User:WillowW/List of non-coding RNA
The following table lists the 574 known families of non-coding RNA and other types of structural or regulatory RNA. We may very well want to change the names in the first column, to make them more explanatory for casual readers. :)
By clicking on the arrows in the top line of the Table, you can sort the whole table by the entries in that column; nifty, no? :)
| Full name | Rfam ID | Type | # of sequences in seed alignment | # of sequences in full alignment | Average length | Average sequence identity | Abbreviated name |
|---|---|---|---|---|---|---|---|
| 5S ribosomal RNA | RF00001 | Gene; rRNA; | 602 | 12117 | 116.8 | 61 | RF00001 |
| 5.8S ribosomal RNA | RF00002 | Gene; rRNA; | 63 | 84358 | 153.4 | 78 | RF00002 |
| U1 spliceosomal RNA | RF00003 | Gene; snRNA; splicing; | 100 | 857 | 161.1 | 69 | RF00003 |
| U2 spliceosomal RNA | RF00004 | Gene; snRNA; splicing; | 77 | 551 | 177.6 | 62 | RF00004 |
| tRNA | RF00005 | Gene; tRNA; | 1088 | 84974 | 72.7 | 44 | RF00005 |
| Vault RNA | RF00006 | Gene; | 11 | 22 | 103.0 | 74 | RF00006 |
| U12 minor spliceosomal RNA | RF00007 | Gene; snRNA; splicing; | 8 | 21 | 160.4 | 67 | RF00007 |
| Hammerhead ribozyme (type III) | RF00008 | Gene; ribozyme; | 84 | 252 | 54.2 | 77 | RF00008 |
| Nuclear RNase P | RF00009 | Gene; ribozyme; | 59 | 110 | 298.8 | 42 | RF00009 |
| Bacterial RNase P class A | RF00010 | Gene; ribozyme; | 116 | 473 | 310.0 | 59 | RF00010 |
| Bacterial RNase P class B | RF00011 | Gene; ribozyme; | 31 | 164 | 369.7 | 67 | RF00011 |
| Small nucleolar RNA U3 | RF00012 | Gene; snRNA; guide; CD-box; | 21 | 227 | 227.2 | 51 | RF00012 |
| 6S / SsrS RNA | RF00013 | Gene; | 77 | 172 | 182.4 | 43 | RF00013 |
| DsrA RNA | RF00014 | Gene; sRNA; | 4 | 16 | 85.8 | 93 | RF00014 |
| U4 spliceosomal RNA | RF00015 | Gene; snRNA; splicing; | 30 | 270 | 137.9 | 63 | RF00015 |
| Small nucleolar RNA SNORD14 | RF00016 | Gene; snRNA; guide; CD-box; | 18 | 218 | 108.6 | 64 | RF00016 |
| Eukaryotic type signal recognition particle RNA | RF00017 | Gene; | 50 | 433 | 292.5 | 39 | RF00017 |
| CsrB/RsmB RNA family | RF00018 | Gene; sRNA; | 7 | 43 | 359.7 | 54 | RF00018 |
| Y RNA | RF00019 | Gene; | 16 | 1278 | 101.7 | 67 | RF00019 |
| U5 spliceosomal RNA | RF00020 | Gene; snRNA; splicing; | 33 | 273 | 117.7 | 61 | RF00020 |
| Spot 42 RNA | RF00021 | Gene; sRNA; | 6 | 27 | 117.9 | 90 | RF00021 |
| GcvB RNA | RF00022 | Gene; | 17 | 29 | 140.6 | 64 | RF00022 |
| tmRNA | RF00023 | Gene; | 178 | 350 | 351.3 | 46 | RF00023 |
| Vertebrate telomerase RNA | RF00024 | Gene; | 37 | 60 | 430.7 | 57 | RF00024 |
| Ciliate telomerase RNA | RF00025 | Gene; | 24 | 22 | 179.0 | 52 | RF00025 |
| U6 spliceosomal RNA | RF00026 | Gene; snRNA; splicing; | 53 | 2599 | 105.7 | 77 | RF00026 |
| let-7 microRNA precursor | RF00027 | Gene; miRNA; | 14 | 94 | 82.1 | 73 | RF00027 |
| Group I catalytic intron | RF00028 | Intron; | 30 | 20085 | 397.7 | 53 | RF00028 |
| Group II catalytic intron | RF00029 | Intron; | 114 | 8189 | 77.9 | 54 | RF00029 |
| RNase MRP | RF00030 | Gene; ribozyme; | 27 | 45 | 264.5 | 51 | RF00030 |
| Selenocysteine insertion sequence | RF00031 | Cis-reg; | 63 | 299 | 64.2 | 43 | RF00031 |
| Histone 3' UTR stem-loop | RF00032 | Cis-reg; | 64 | 1046 | 26.0 | 78 | RF00032 |
| MicF RNA | RF00033 | Gene; antisense; | 8 | 24 | 91.6 | 83 | RF00033 |
| RprA RNA | RF00034 | Gene; sRNA; | 7 | 19 | 108.7 | 81 | RF00034 |
| OxyS RNA | RF00035 | Gene; sRNA; | 5 | 18 | 106.2 | 93 | RF00035 |
| HIV Rev response element | RF00036 | Cis-reg; | 65 | 3972 | 311.9 | 87 | RF00036 |
| Iron response element | RF00037 | Cis-reg; | 39 | 318 | 29.0 | 63 | RF00037 |
| PrfA thermoregulator UTR | RF00038 | Cis-reg; thermoregulator; | 11 | 130 | 130.2 | 97 | RF00038 |
| DicF RNA | RF00039 | Gene; antisense; | 6 | 29 | 52.0 | 73 | RF00039 |
| RNase E 5' UTR element | RF00040 | Cis-reg; | 9 | 25 | 336.6 | 76 | RF00040 |
| Enteroviral 3' UTR element | RF00041 | Cis-reg; | 60 | 96 | 119.5 | 87 | RF00041 |
| CopA-like RNA | RF00042 | Gene; antisense; | 17 | 42 | 90.2 | 84 | RF00042 |
| R1162-like plasmid antisense RNA | RF00043 | Gene; antisense; | 3 | 9 | 73.2 | 67 | RF00043 |
| Bacteriophage pRNA | RF00044 | Gene; | 3 | 5 | 215.2 | 76 | RF00044 |
| Small nucleolar RNA SNORA73 | RF00045 | Gene; snRNA; guide; HACA-box; | 23 | 71 | 207.7 | 71 | RF00045 |
| Small nucleolar RNA R30/Z108 | RF00046 | Gene; snRNA; guide; CD-box; | 6 | 30 | 95.6 | 89 | RF00046 |
| mir-2 microRNA precursor | RF00047 | Gene; miRNA; | 9 | 25 | 70.1 | 71 | RF00047 |
| Enterovirus cis-acting replication element | RF00048 | Cis-reg; | 56 | 262 | 61.0 | 81 | RF00048 |
| Small nucleolar RNA SNORD36 | RF00049 | Gene; snRNA; guide; CD-box; | 20 | 129 | 78.5 | 66 | RF00049 |
| FMN riboswitch (RFN element) | RF00050 | Cis-reg; riboswitch; | 34 | 183 | 144.7 | 65 | RF00050 |
| mir-17 microRNA precursor family | RF00051 | Gene; miRNA; | 54 | 63 | 82.1 | 69 | RF00051 |
| lin-4 microRNA precursor | RF00052 | Gene; miRNA; | 9 | 39 | 70.1 | 73 | RF00052 |
| mir-7 microRNA precursor | RF00053 | Gene; miRNA; | 6 | 29 | 88.2 | 73 | RF00053 |
| Small nucleolar RNA SNORD25 | RF00054 | Gene; snRNA; guide; CD-box; | 8 | 39 | 81.4 | 65 | RF00054 |
| Small nucleolar RNA Z37 | RF00055 | Gene; snRNA; guide; CD-box; | 9 | 39 | 90.5 | 65 | RF00055 |
| Small nucleolar RNA SNORA71 | RF00056 | Gene; snRNA; guide; HACA-box; | 15 | 37 | 128.6 | 71 | RF00056 |
| RyhB RNA | RF00057 | Gene; sRNA; | 13 | 41 | 83.0 | 72 | RF00057 |
| HgcF RNA | RF00058 | Gene; | 3 | 5 | 168.6 | 89 | RF00058 |
| TPP riboswitch (THI element) | RF00059 | Cis-reg; riboswitch; | 174 | 496 | 109.2 | 52 | RF00059 |
| HgcE RNA | RF00060 | Gene; | 3 | 5 | 130.0 | 81 | RF00060 |
| Hepatitis C virus internal ribosome entry site | RF00061 | Cis-reg; IRES; | 821 | 3632 | 206.5 | 90 | RF00061 |
| HgcC family RNA | RF00062 | Gene; | 4 | 38 | 166.7 | 60 | RF00062 |
| SscA RNA | RF00063 | Gene; | 4 | 6 | 96.3 | 75 | RF00063 |
| HgcG RNA | RF00064 | Gene; | 2 | 6 | 239.5 | 76 | RF00064 |
| Small nucleolar RNA snoR9 | RF00065 | Gene; snRNA; guide; CD-box; | 3 | 5 | 127.8 | 84 | RF00065 |
| U7 small nuclear RNA | RF00066 | Gene; snRNA; | 24 | 353 | 49.0 | 69 | RF00066 |
| Small nucleolar RNA SNORD15 | RF00067 | Gene; snRNA; guide; CD-box; | 18 | 49 | 113.1 | 63 | RF00067 |
| Small nucleolar RNA SNORD21 | RF00068 | Gene; snRNA; guide; CD-box; | 5 | 12 | 89.1 | 66 | RF00068 |
| Small nucleolar RNA SNORD24 | RF00069 | Gene; snRNA; guide; CD-box; | 14 | 102 | 81.6 | 72 | RF00069 |
