary structures are predicted. |
| 153 | RF00511 | Kaposi's sarcoma-associated herpesvirus internal ribosome entry site (IRES) | 4 | PMID:11160685 | Published; 11160685 | NO Secondary structures predicted with Mfold. |
| 154 | RF00512 | Leucine operon leader | 3 | PMID:6186194 | Bateman A | NO Cannot access the paper, but it's a review paper from 1982, I doubt it determines the secondary structure. |
| 155 | RF00513 | Tryptophan operon leader | 11 | PMID:6186194 | Bateman A | NO Cannot access the paper, but it's a review paper from 1982, I doubt it determines the secondary structure. |
| 156 | RF00514 | Histidine operon leader | 12 | PMID:6186194 | Bateman A | NO Cannot access the paper, but it's a review paper from 1982, I doubt it determines the secondary structure. |
| 157 | RF00515 | PyrR binding site | 72 | PMID:11726695 | Bateman A | NO Secondary structures are predicted with Mfold. |
| 158 | RF00523 | Prion pseudoknot | 167 | PMID:11160898 | PMID:11160898 |
NO Pseudoknot secondary structure was predicted by Wills (1992) (reference 13 in the secondary structure paper). |
| 159 | RF00524 | R2 RNA element | 15 | PMID:15146081 | PMID:15146081 |
YES Phylogenetic analysis and alignment on 27 species, thermodynamic predictions and chemical probing. |
| 160 | RF00525 | Flavivirus DB element | 111 | PMID:15956576 | PMID:15956576 |
NO Secondary structure fragments were proposed by other papers, and put together in this paper. |
| 161 | RF00548 | U11 spliceosomal RNA | 9 | PMID:15210936 | Griffiths-Jones S | NO U RNAs heavily interact with other molecules. |
| 162 | RF00550 | Hepatitis E virus cis-reactive element | 46 | PMID:15890906 | PMID:15890906 |
NO Secondary structure is predicted. |
| 163 | RF00551 | Bicoid 3'-UTR regulatory element | 15 | PMID:15016447 | PMID:15016447 |
YES Secondary structure determined by a variety of enzymatic and chemical modifications. |
| 164 | RF00552 | rncO | 6 | PMID:8972772 | PMID:8972772 |
NO Secondary structures were predicted with Mfold, chemical modification, and phylogenetic analysis only with one other structure. |
| 165 | RF00615 | Listeria Hfq binding LhrA | 3 | PMID:16682563 | Daub J | NO Secondary structures are predicted with Mfold. |
| 166 | RF00616 | Listeria Hfq binding LhrC | 4 | PMID:16682563 | Daub J | NO Secondary structures are predicted with Mfold. |
| 167 | RF00617 | flavivirus capsid hairpin cHP | 59 | PMID:16474125 | PMID:16474125 |
NO Secondary structures predicted with Mfold and RNAalifold. |
| 168 | RF00618 | U4atac minor spliceosomal RNA | 4 | PMID:11911359 | PMID:15987817 ; Daub J |
NO Spliceosomal RNAs interact with many other molecules. |
| 169 | RF00619 | U6atac minor spliceosomal RNA | 4 | PMID:11911359 | PMID:10199569 ; Daub J |
NO Spliceosomal RNAs interact with many other molecules. |
| 170 | RF00621 | Beta-globin co-transcriptional cleavage ribozyme | 10 | PMID:15565159 | Daub J | NO Secondary structures are predicted, and chemical modifications are added, but it's not clear exactly what. |
| 171 | RF00622 | Mammalian CPEB3 ribozyme | 3 | PMID:16990549 | PMID:16990549 Published; |
YES Secondary structure is believed to be similar to the HDV (human delta virus) ribozyme. To test that, they performed covariation and mutational analyses. |
| 172 | RF00626 | Gurken localisation signal | 2 | PMID:15992540 | Bateman A | NO Predicted with mfold. |