| Small nucleolar RNA SNORD29 | RF00070 | Gene; snRNA; guide; CD-box; | 10 | 19 | 75.1 | 70 | RF00070 |
| Small nucleolar RNA SNORD73 | RF00071 | Gene; snRNA; guide; CD-box; | 4 | 15 | 68.7 | 84 | RF00071 |
| Small nucleolar RNA SNORA75 | RF00072 | Gene; snRNA; guide; HACA-box; | 6 | 23 | 130.4 | 73 | RF00072 |
| mir-156 microRNA precursor | RF00073 | Gene; miRNA; | 10 | 47 | 93.5 | 67 | RF00073 |
| mir-29 microRNA precursor | RF00074 | Gene; miRNA; | 10 | 53 | 67.9 | 80 | RF00074 |
| mir-166 microRNA precursor | RF00075 | Gene; miRNA; | 30 | 63 | 123.2 | 57 | RF00075 |
| mir-181 microRNA precursor | RF00076 | Gene; miRNA; | 4 | 25 | 75.3 | 83 | RF00076 |
| SraB RNA | RF00077 | Gene; sRNA; | 3 | 14 | 168.6 | 90 | RF00077 |
| SraD RNA | RF00078 | Gene; sRNA; | 3 | 25 | 75.5 | 87 | RF00078 |
| SraE/RygA/RygB family RNA | RF00079 | Gene; sRNA; | 4 | 30 | 86.9 | 82 | RF00079 |
| yybP-ykoY leader | RF00080 | Cis-reg; | 50 | 142 | 124.5 | 45 | RF00080 |
| SraH RNA | RF00081 | Gene; sRNA; | 2 | 19 | 108.4 | 79 | RF00081 |
| SraG RNA | RF00082 | Gene; sRNA; | 5 | 26 | 173.4 | 82 | RF00082 |
| SraJ RNA | RF00083 | Gene; sRNA; | 4 | 16 | 173.9 | 91 | RF00083 |
| CsrC RNA family | RF00084 | Gene; sRNA; | 4 | 18 | 254.6 | 77 | RF00084 |
| Small nucleolar RNA SNORD28 | RF00085 | Gene; snRNA; guide; CD-box; | 4 | 8 | 77.2 | 72 | RF00085 |
| Small nucleolar RNA SNORD27 | RF00086 | Gene; snRNA; guide; CD-box; | 11 | 28 | 77.9 | 68 | RF00086 |
| Small nucleolar RNA SNORD26 | RF00087 | Gene; snRNA; guide; CD-box; | 4 | 8 | 74.4 | 82 | RF00087 |
| Small nucleolar RNA SNORD30 | RF00088 | Gene; snRNA; guide; CD-box; | 3 | 10 | 70.0 | 78 | RF00088 |
| Small nucleolar RNA SNORD31 | RF00089 | Gene; snRNA; guide; CD-box; | 4 | 12 | 69.0 | 79 | RF00089 |
| Small nucleolar RNA SNORA74 | RF00090 | Gene; snRNA; guide; HACA-box; | 3 | 9 | 197.8 | 76 | RF00090 |
| Small nucleolar RNA SNORA62 | RF00091 | Gene; snRNA; guide; HACA-box; | 10 | 26 | 148.2 | 71 | RF00091 |
| Small nucleolar RNA SNORA63 | RF00092 | Gene; snRNA; guide; HACA-box; | 8 | 37 | 126.3 | 71 | RF00092 |
| Small nucleolar RNA SNORD18 | RF00093 | Gene; snRNA; guide; CD-box; | 16 | 70 | 76.4 | 60 | RF00093 |
| Hepatitis delta virus ribozyme | RF00094 | Gene; ribozyme; | 15 | 82 | 88.8 | 95 | RF00094 |
| Pyrococcus C/D box small nucleolar RNA | RF00095 | Gene; snRNA; guide; CD-box; | 38 | 58 | 56.2 | 59 | RF00095 |
| U8 small nucleolar RNA | RF00096 | Gene; snRNA; guide; CD-box; | 6 | 38 | 133.8 | 60 | RF00096 |
| Plant small nucleolar RNA R71 | RF00097 | Gene; snRNA; guide; CD-box; | 21 | 370 | 106.5 | 77 | RF00097 |
| Snake H/ACA box small nucleolar RNA | RF00098 | Gene; snRNA; guide; HACA-box; | 22 | 55 | 140.3 | 90 | RF00098 |
| Small nucleolar RNA SNORD22 | RF00099 | Gene; snRNA; guide; CD-box; | 3 | 9 | 125.8 | 84 | RF00099 |
| 7SK RNA | RF00100 | Gene; | 6 | 171 | 317.0 | 72 | RF00100 |
| SraC/RyeA RNA | RF00101 | Gene; sRNA; | 4 | 19 | 242.7 | 76 | RF00101 |
| VA RNA | RF00102 | Gene; | 54 | 157 | 158.9 | 70 | RF00102 |
| mir-1 microRNA precursor family | RF00103 | Gene; miRNA; | 7 | 27 | 76.7 | 71 | RF00103 |
| mir-10 microRNA precursor family | RF00104 | Gene; miRNA; | 11 | 73 | 73.8 | 67 | RF00104 |
| Small nucleolar RNA SNORD115 | RF00105 | Gene; snRNA; guide; CD-box; | 23 | 133 | 81.1 | 90 | RF00105 |
| RNAI | RF00106 | Gene; antisense; | 10 | 138 | 103.5 | 71 | RF00106 |
| FinP | RF00107 | Gene; | 6 | 15 | 77.6 | 91 | RF00107 |
| Small nucleolar RNA SNORD116 | RF00108 | Gene; snRNA; guide; CD-box; | 7 | 85 | 92.2 | 80 | RF00108 |
| Vimentin 3' UTR protein-binding region | RF00109 | Cis-reg; | 19 | 45 | 66.1 | 80 | RF00109 |
| RybB RNA | RF00110 | Gene; sRNA; | 3 | 19 | 79.5 | 89 | RF00110 |
| RyeB RNA | RF00111 | Gene; sRNA; | 4 | 19 | 97.3 | 92 | RF00111 |
| RyeE RNA | RF00112 | Gene; sRNA; | 2 | 22 | 84.8 | 80 | RF00112 |
| QUAD RNA | RF00113 | Gene; sRNA; | 14 | 50 | 146.9 | 77 | RF00113 |
| Ribosomal S15 leader | RF00114 | Cis-reg; leader; | 47 | 51 | 117.4 | 64 | RF00114 |
| IS061 RNA | RF00115 | Gene; sRNA; | 6 | 9 | 180.4 | 93 | RF00115 |
| C0465 RNA | RF00116 | Gene; sRNA; | 2 | 10 | 77.6 | 100 | RF00116 |
| C0719 RNA | RF00117 | Gene; sRNA; | 2 | 7 | 210.3 | 99 | RF00117 |
| rydB RNA | RF00118 | Gene; sRNA; | 2 | 13 | 67.6 | 96 | RF00118 |
| C0299 RNA | RF00119 | Gene; sRNA; | 2 | 11 | 79.0 | 98 | RF00119 |
| C0343 RNA | RF00120 | Gene; sRNA; | 2 | 14 | 75.0 | 87 | RF00120 |
| MicC RNA | RF00121 | Gene; sRNA; | 5 | 15 | 121.6 | 86 | RF00121 |
| GadY | RF00122 | Gene; sRNA; | 2 | 8 | 114.0 | 100 | RF00122 |
| IS102 RNA | RF00124 | Gene; sRNA; | 7 | 13 | 202.3 | 91 | RF00124 |
| IS128 RNA | RF00125 | Gene; sRNA; | 2 | 5 | 209.0 | 99 | RF00125 |
| ryfA RNA | RF00126 | Gene; sRNA; | 4 | 13 | 301.1 | 85 | RF00126 |
| t44 RNA | RF00127 | Gene; sRNA; | 7 | 27 | 145.8 | 72 | RF00127 |
| tke1 RNA | RF00128 | Gene; sRNA; | 4 | 18 | 153.4 | 87 | RF00128 |
| mir-103/107 microRNA precursor | RF00129 | Gene; miRNA; | 5 | 29 | 78.0 | 85 | RF00129 |
| mir-192/215 microRNA precursor | RF00130 | Gene; miRNA; | 4 | 12 | 106.0 | 75 | RF00130 |
| mir-30 microRNA precursor | RF00131 | Gene; miRNA; | 4 | 21 | 70.8 | 82 | RF00131 |
| Small nucleolar RNA R24 | RF00132 | Gene; snRNA; guide; CD-box; | 12 | 45 | 92.4 | 81 | RF00132 |
| Small nucleolar RNA Z195/SNORD33 family | RF00133 | Gene; snRNA; guide; CD-box; | 17 | 43 | 85.0 | 65 | RF00133 |
| Small nucleolar RNA Z196/R39/R59 family | RF00134 | Gene; snRNA; guide; CD-box; | 23 | 43 | 84.4 | 64 | RF00134 |
| Small nucleolar RNA Z223 | RF00135 | Gene; snRNA; guide; CD-box; | 5 | 35 | 90.4 | 82 | RF00135 |
| Small nucleolar RNA SNORD81 | RF00136 | Gene; snRNA; guide; CD-box; | 3 | 19 | 76.5 | 82 | RF00136 |
| Small nucleolar RNA SNORD83 | RF00137 | Gene; snRNA; guide; CD-box; | 7 | 56 | 76.9 | 85 | RF00137 |
| Small nucleolar RNA SNORD16 | RF00138 | Gene; snRNA; guide; CD-box; | 5 | 11 | 98.5 | 81 | RF00138 |
| Small nucleolar RNA SNORA72 | RF00139 | Gene; snRNA; guide; HACA-box; | 7 | 17 | 136.5 | 81 | RF00139 |
| Alpha operon ribosome binding site | RF00140 | Cis-reg; | 15 | 44 | 109.2 | 69 | RF00140 |
| Small nucleolar RNA Z118/Z121/Z120 | RF00142 | Gene; snRNA; guide; CD-box; | 7 | 42 | 103.2 | 81 | RF00142 |
| mir-6 microRNA precursor | RF00143 | Gene; miRNA; | 3 | 9 | 77.0 | 79 | RF00143 |
| mir-199 microRNA precursor | RF00144 | Gene; miRNA; | 3 | 18 | 99.9 | 88 | RF00144 |
| Small nucleolar RNA Z105 | RF00145 | Gene; snRNA; guide; CD-box; | 5 | 17 | 69.0 | 79 | RF00145 |
| Small nucleolar RNA SNORD34 | RF00147 | Gene; snRNA; guide; CD-box; | 9 | 34 | 79.4 | 67 | RF00147 |
| Small nucleolar RNA Z103 | RF00149 | Gene; snRNA; guide; CD-box; | 9 | 42 | 98.3 | 78 | RF00149 |
| Small nucleolar RNA SNORD42 | RF00150 | Gene; snRNA; guide; CD-box; | 7 | 14 | 64.3 | 76 | RF00150 |
| Small nucleolar RNA SNORD58 | RF00151 | Gene; snRNA; guide; CD-box; | 3 | 20 | 65.6 | 81 | RF00151 |
| Small nucleolar RNA SNORD79 | RF00152 | Gene; snRNA; guide; CD-box; | 6 | 9 | 74.4 | 83 | RF00152 |
| Small nucleolar RNA SNORD62 | RF00153 | Gene; snRNA; guide; CD-box; | 3 | 8 | 85.5 | 94 | RF00153 |
| Small nucleolar RNA SNORD63 | RF00154 | Gene; snRNA; guide; CD-box; | 2 | 3 | 68.7 | 90 | RF00154 |
| Small nucleolar RNA SNORA66 | RF00155 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 132.2 | 85 | RF00155 |
| Small nucleolar RNA SNORA70 | RF00156 | Gene; snRNA; guide; HACA-box; | 13 | 90 | 130.7 | 70 | RF00156 |
| Small nucleolar RNA SNORD39 | RF00157 | Gene; snRNA; guide; CD-box; | 4 | 15 | 78.3 | 79 | RF00157 |
| Small nucleolar RNA SNORD82 | RF00158 | Gene; snRNA; guide; CD-box; | 3 | 10 | 69.8 | 88 | RF00158 |
| Small nucleolar RNA Z168/Z174 | RF00159 | Gene; snRNA; guide; CD-box; | 6 | 18 | 82.2 | 87 | RF00159 |
| Small nucleolar RNA Z159/U59 | RF00160 | Gene; snRNA; guide; CD-box; | 10 | 37 | 87.7 | 76 | RF00160 |
| Nanos 3' UTR translation control element | RF00161 | Cis-reg; | 3 | 16 | 63.1 | 90 | RF00161 |
| SAM riboswitch (S box leader) | RF00162 | Cis-reg; riboswitch; | 48 | 298 | 110.8 | 66 | RF00162 |
| Hammerhead ribozyme (type I) | RF00163 | Gene; ribozyme; | 75 | 62 | 47.0 | 69 | RF00163 |
| Coronavirus 3' stem-loop II-like motif (s2m) | RF00164 | Cis-reg; | 38 | 302 | 43.0 | 79 | RF00164 |
| Coronavirus 3' UTR pseudoknot | RF00165 | Cis-reg; | 14 | 85 | 62.5 | 70 | RF00165 |
| PrrB/RsmZ RNA family | RF00166 | Gene; sRNA; | 12 | 17 | 157.4 | 75 | RF00166 |
| Purine riboswitch | RF00167 | Cis-reg; riboswitch; | 22 | 122 | 102.1 | 56 | RF00167 |
| Lysine riboswitch | RF00168 | Cis-reg; riboswitch; | 43 | 112 | 182.2 | 49 | RF00168 |
| Bacterial signal recognition particle RNA | RF00169 | Gene; | 62 | 285 | 98.9 | 50 | RF00169 |
| Retron msr RNA | RF00170 | Gene; | 8 | 12 | 71.3 | 58 | RF00170 |
| Tombusvirus 5' UTR | RF00171 | Cis-reg; | 9 | 40 | 108.1 | 59 | RF00171 |
| ctgf/hcs24 CAESAR | RF00172 | Cis-reg; | 9 | 41 | 78.9 | 83 | RF00172 |
| Hairpin ribozyme | RF00173 | Gene; ribozyme; | 3 | 5 | 51.2 | 82 | RF00173 |
| Cobalamin riboswitch | RF00174 | Cis-reg; riboswitch; | 128 | 306 | 204.5 | 47 | RF00174 |
| Retroviral Psi packaging element | RF00175 | Cis-reg; | 173 | 1364 | 105.7 | 84 | RF00175 |
| Tombusvirus 3' UTR region IV | RF00176 | Cis-reg; | 18 | 77 | 64.5 | 94 | RF00176 |
| Small subunit ribosomal RNA, 5' domain | RF00177 | Gene; rRNA; | 358 | 343 | 487.3 | 48 | RF00177 |
| mir-24 microRNA precursor family | RF00178 | Gene; miRNA; | 3 | 21 | 67.7 | 86 | RF00178 |
| GAIT element | RF00179 | Cis-reg; | 8 | 11 | 71.1 | 96 | RF00179 |
| Renin stability regulatory element (REN-SRE) | RF00180 | Cis-reg; | 13 | 30 | 37.0 | 90 | RF00180 |
| C/D box small nucleolar RNA SNORD113/SNORD114 family | RF00181 | Gene; snRNA; guide; CD-box; | 59 | 81 | 75.3 | 64 | RF00181 |
| Coronavirus packaging signal | RF00182 | Cis-reg; | 15 | 23 | 129.0 | 82 | RF00182 |
| G-CSF factor stem-loop destabilising element (SLDE) | RF00183 | Cis-reg; | 6 | 19 | 94.2 | 86 | RF00183 |
| Potato virus X cis-acting regulatory element | RF00184 | Cis-reg; | 3 | 21 | 54.0 | 97 | RF00184 |
| Flavivirus 3' UTR cis-acting replication element (CRE) | RF00185 | Cis-reg; | 84 | 303 | 95.4 | 69 | RF00185 |
| Small nucleolar RNA SNORD101 | RF00186 | Gene; snRNA; guide; CD-box; | 3 | 6 | 73.2 | 89 | RF00186 |
| Small nucleolar RNA SNORD102 | RF00187 | Gene; snRNA; guide; CD-box; | 2 | 4 | 71.8 | 94 | RF00187 |
| Small nucleolar RNA SNORD103 | RF00188 | Gene; snRNA; guide; CD-box; | 3 | 5 | 89.8 | 96 | RF00188 |
| Small nucleolar RNA SNORD95 | RF00189 | Gene; snRNA; guide; CD-box; | 5 | 12 | 68.3 | 80 | RF00189 |
| U98 small nucleolar RNA | RF00190 | Gene; snRNA; guide; HACA-box; | 3 | 14 | 133.3 | 78 | RF00190 |
| Small nucleolar RNA SNORA57 | RF00191 | Gene; snRNA; guide; HACA-box; | 3 | 10 | 145.1 | 83 | RF00191 |
| Bovine leukaemia virus RNA packaging signal | RF00192 | Cis-reg; | 5 | 5 | 55.0 | 97 | RF00192 |
| Citrus tristeza virus replication signal | RF00193 | Cis-reg; | 9 | 24 | 258.2 | 91 | RF00193 |
| Rubella virus 3' cis-acting element | RF00194 | Cis-reg; | 25 | 93 | 63.2 | 97 | RF00194 |
| RsmY RNA family | RF00195 | Gene; sRNA; | 4 | 9 | 121.4 | 84 | RF00195 |
| Alfalfa mosaic virus RNA 1 5' UTR stem-loop | RF00196 | Cis-reg; | 4 | 8 | 35.0 | 96 | RF00196 |
| rbcL 5' UTR RNA stabilising element | RF00197 | Cis-reg; | 3 | 25 | 45.6 | 67 | RF00197 |
| SL1 RNA | RF00198 | Gene; | 32 | 98 | 103.4 | 73 | RF00198 |
| SL2 RNA | RF00199 | Gene; | 32 | 37 | 109.0 | 73 | RF00199 |
| Small nucleolar RNA Z199 | RF00200 | Gene; snRNA; guide; CD-box; | 17 | 38 | 83.1 | 79 | RF00200 |
| Small nucleolar RNA Z278 | RF00201 | Gene; snRNA; guide; CD-box; | 7 | 19 | 114.7 | 94 | RF00201 |
| Small nucleolar RNA R66 | RF00202 | Gene; snRNA; guide; CD-box; | 6 | 35 | 73.2 | 89 | RF00202 |
| Small nucleolar RNA R160 | RF00203 | Gene; snRNA; guide; CD-box; | 9 | 21 | 78.4 | 76 | RF00203 |
| Small nucleolar RNA R12 | RF00204 | Gene; snRNA; guide; CD-box; | 9 | 66 | 80.8 | 82 | RF00204 |
| Small nucleolar RNA R41 | RF00205 | Gene; snRNA; guide; CD-box; | 7 | 15 | 95.4 | 85 | RF00205 |
| Small nucleolar RNA SNORD54 | RF00206 | Gene; snRNA; guide; CD-box; | 22 | 45 | 80.2 | 70 | RF00206 |
| K10 transport/localisation element (TLS) | RF00207 | Cis-reg; | 3 | 6 | 44.0 | 100 | RF00207 |
| Small nucleolar RNA R72 | RF00208 | Gene; snRNA; guide; CD-box; | 4 | 10 | 87.0 | 98 | RF00208 |
| Pestivirus internal ribosome entry site (IRES) | RF00209 | Cis-reg; IRES; | 25 | 997 | 249.1 | 80 | RF00209 |
| Aphthovirus internal ribosome entry site (IRES) | RF00210 | Cis-reg; IRES; | 92 | 188 | 461.5 | 73 | RF00210 |
| Small nucleolar RNA SNORD35 | RF00211 | Gene; snRNA; guide; CD-box; | 8 | 17 | 88.1 | 76 | RF00211 |
| Small nucleolar RNA SNORD38 | RF00212 | Gene; snRNA; guide; CD-box; | 7 | 23 | 69.0 | 76 | RF00212 |
| Small nucleolar RNA R38 | RF00213 | Gene; snRNA; guide; CD-box; | 19 | 50 | 84.4 | 58 | RF00213 |
| Retrovirus direct repeat 1 (dr1) | RF00214 | Cis-reg; | 26 | 124 | 89.2 | 86 | RF00214 |
| Tombus virus defective interfering (DI) RNA region 3 | RF00215 | Cis-reg; | 28 | 66 | 69.6 | 79 | RF00215 |
| c-myc internal ribosome entry site (IRES) | RF00216 | Cis-reg; IRES; | 23 | 54 | 296.5 | 79 | RF00216 |
| Small nucleolar RNA SNORD20 | RF00217 | Gene; snRNA; guide; CD-box; | 4 | 6 | 80.2 | 100 | RF00217 |
| Small nucleolar RNA SNORD46 | RF00218 | Gene; snRNA; guide; CD-box; | 9 | 27 | 87.9 | 70 | RF00218 |
| Small nucleolar RNA SNORD32 | RF00219 | Gene; snRNA; guide; CD-box; | 4 | 21 | 82.0 | 90 | RF00219 |
| Human rhinovirus internal cis-acting regulatory element (CRE) | RF00220 | Cis-reg; | 12 | 60 | 85.5 | 72 | RF00220 |
| Small nucleolar RNA SNORD43 | RF00221 | Gene; snRNA; guide; CD-box; | 7 | 19 | 85.7 | 61 | RF00221 |
| Bag-1 internal ribosome entry site (IRES) | RF00222 | Cis-reg; IRES; | 4 | 15 | 349.8 | 86 | RF00222 |
| bip internal ribosome entry site (IRES) | RF00223 | Cis-reg; IRES; | 4 | 10 | 236.4 | 74 | RF00223 |
| FGF-2 internal ribosome entry site (IRES) | RF00224 | Cis-reg; IRES; | 3 | 9 | 435.2 | 95 | RF00224 |
| Tobamovirus internal ribosome entry site (IRES) | RF00225 | Cis-reg; IRES; | 7 | 11 | 152.1 | 86 | RF00225 |
| n-myc internal ribosome entry site (IRES) | RF00226 | Cis-reg; IRES; | 6 | 29 | 269.7 | 57 | RF00226 |
| FIE3 (ftz instability element 3') element | RF00227 | Cis-reg; | 5 | 10 | 65.0 | 77 | RF00227 |
| Hepatitis A virus internal ribosome entry site (IRES) | RF00228 | Cis-reg; IRES; | 23 | 137 | 389.0 | 95 | RF00228 |
| Picornavirus internal ribosome entry site (IRES) | RF00229 | Cis-reg; IRES; | 208 | 1512 | 205.1 | 80 | RF00229 |
| T-box leader | RF00230 | Cis-reg; | 103 | 716 | 226.8 | 46 | RF00230 |
| Small Cajal body specific RNA 13 | RF00231 | Gene; snRNA; guide; scaRNA; | 3 | 7 | 273.4 | 86 | RF00231 |
| Spi-1 (PU.1) 5' UTR regulatory element | RF00232 | Cis-reg; | 5 | 10 | 165.2 | 89 | RF00232 |
| Tymovirus/Pomovirus tRNA-like 3' UTR element | RF00233 | Cis-reg; | 28 | 82 | 78.5 | 64 | RF00233 |
| glmS glucosamine-6-phosphate activated ribozyme | RF00234 | Cis-reg; riboswitch; | 11 | 44 | 186.5 | 60 | RF00234 |
| Plasmid RNAIII | RF00235 | Gene; | 7 | 9 | 130.0 | 95 | RF00235 |
| ctRNA | RF00236 | Gene; antisense; | 15 | 21 | 78.6 | 72 | RF00236 |
| mir-9/mir-79 microRNA precursor family | RF00237 | Gene; miRNA; | 5 | 34 | 61.3 | 85 | RF00237 |
| ctRNA | RF00238 | Gene; antisense; | 48 | 52 | 85.3 | 71 | RF00238 |
| mir-124 microRNA precursor family | RF00239 | Gene; miRNA; | 6 | 25 | 80.6 | 85 | RF00239 |
| RNA-OUT | RF00240 | Gene; | 4 | 172 | 70.0 | 96 | RF00240 |
| mir-8/mir-141/mir-200 microRNA precursor family | RF00241 | Gene; miRNA; | 9 | 24 | 77.2 | 64 | RF00241 |
| ctRNA | RF00242 | Gene; antisense; | 16 | 21 | 95.0 | 77 | RF00242 |
| traJ 5' UTR | RF00243 | Cis-reg; | 6 | 15 | 108.8 | 88 | RF00243 |
| mir-26 microRNA precursor family | RF00244 | Gene; miRNA; | 5 | 24 | 73.5 | 80 | RF00244 |
| mir-19 microRNA precursor family | RF00245 | Gene; miRNA; | 3 | 43 | 75.4 | 82 | RF00245 |
| mir-135 microRNA precursor family | RF00246 | Gene; miRNA; | 5 | 22 | 90.2 | 75 | RF00246 |
| mir-160 microRNA precursor family | RF00247 | Gene; miRNA; | 7 | 33 | 94.5 | 65 | RF00247 |
| mir-148/mir-152 microRNA precursor family | RF00248 | Gene; miRNA; | 5 | 9 | 86.2 | 71 | RF00248 |
| mir-46/mir-47/mir-281 microRNA precursor family | RF00249 | Gene; miRNA; | 4 | 8 | 76.0 | 78 | RF00249 |
| Trans-activation response element (TAR) | RF00250 | Cis-reg; | 426 | 2004 | 56.7 | 91 | RF00250 |
| mir-219 microRNA precursor family | RF00251 | Gene; miRNA; | 7 | 31 | 72.3 | 79 | RF00251 |
| Alfalfa mosaic virus coat protein binding (CPB) RNA | RF00252 | Cis-reg; | 18 | 23 | 159.4 | 90 | RF00252 |
| mir-101 microRNA precursor family | RF00253 | Gene; miRNA; | 4 | 20 | 75.0 | 89 | RF00253 |
| mir-16 microRNA precursor family | RF00254 | Gene; miRNA; | 12 | 37 | 80.4 | 76 | RF00254 |
| mir-218 microRNA precursor family | RF00255 | Gene; miRNA; | 3 | 23 | 96.1 | 80 | RF00255 |
| mir-196 microRNA precursor family | RF00256 | Gene; miRNA; | 14 | 45 | 91.1 | 73 | RF00256 |
| mir-194 microRNA precursor family | RF00257 | Gene; miRNA; | 4 | 13 | 85.0 | 79 | RF00257 |
| mir-130 microRNA precursor family | RF00258 | Gene; miRNA; | 3 | 15 | 82.5 | 72 | RF00258 |
| Interferon gamma 5' UTR regulatory element | RF00259 | Cis-reg; | 5 | 13 | 160.2 | 85 | RF00259 |
| Hepatitis C virus (HCV) cis-acting replication element (CRE) | RF00260 | Cis-reg; | 52 | 348 | 51.0 | 87 | RF00260 |
| L-myc internal ribosome entry site (IRES) | RF00261 | Cis-reg; IRES; | 3 | 5 | 220.2 | 94 | RF00261 |
| sar RNA | RF00262 | Gene; antisense; | 4 | 7 | 65.9 | 87 | RF00262 |
| Small nucleolar RNA SNORA68 | RF00263 | Gene; snRNA; guide; HACA-box; | 4 | 12 | 127.4 | 76 | RF00263 |
| Small nucleolar RNA SNORA64/SNORA10 family | RF00264 | Gene; snRNA; guide; HACA-box; | 9 | 17 | 132.4 | 70 | RF00264 |
| Small nucleolar RNA SNORA69 | RF00265 | Gene; snRNA; guide; HACA-box; | 3 | 9 | 132.1 | 76 | RF00265 |
| Small nucleolar RNA Z17 | RF00266 | Gene; snRNA; guide; CD-box; | 4 | 8 | 71.8 | 79 | RF00266 |
| Small nucleolar RNA R64/Z200 family | RF00267 | Gene; snRNA; guide; CD-box; | 11 | 24 | 94.2 | 70 | RF00267 |
| Small nucleolar RNA snoZ7/snoR77 | RF00268 | Gene; snRNA; guide; CD-box; | 3 | 9 | 80.2 | 82 | RF00268 |
| Small nucleolar RNA SNORD61 | RF00270 | Gene; snRNA; guide; CD-box; | 3 | 6 | 71.3 | 87 | RF00270 |
| Small nucleolar RNA SNORD60 | RF00271 | Gene; snRNA; guide; CD-box; | 3 | 9 | 81.7 | 87 | RF00271 |
| Small nucleolar RNA SNORA67 | RF00272 | Gene; snRNA; guide; HACA-box; | 10 | 21 | 139.9 | 73 | RF00272 |
| Small nucleolar RNA SNORD59 | RF00273 | Gene; snRNA; guide; CD-box; | 4 | 11 | 72.1 | 83 | RF00273 |
| Small nucleolar RNA SNORD57 | RF00274 | Gene; snRNA; guide; CD-box; | 3 | 5 | 69.6 | 88 | RF00274 |
| Small nucleolar RNA SNORD56 | RF00275 | Gene; snRNA; guide; CD-box; | 7 | 14 | 70.8 | 84 | RF00275 |
| Small nucleolar RNA SNORD52 | RF00276 | Gene; snRNA; guide; CD-box; | 4 | 19 | 66.4 | 80 | RF00276 |
| Small nucleolar RNA SNORD49 | RF00277 | Gene; snRNA; guide; CD-box; | 4 | 10 | 68.6 | 73 | RF00277 |
| Small nucleolar RNA SNORD50 | RF00278 | Gene; snRNA; guide; CD-box; | 6 | 12 | 70.8 | 83 | RF00278 |
| Small nucleolar RNA SNORD45 | RF00279 | Gene; snRNA; guide; CD-box; | 11 | 18 | 75.7 | 80 | RF00279 |
| Small nucleolar RNA SNORD51 | RF00280 | Gene; snRNA; guide; CD-box; | 3 | 4 | 75.0 | 88 | RF00280 |
| Small nucleolar RNA SNORD47 | RF00281 | Gene; snRNA; guide; CD-box; | 3 | 11 | 74.9 | 88 | RF00281 |
| Small nucleolar RNA SNORD48 | RF00282 | Gene; snRNA; guide; CD-box; | 3 | 13 | 63.2 | 92 | RF00282 |
| small Cajal body-specific RNA 18 | RF00283 | Gene; snRNA; guide; scaRNA; | 4 | 18 | 80.3 | 86 | RF00283 |
| Z18 small nucleolar RNA | RF00284 | Gene; snRNA; guide; CD-box; | 4 | 19 | 76.2 | 76 | RF00284 |
| Z6 small nucleolar RNA | RF00285 | Gene; snRNA; guide; CD-box; | 3 | 18 | 86.0 | 77 | RF00285 |
| Small Cajal body specific RNA 8 | RF00286 | Gene; snRNA; guide; scaRNA; | 3 | 5 | 128.4 | 81 | RF00286 |
| Small nucleolar RNA SNORD44 | RF00287 | Gene; snRNA; guide; CD-box; | 3 | 5 | 60.6 | 92 | RF00287 |
| Z30 small nucleolar RNA | RF00288 | Gene; snRNA; guide; CD-box; | 4 | 12 | 97.4 | 83 | RF00288 |
| Z12 small nucleolar RNA | RF00289 | Gene; snRNA; guide; CD-box; | 3 | 5 | 70.0 | 87 | RF00289 |
| Bamboo mosaic potexvirus (BaMV) cis-regulatory element | RF00290 | Cis-reg; | 4 | 14 | 140.0 | 100 | RF00290 |
| Small nucleolar RNA snoR639/H1 | RF00291 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 138.0 | 100 | RF00291 |
| Small nucleolar RNA TBR5 | RF00292 | Gene; snRNA; guide; CD-box; | 3 | 5 | 90.0 | 80 | RF00292 |
| Small nucleolar RNA snoM1 | RF00293 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 99.6 | 91 | RF00293 |
| Small nucleolar RNA TBR17 | RF00294 | Gene; snRNA; guide; CD-box; | 5 | 8 | 270.5 | 74 | RF00294 |
| Small nucleolar RNA TBR7 | RF00295 | Gene; snRNA; guide; CD-box; | 6 | 9 | 74.8 | 80 | RF00295 |
| Small nucleolar RNA R16 | RF00296 | Gene; snRNA; guide; CD-box; | 17 | 18 | 84.8 | 77 | RF00296 |
| Small nucleolar RNA Z221 | RF00300 | Gene; snRNA; guide; CD-box; | 3 | 7 | 112.4 | 96 | RF00300 |
| Small nucleolar RNA Z256 | RF00301 | Gene; snRNA; guide; CD-box; | 5 | 10 | 94.4 | 75 | RF00301 |
| Small nucleolar RNA SNORA65 | RF00302 | Gene; snRNA; guide; HACA-box; | 8 | 9 | 123.9 | 81 | RF00302 |
| Small nucleolar RNA snoR86 | RF00303 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 125.3 | 87 | RF00303 |
| Small nucleolar RNA Z279 | RF00304 | Gene; snRNA; guide; CD-box; | 3 | 7 | 111.1 | 94 | RF00304 |
| Small nucleolar RNA Z248 | RF00305 | Gene; snRNA; guide; CD-box; | 4 | 10 | 137.0 | 98 | RF00305 |
| Small nucleolar RNA Z178 | RF00306 | Gene; snRNA; guide; CD-box; | 4 | 6 | 152.0 | 100 | RF00306 |
| Small nucleolar RNA snoR98 | RF00307 | Gene; snRNA; guide; HACA-box; | 4 | 5 | 110.4 | 87 | RF00307 |
| Small nucleolar RNA snR60/Z15/Z230/Z193/J17 | RF00309 | Gene; snRNA; guide; CD-box; | 23 | 43 | 93.4 | 64 | RF00309 |
| Small nucleolar RNA Z165 | RF00310 | Gene; snRNA; guide; CD-box; | 3 | 8 | 90.9 | 95 | RF00310 |
| Small nucleolar RNA Z188 | RF00311 | Gene; snRNA; guide; CD-box; | 7 | 20 | 119.7 | 78 | RF00311 |
| Small nucleolar RNA Z206 | RF00312 | Gene; snRNA; guide; CD-box; | 3 | 12 | 130.3 | 89 | RF00312 |
| Small nucleolar RNA Z173 | RF00313 | Gene; snRNA; guide; CD-box; | 3 | 5 | 106.6 | 100 | RF00313 |
| Small nucleolar RNA Z182 | RF00314 | Gene; snRNA; guide; CD-box; | 4 | 9 | 88.7 | 96 | RF00314 |
| Small nucleolar RNA J33 | RF00315 | Gene; snRNA; guide; CD-box; | 3 | 24 | 80.9 | 67 | RF00315 |
| Small nucleolar RNA R43 | RF00316 | Gene; snRNA; guide; CD-box; | 16 | 20 | 73.1 | 83 | RF00316 |
| Small nucleolar RNA Z163/Z177 family | RF00317 | Gene; snRNA; guide; CD-box; | 7 | 15 | 88.5 | 85 | RF00317 |
| Small nucleolar RNA Z175 | RF00318 | Gene; snRNA; guide; CD-box; | 3 | 5 | 81.0 | 99 | RF00318 |
| Small nucleolar RNA MBI-1 | RF00319 | Gene; snRNA; guide; HACA-box; | 5 | 7 | 182.4 | 83 | RF00319 |
| Small nucleolar RNA Z185 | RF00320 | Gene; snRNA; guide; CD-box; | 2 | 8 | 84.2 | 92 | RF00320 |
| Small nucleolar RNA Z247 | RF00321 | Gene; snRNA; guide; CD-box; | 8 | 32 | 137.3 | 71 | RF00321 |
| Small nucleolar RNA MBI-161 | RF00322 | Gene; snRNA; guide; HACA-box; | 5 | 8 | 127.1 | 88 | RF00322 |
| Small nucleolar RNA R79 | RF00323 | Gene; snRNA; guide; CD-box; | 4 | 9 | 63.1 | 96 | RF00323 |
| Small nucleolar RNA MBII-202 | RF00324 | Gene; snRNA; guide; CD-box; | 5 | 11 | 78.0 | 80 | RF00324 |
| Small nucleolar RNA SNORD53 | RF00325 | Gene; snRNA; guide; CD-box; | 3 | 8 | 76.2 | 82 | RF00325 |
| Small nucleolar RNA Z155 | RF00326 | Gene; snRNA; guide; CD-box; | 8 | 14 | 78.0 | 81 | RF00326 |
| Small nucleolar RNA Z194 | RF00327 | Gene; snRNA; guide; CD-box; | 3 | 7 | 106.3 | 99 | RF00327 |
| Small nucleolar RNA Z161/Z228 | RF00328 | Gene; snRNA; guide; CD-box; | 7 | 15 | 92.2 | 82 | RF00328 |
| Small nucleolar RNA Z162 | RF00329 | Gene; snRNA; guide; CD-box; | 3 | 7 | 88.1 | 90 | RF00329 |
| Small nucleolar RNA Z43 | RF00330 | Gene; snRNA; guide; CD-box; | 4 | 13 | 99.2 | 82 | RF00330 |
| Small nucleolar RNA Z169 | RF00331 | Gene; snRNA; guide; CD-box; | 3 | 8 | 66.8 | 90 | RF00331 |
| Small nucleolar RNA Z266 | RF00332 | Gene; snRNA; guide; CD-box; | 4 | 22 | 87.0 | 81 | RF00332 |
| Small nucleolar RNA Z157/R69/R10 | RF00333 | Gene; snRNA; guide; CD-box; | 10 | 26 | 97.4 | 73 | RF00333 |
| Small nucleolar RNA MBI-28 | RF00334 | Gene; snRNA; guide; HACA-box; | 3 | 18 | 115.6 | 77 | RF00334 |
| Small nucleolar RNA Z13/snr52 | RF00335 | Gene; snRNA; guide; CD-box; | 4 | 10 | 95.9 | 74 | RF00335 |
| Small nucleolar RNA J26 | RF00336 | Gene; snRNA; guide; CD-box; | 5 | 18 | 146.4 | 91 | RF00336 |
| Small nucleolar RNA Z112 | RF00337 | Gene; snRNA; guide; CD-box; | 3 | 29 | 182.7 | 92 | RF00337 |
| Small nucleolar RNA snR53 | RF00338 | Gene; snRNA; guide; CD-box; | 3 | 3 | 89.7 | 94 | RF00338 |
| Small nucleolar RNA snoR60 | RF00339 | Gene; snRNA; guide; CD-box; | 3 | 26 | 73.8 | 84 | RF00339 |
| Small nucleolar RNA snoMBI-87 | RF00340 | Gene; snRNA; guide; HACA-box; | 6 | 25 | 131.4 | 79 | RF00340 |
| Small nucleolar RNA Z39 | RF00341 | Gene; snRNA; guide; CD-box; | 5 | 8 | 61.6 | 88 | RF00341 |
| Small nucleolar RNA Z40 | RF00342 | Gene; snRNA; guide; CD-box; | 5 | 11 | 73.0 | 89 | RF00342 |
| Small nucleolar RNA Z122 | RF00343 | Gene; snRNA; guide; CD-box; | 3 | 16 | 84.9 | 75 | RF00343 |
| Small nucleolar RNA Z267 | RF00344 | Gene; snRNA; guide; CD-box; | 5 | 12 | 73.1 | 78 | RF00344 |
| Small nucleolar RNA snoR1 | RF00345 | Gene; snRNA; guide; CD-box; | 7 | 20 | 95.1 | 80 | RF00345 |
| Small nucleolar RNA Z50 | RF00347 | Gene; snRNA; guide; CD-box; | 3 | 4 | 65.8 | 93 | RF00347 |
| Small nucleolar RNA snoR9 | RF00348 | Gene; snRNA; guide; CD-box; | 7 | 32 | 126.0 | 76 | RF00348 |
| Small nucleolar RNA R11/Z151 | RF00349 | Gene; snRNA; guide; CD-box; | 5 | 19 | 91.9 | 84 | RF00349 |
| Small nucleolar RNA Z152/R70/R12/ | RF00350 | Gene; snRNA; guide; CD-box; | 4 | 12 | 98.8 | 80 | RF00350 |
| Small nucleolar RNA R20 | RF00351 | Gene; snRNA; guide; CD-box; | 3 | 4 | 91.0 | 93 | RF00351 |
| Small nucleolar RNA R21 | RF00352 | Gene; snRNA; guide; CD-box; | 4 | 8 | 82.0 | 88 | RF00352 |
| Small nucleolar RNA snoR31/Z110/Z27 | RF00353 | Gene; snRNA; guide; CD-box; | 8 | 35 | 95.3 | 87 | RF00353 |
| Small nucleolar RNA snoR28 | RF00355 | Gene; snRNA; guide; CD-box; | 4 | 11 | 74.0 | 94 | RF00355 |
| Small nucleolar RNA R32/R81/Z41 | RF00356 | Gene; snRNA; guide; CD-box; | 6 | 8 | 95.6 | 84 | RF00356 |
| Small nucleolar RNA R44/J54/Z268 family | RF00357 | Gene; snRNA; guide; CD-box; | 19 | 39 | 97.6 | 70 | RF00357 |
| Small nucleolar RNA Z101 | RF00358 | Gene; snRNA; guide; CD-box; | 3 | 18 | 94.4 | 71 | RF00358 |
| Small nucleolar RNA Z102/R77 | RF00359 | Gene; snRNA; guide; CD-box; | 4 | 11 | 86.5 | 89 | RF00359 |
| Small nucleolar RNA Z107/R87 | RF00360 | Gene; snRNA; guide; CD-box; | 6 | 38 | 112.8 | 81 | RF00360 |
| Small nucleolar RNA Z119 | RF00361 | Gene; snRNA; guide; CD-box; | 3 | 12 | 97.2 | 94 | RF00361 |
| Pospiviroid RY motif stem loop | RF00362 | Cis-reg; | 16 | 175 | 77.8 | 89 | RF00362 |
| mir-BART1 microRNA precursor family | RF00363 | Gene; miRNA; | 3 | 4 | 70.0 | 93 | RF00363 |
| mir-BART2 microRNA precursor family | RF00364 | Gene; miRNA; | 8 | 14 | 60.4 | 93 | RF00364 |
| mir-BHRF1-1 microRNA precursor family | RF00365 | Gene; miRNA; | 3 | 6 | 66.0 | 97 | RF00365 |
| mir-BHRF1-2 microRNA precursor family | RF00366 | Gene; miRNA; | 4 | 9 | 65.0 | 90 | RF00366 |
| mir-BHRF1-3 microRNA precursor family | RF00367 | Gene; miRNA; | 3 | 6 | 65.0 | 100 | RF00367 |
| sroB RNA | RF00368 | Gene; sRNA; | 4 | 17 | 81.6 | 86 | RF00368 |
| sroC RNA | RF00369 | Gene; sRNA; | 4 | 14 | 162.2 | 86 | RF00369 |
| sroD RNA | RF00370 | Gene; sRNA; | 3 | 17 | 86.8 | 96 | RF00370 |
| sroE RNA | RF00371 | Gene; sRNA; | 3 | 14 | 89.7 | 94 | RF00371 |
| sroH RNA | RF00372 | Gene; sRNA; | 4 | 7 | 160.9 | 100 | RF00372 |
| Archaeal RNase P | RF00373 | Gene; ribozyme; | 34 | 97 | 263.1 | 64 | RF00373 |
| Gammaretrovirus core encapsidation signal | RF00374 | Cis-reg; | 23 | 141 | 101.0 | 93 | RF00374 |
| HIV primer binding site (PBS) | RF00375 | Cis-reg; | 388 | 1609 | 94.8 | 79 | RF00375 |
| HIV gag stem loop 3 (GSL3) | RF00376 | Cis-reg; | 1403 | 6923 | 81.1 | 87 | RF00376 |
| Small nucleolar RNA U6-53/MBII-28 | RF00377 | Gene; snRNA; guide; CD-box; | 4 | 8 | 106.9 | 83 | RF00377 |
| Qrr RNA | RF00378 | Gene; sRNA; | 6 | 25 | 103.0 | 79 | RF00378 |
| ydaO/yuaA leader | RF00379 | Cis-reg; | 25 | 80 | 155.4 | 55 | RF00379 |
| ykoK leader | RF00380 | Cis-reg; | 36 | 57 | 168.1 | 61 | RF00380 |
| Antizyme RNA frameshifting stimulation element | RF00381 | Cis-reg; frameshift_element; | 13 | 53 | 57.6 | 87 | RF00381 |
| DnaX ribosomal frameshifting element | RF00382 | Cis-reg; frameshift_element; | 3 | 20 | 65.0 | 85 | RF00382 |
| Insertion sequence IS1222 ribosomal frameshifting element | RF00383 | Cis-reg; frameshift_element; | 6 | 13 | 117.8 | 95 | RF00383 |
| Poxvirus AX element late mRNA cis-regulatory element | RF00384 | Cis-reg; | 7 | 22 | 62.0 | 96 | RF00384 |
| Infectious bronchitis virus D-RNA | RF00385 | Cis-reg; | 10 | 41 | 41.8 | 96 | RF00385 |
| Enterovirus 5' cloverleaf cis-acting replication element | RF00386 | Cis-reg; | 160 | 287 | 88.1 | 84 | RF00386 |
| FGF-1 internal ribosome entry site (IRES) | RF00387 | Cis-reg; IRES; | 6 | 10 | 166.9 | 84 | RF00387 |
| Qa RNA | RF00388 | Gene; antisense; | 5 | 7 | 103.7 | 73 | RF00388 |
| Bamboo mosaic virus satellite RNA cis-regulatory element | RF00389 | Cis-reg; | 42 | 74 | 157.6 | 94 | RF00389 |
| UPSK RNA | RF00390 | Cis-reg; | 4 | 25 | 23.0 | 97 | RF00390 |
| RtT RNA | RF00391 | Cis-reg; | 16 | 91 | 169.4 | 67 | RF00391 |
| Small nucleolar RNA SNORA5 | RF00392 | Gene; snRNA; guide; HACA-box; | 6 | 12 | 131.1 | 74 | RF00392 |
| Small nucleolar RNA SNORA8 | RF00393 | Gene; snRNA; guide; HACA-box; | 5 | 14 | 135.1 | 85 | RF00393 |
| Small nucleolar RNA SNORA4 | RF00394 | Gene; snRNA; guide; HACA-box; | 7 | 13 | 138.9 | 76 | RF00394 |
| Small nucleolar RNA SNORA13 | RF00396 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 132.5 | 87 | RF00396 |
| Small nucleolar RNA SNORA14 | RF00397 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 134.7 | 92 | RF00397 |
| Small nucleolar RNA SNORA15 | RF00398 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 128.2 | 84 | RF00398 |
| Small nucleolar RNA SNORA24 | RF00399 | Gene; snRNA; guide; HACA-box; | 5 | 17 | 125.5 | 74 | RF00399 |
| Small nucleolar RNA SNORA28 | RF00400 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 124.7 | 95 | RF00400 |
| Small nucleolar RNA SNORA20 | RF00401 | Gene; snRNA; guide; HACA-box; | 17 | 34 | 128.7 | 88 | RF00401 |
| Small nucleolar RNA SNORA25 | RF00402 | Gene; snRNA; guide; HACA-box; | 9 | 29 | 128.1 | 74 | RF00402 |
| Small nucleolar RNA SNORA41 | RF00403 | Gene; snRNA; guide; HACA-box; | 6 | 8 | 129.0 | 88 | RF00403 |
| Small nucleolar RNA SNORA46 | RF00404 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 125.4 | 81 | RF00404 |
| Small nucleolar RNA SNORA44 | RF00405 | Gene; snRNA; guide; HACA-box; | 6 | 17 | 127.5 | 81 | RF00405 |
| Small nucleolar RNA SNORA42 | RF00406 | Gene; snRNA; guide; HACA-box; | 4 | 44 | 131.1 | 79 | RF00406 |
| Small nucleolar RNA SNORA50 | RF00407 | Gene; snRNA; guide; HACA-box; | 3 | 4 | 135.5 | 98 | RF00407 |
| Small nucleolar RNA SNORA1 | RF00408 | Gene; snRNA; guide; HACA-box; | 6 | 11 | 132.8 | 87 | RF00408 |
| Small nucleolar RNA SNORA7 | RF00409 | Gene; snRNA; guide; HACA-box; | 8 | 45 | 137.8 | 69 | RF00409 |
| Small nucleolar RNA SNORA2 | RF00410 | Gene; snRNA; guide; HACA-box; | 18 | 27 | 134.0 | 72 | RF00410 |
| Small nucleolar RNA SNORA9 | RF00411 | Gene; snRNA; guide; HACA-box; | 6 | 14 | 130.4 | 87 | RF00411 |
| Small nucleolar RNA SNORA21 | RF00412 | Gene; snRNA; guide; HACA-box; | 5 | 13 | 133.5 | 86 | RF00412 |
| Small nucleolar RNA SNORA19 | RF00413 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 121.3 | 91 | RF00413 |
| Small nucleolar RNA SNORA22 | RF00414 | Gene; snRNA; guide; HACA-box; | 5 | 6 | 135.0 | 91 | RF00414 |
| Small nucleolar RNA SNORA30 | RF00415 | Gene; snRNA; guide; HACA-box; | 11 | 14 | 129.1 | 70 | RF00415 |
| Small nucleolar RNA SNORA43 | RF00416 | Gene; snRNA; guide; HACA-box; | 7 | 20 | 135.1 | 71 | RF00416 |
| Small nucleolar RNA SNORA56 | RF00417 | Gene; snRNA; guide; HACA-box; | 4 | 7 | 129.9 | 97 | RF00417 |
| Small nucleolar RNA SNORA58 | RF00418 | Gene; snRNA; guide; HACA-box; | 4 | 7 | 134.9 | 85 | RF00418 |
| Small nucleolar RNA SNORA52 | RF00419 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 135.1 | 74 | RF00419 |
| Small nucleolar RNA SNORA61 | RF00420 | Gene; snRNA; guide; HACA-box; | 4 | 15 | 128.7 | 77 | RF00420 |
| Small nucleolar RNA SNORA32 | RF00421 | Gene; snRNA; guide; HACA-box; | 9 | 33 | 116.7 | 78 | RF00421 |
| Small Cajal body specific RNA 24 | RF00422 | Gene; snRNA; guide; scaRNA; | 3 | 7 | 133.1 | 84 | RF00422 |
| Small Cajal body specific RNA 4 | RF00423 | Gene; snRNA; guide; scaRNA; | 3 | 12 | 127.2 | 88 | RF00423 |
| Small Cajal body specific RNA 16 | RF00424 | Gene; snRNA; guide; scaRNA; | 6 | 9 | 182.8 | 80 | RF00424 |
| Small nucleolar RNA SNORA18 | RF00425 | Gene; snRNA; guide; HACA-box; | 6 | 19 | 126.4 | 79 | RF00425 |
| Small Cajal body specific RNA 15 | RF00426 | Gene; snRNA; guide; scaRNA; | 3 | 8 | 124.2 | 96 | RF00426 |
| Small Cajal body specific RNA 23 | RF00427 | Gene; snRNA; guide; scaRNA; | 3 | 4 | 126.0 | 92 | RF00427 |
| Small nucleolar RNA SNORA38 | RF00428 | Gene; snRNA; guide; HACA-box; | 5 | 26 | 132.2 | 84 | RF00428 |
| Small nucleolar RNA SNORA29 | RF00429 | Gene; snRNA; guide; HACA-box; | 3 | 10 | 137.3 | 82 | RF00429 |
| Small nucleolar RNA SNORA54 | RF00430 | Gene; snRNA; guide; HACA-box; | 5 | 10 | 126.0 | 72 | RF00430 |
| Small nucleolar RNA SNORA55 | RF00431 | Gene; snRNA; guide; HACA-box; | 3 | 14 | 126.6 | 84 | RF00431 |
| Small nucleolar RNA SNORA51 | RF00432 | Gene; snRNA; guide; HACA-box; | 9 | 35 | 131.7 | 74 | RF00432 |
| Hsp90 cis-regulatory element | RF00433 | Cis-reg; thermoregulator; | 4 | 7 | 152.0 | 98 | RF00433 |
| Luteovirus cap-independent translation element (BTE) | RF00434 | Cis-reg; | 17 | 32 | 101.2 | 73 | RF00434 |
| Repression of heat shock gene expression (ROSE) element | RF00435 | Cis-reg; thermoregulator; | 13 | 20 | 94.3 | 65 | RF00435 |
| UnaL2 LINE 3' element | RF00436 | Cis-reg; | 30 | 5255 | 54.0 | 78 | RF00436 |
| Hairy RNA localisation element (HLE) | RF00437 | Cis-reg; | 4 | 20 | 130.5 | 89 | RF00437 |
| Small nucleolar RNA SNORA33 | RF00438 | Gene; snRNA; guide; HACA-box; | 5 | 11 | 125.8 | 77 | RF00438 |
| Small nucleolar RNA SNORD87 | RF00439 | Gene; snRNA; guide; CD-box; | 4 | 7 | 81.9 | 93 | RF00439 |
| Small nucleolar RNA SNORD37 | RF00440 | Gene; snRNA; guide; CD-box; | 7 | 11 | 64.5 | 78 | RF00440 |
| Small nucleolar RNA Z242 | RF00441 | Gene; snRNA; guide; CD-box; | 4 | 11 | 191.1 | 82 | RF00441 |
| ykkC-yxkD leader | RF00442 | Cis-reg; | 11 | 35 | 106.5 | 62 | RF00442 |
| Small nucleolar RNA SNORA27 | RF00443 | Gene; snRNA; guide; HACA-box; | 3 | 11 | 127.9 | 87 | RF00443 |
| PrrF RNA | RF00444 | Gene; sRNA; | 5 | 14 | 148.4 | 84 | RF00444 |
| mir-399 microRNA precursor family | RF00445 | Gene; miRNA; | 13 | 41 | 113.7 | 57 | RF00445 |
| mir-133 microRNA precursor family | RF00446 | Gene; miRNA; | 9 | 27 | 88.9 | 82 | RF00446 |
| Voltage-gated potassium-channel Kv1.4 IRES | RF00447 | Cis-reg; IRES; | 6 | 9 | 255.8 | 90 | RF00447 |
| Epstein-Barr virus nuclear antigen (EBNA) IRES | RF00448 | Cis-reg; IRES; | 9 | 14 | 214.9 | 66 | RF00448 |
| HIF-1 alpha IRES | RF00449 | Cis-reg; IRES; | 7 | 12 | 270.8 | 84 | RF00449 |
| Small nucleolar RNA R105/R108 | RF00450 | Gene; snRNA; guide; CD-box; | 7 | 7 | 103.3 | 77 | RF00450 |
| mir-395 microRNA precursor family | RF00451 | Gene; miRNA; | 21 | 107 | 99.7 | 64 | RF00451 |
| mir-172 microRNA precursor family | RF00452 | Gene; miRNA; | 8 | 19 | 113.5 | 65 | RF00452 |
| Cardiovirus cis-acting replication element (CRE) | RF00453 | Cis-reg; | 12 | 30 | 33.0 | 85 | RF00453 |
| p27 cis-regulatory element | RF00454 | Cis-reg; | 4 | 9 | 58.3 | 92 | RF00454 |
| mir-15 microRNA precursor family | RF00455 | Gene; miRNA; | 4 | 29 | 85.4 | 80 | RF00455 |
| mir-34 microRNA precursor family | RF00456 | Gene; miRNA; | 18 | 20 | 87.2 | 70 | RF00456 |
| Mnt IRES | RF00457 | Cis-reg; IRES; | 4 | 7 | 203.1 | 97 | RF00457 |
| Cripavirus internal ribosome entry site (IRES) | RF00458 | Cis-reg; IRES; | 7 | 8 | 198.8 | 56 | RF00458 |
| Mason-Pfizer monkey virus packaging signal | RF00459 | Cis-reg; | 4 | 14 | 274.5 | 80 | RF00459 |
| U1A polyadenylation inhibition element (PIE) | RF00460 | Cis-reg; | 8 | 27 | 74.0 | 80 | RF00460 |
| Vascular endothelial growth factor (VEGF) IRES A | RF00461 | Cis-reg; IRES; | 7 | 13 | 305.5 | 92 | RF00461 |
| APC internal ribosome entry site (IRES) | RF00462 | Cis-reg; IRES; | 6 | 8 | 53.0 | 85 | RF00462 |
| Apolipoprotein B (apoB) 5' UTR cis-regulatory element | RF00463 | Cis-reg; | 3 | 12 | 118.9 | 94 | RF00463 |
| mir-92 microRNA precursor family | RF00464 | Gene; miRNA; | 33 | 45 | 79.2 | 62 | RF00464 |
| Japanese encephalitis virus (JEV) hairpin structure | RF00465 | Cis-reg; | 20 | 213 | 59.5 | 84 | RF00465 |
| Rous sarcoma virus (RSV) primer binding site (PBS) | RF00467 | Cis-reg; | 23 | 101 | 72.6 | 83 | RF00467 |
| Hepatitis C virus stem-loop VII | RF00468 | Cis-reg; | 110 | 497 | 65.0 | 78 | RF00468 |
| Hepatitis C stem-loop IV | RF00469 | Cis-reg; | 110 | 344 | 37.0 | 89 | RF00469 |
| Togavirus 5' plus strand cis-regulatory element | RF00470 | Cis-reg; | 33 | 78 | 255.3 | 72 | RF00470 |
| Small nucleolar RNA snR48 | RF00471 | Gene; snRNA; guide; CD-box; | 6 | 8 | 109.4 | 78 | RF00471 |
| Small nucleolar RNA snR55/Z10 | RF00472 | Gene; snRNA; guide; CD-box; | 6 | 9 | 88.4 | 74 | RF00472 |
| Small nucleolar RNA snR54 | RF00473 | Gene; snRNA; guide; CD-box; | 9 | 16 | 81.8 | 76 | RF00473 |
| Small nucleolar RNA snR57 | RF00474 | Gene; snRNA; guide; CD-box; | 6 | 8 | 91.6 | 75 | RF00474 |
| Small nucleolar RNA snR69 | RF00475 | Gene; snRNA; guide; CD-box; | 7 | 14 | 95.6 | 61 | RF00475 |
| Small nucleolar RNA snR61/Z1/Z11 | RF00476 | Gene; snRNA; guide; CD-box; | 17 | 20 | 82.3 | 69 | RF00476 |
| Small nucleolar RNA snR66 | RF00477 | Gene; snRNA; guide; CD-box; | 5 | 9 | 100.7 | 82 | RF00477 |
| Small Cajal body specific RNA 6 | RF00478 | Gene; snRNA; guide; scaRNA; | 4 | 9 | 265.7 | 63 | RF00478 |
| Small nucleolar RNA snR71 | RF00479 | Gene; snRNA; guide; CD-box; | 7 | 7 | 92.4 | 73 | RF00479 |
| HIV Ribosomal frameshift signal | RF00480 | Cis-reg; frameshift_element; | 853 | 4437 | 51.9 | 90 | RF00480 |
| Hepatitis C virus 3'X element | RF00481 | Cis-reg; | 22 | 77 | 100.0 | 97 | RF00481 |
| Small nucleolar RNA F1/F2/snoR5a | RF00482 | Gene; snRNA; guide; HACA-box; | 8 | 19 | 136.3 | 85 | RF00482 |
| Insulin-like growth factor II IRES | RF00483 | Cis-reg; IRES; | 9 | 36 | 118.4 | 95 | RF00483 |
| Connexin-32 internal ribosome entry site (IRES) | RF00484 | Cis-reg; IRES; | 6 | 11 | 147.5 | 93 | RF00484 |
| Potassium channel RNA editing signal | RF00485 | Cis-reg; | 85 | 364 | 113.7 | 65 | RF00485 |
| mir-129 microRNA precursor family | RF00486 | Gene; miRNA; | 6 | 10 | 91.1 | 82 | RF00486 |
| Connexin-43 internal ribosome entry site (IRES) | RF00487 | Cis-reg; IRES; | 14 | 30 | 195.6 | 79 | RF00487 |
| Yeast U1 spliceosomal RNA | RF00488 | Gene; snRNA; splicing; | 5 | 9 | 553.2 | 61 | RF00488 |
| ctRNA | RF00489 | Gene; antisense; | 14 | 33 | 76.6 | 67 | RF00489 |
| S-element | RF00490 | Cis-reg; | 12 | 24 | 68.0 | 77 | RF00490 |
| Simian virus 40 late polyadenylation signal (SVLPA) | RF00491 | Cis-reg; | 6 | 38 | 54.4 | 99 | RF00491 |
| small Cajal body-specific RNA 17 | RF00492 | Gene; snRNA; guide; scaRNA; | 6 | 16 | 141.8 | 81 | RF00492 |
| Small nucleolar RNA U2-30 | RF00493 | Gene; snRNA; guide; CD-box; | 3 | 7 | 69.3 | 86 | RF00493 |
| Small nucleolar RNA U2-19 | RF00494 | Gene; snRNA; guide; CD-box; | 4 | 7 | 78.9 | 87 | RF00494 |
| Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) | RF00495 | Cis-reg; IRES; | 14 | 38 | 209.7 | 81 | RF00495 |
| Coronavirus SL-III cis-acting replication element (CRE) | RF00496 | Cis-reg; | 5 | 13 | 42.0 | 96 | RF00496 |
| Equine arteritis virus leader TRS hairpin (LTH) | RF00498 | Cis-reg; | 4 | 12 | 45.0 | 99 | RF00498 |
| Human parechovirus 1 (HPeV1) cis regulatory element (CRE) | RF00499 | Cis-reg; | 5 | 6 | 112.8 | 86 | RF00499 |
| Turnip crinkle virus (TCV) repressor of minus strand synthesis H5 | RF00500 | Cis-reg; | 3 | 5 | 45.2 | 97 | RF00500 |
| Rotavirus cis-acting replication element (CRE) | RF00501 | Cis-reg; | 14 | 17 | 67.8 | 86 | RF00501 |
| Turnip crinkle virus (TCV) core promoter hairpin (Pr) | RF00502 | Cis-reg; | 4 | 5 | 52.2 | 95 | RF00502 |
| RNAIII | RF00503 | Gene; | 12 | 16 | 506.6 | 86 | RF00503 |
| Glycine riboswitch | RF00504 | Cis-reg; riboswitch; | 93 | 217 | 102.4 | 50 | RF00504 |
| RydC RNA | RF00505 | Gene; sRNA; | 2 | 12 | 64.7 | 91 | RF00505 |
| Threonine operon leader | RF00506 | Cis-reg; | 24 | 33 | 124.1 | 81 | RF00506 |
| Coronavirus frameshifting stimulation element | RF00507 | Cis-reg; frameshift_element; | 23 | 183 | 82.5 | 80 | RF00507 |
| Small nucleolar RNA snR64 | RF00509 | Gene; snRNA; guide; CD-box; | 3 | 9 | 102.8 | 89 | RF00509 |
| Tombusvirus internal replication element (IRE) | RF00510 | Cis-reg; | 22 | 41 | 88.7 | 85 | RF00510 |
| Kaposi's sarcoma-associated herpesvirus internal ribosome entry site (IRES) | RF00511 | Cis-reg; IRES; | 4 | 5 | 248.0 | 99 | RF00511 |
| Leucine operon leader | RF00512 | Cis-reg; leader; | 3 | 25 | 149.0 | 81 | RF00512 |
| Tryptophan operon leader | RF00513 | Cis-reg; leader; | 11 | 30 | 96.6 | 74 | RF00513 |
| Histidine operon leader | RF00514 | Cis-reg; leader; | 12 | 36 | 126.9 | 79 | RF00514 |
| PyrR binding site | RF00515 | Cis-reg; | 72 | 109 | 114.9 | 48 | RF00515 |
| ylbH leader | RF00516 | Cis-reg; | 5 | 16 | 121.7 | 75 | RF00516 |
| serC leader | RF00517 | Cis-reg; | 6 | 10 | 52.4 | 76 | RF00517 |
| speF leader | RF00518 | Cis-reg; | 6 | 11 | 326.2 | 69 | RF00518 |
| suhB | RF00519 | Gene; sRNA; | 13 | 31 | 74.9 | 51 | RF00519 |
| ybhL leader | RF00520 | Cis-reg; | 2 | 7 | 74.4 | 75 | RF00520 |
| SAM riboswitch (alpha-proteobacteria) | RF00521 | Cis-reg; riboswitch; | 12 | 32 | 76.8 | 59 | RF00521 |
| PreQ1 riboswitch | RF00522 | Cis-reg; riboswitch; | 22 | 63 | 45.9 | 61 | RF00522 |
| Prion pseudoknot | RF00523 | Cis-reg; | 167 | 1598 | 40.8 | 86 | RF00523 |
| R2 RNA element | RF00524 | Cis-reg; | 15 | 15 | 217.1 | 69 | RF00524 |
| Flavivirus DB element | RF00525 | Cis-reg; | 111 | 889 | 71.5 | 70 | RF00525 |
| Small nucleolar RNA Me28S-U3344 | RF00526 | Gene; snRNA; guide; CD-box; | 3 | 6 | 81.3 | 88 | RF00526 |
| Small nucleolar RNA Me28S-Gm3255 | RF00527 | Gene; snRNA; guide; CD-box; | 4 | 14 | 83.5 | 86 | RF00527 |
| Small nucleolar RNA Me28S-Gm1083 | RF00528 | Gene; snRNA; guide; CD-box; | 4 | 30 | 87.5 | 91 | RF00528 |
| Small nucleolar RNA Me28S-Am2589 | RF00529 | Gene; snRNA; guide; CD-box; | 3 | 9 | 108.0 | 74 | RF00529 |
| Small nucleolar RNA Me28S-Cm2645 | RF00530 | Gene; snRNA; guide; CD-box; | 6 | 19 | 75.0 | 92 | RF00530 |
| Small nucleolar RNA Me28S-Gm3113 | RF00531 | Gene; snRNA; guide; CD-box; | 3 | 6 | 83.2 | 84 | RF00531 |
| Small nucleolar RNA Me18S-Um1356 | RF00532 | Gene; snRNA; guide; CD-box; | 3 | 15 | 84.8 | 92 | RF00532 |
| Small nucleolar RNA Me18S-Gm1358 | RF00533 | Gene; snRNA; guide; CD-box; | 3 | 6 | 77.2 | 97 | RF00533 |
| SgrS RNA | RF00534 | Gene; sRNA; | 7 | 15 | 76.0 | 88 | RF00534 |
| Small nucleolar RNA Me28S-Am982 | RF00535 | Gene; snRNA; guide; CD-box; | 4 | 14 | 79.3 | 86 | RF00535 |
| Small nucleolar RNA Me28S-Cm3227 | RF00536 | Gene; snRNA; guide; CD-box; | 4 | 12 | 81.7 | 94 | RF00536 |
| Small nucleolar RNA Me28S-Am2634 | RF00537 | Gene; snRNA; guide; CD-box; | 9 | 24 | 90.2 | 83 | RF00537 |
| Small nucleolar RNA CD11 | RF00538 | Gene; snRNA; guide; CD-box; | 6 | 9 | 70.7 | 91 | RF00538 |
| Small nucleolar RNA Me28S-Cm788 | RF00539 | Gene; snRNA; guide; CD-box; | 3 | 6 | 72.5 | 93 | RF00539 |
| Small nucleolar RNA psi18S-1854 | RF00540 | Gene; snRNA; guide; HACA-box; | 6 | 15 | 150.6 | 87 | RF00540 |
| Small nucleolar RNA psi28S-2876 | RF00541 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 143.3 | 93 | RF00541 |
| Small nucleolar RNA psi28S-1192 | RF00542 | Gene; snRNA; guide; HACA-box; | 5 | 19 | 138.6 | 87 | RF00542 |
| Small nucleolar RNA psi18S-1377 | RF00543 | Gene; snRNA; guide; HACA-box; | 5 | 16 | 132.8 | 78 | RF00543 |
| Small nucleolar RNA psi28S-3327 | RF00544 | Gene; snRNA; guide; HACA-box; | 3 | 10 | 142.4 | 81 | RF00544 |
| Small nucleolar RNA psi18S-841/snoR66 | RF00545 | Gene; snRNA; guide; HACA-box; | 3 | 7 | 139.7 | 76 | RF00545 |
| Small nucleolar RNA psi28S-3316 | RF00546 | Gene; snRNA; guide; HACA-box; | 3 | 15 | 149.2 | 74 | RF00546 |
| TrkB IRES | RF00547 | Cis-reg; IRES; | 4 | 9 | 352.6 | 98 | RF00547 |
| U11 spliceosomal RNA | RF00548 | Gene; snRNA; splicing; | 9 | 29 | 137.8 | 59 | RF00548 |
| c-sis internal ribosome entry site (IRES) | RF00549 | Cis-reg; IRES; | 10 | 14 | 601.9 | 89 | RF00549 |
| Hepatitis E virus cis-reactive element | RF00550 | Cis-reg; | 46 | 82 | 146.7 | 84 | RF00550 |
| Bicoid 3'-UTR regulatory element | RF00551 | Cis-reg; | 15 | 44 | 550.6 | 87 | RF00551 |
| rncO | RF00552 | Cis-reg; | 6 | 24 | 204.1 | 80 | RF00552 |
| Small Cajal body specific RNA 1 | RF00553 | Gene; snRNA; guide; scaRNA; | 3 | 3 | 165.7 | 92 | RF00553 |
| Small nucleolar RNA SNORA48 | RF00554 | Gene; snRNA; guide; HACA-box; | 8 | 34 | 130.9 | 79 | RF00554 |
| Ribosomal protein L13 leader | RF00555 | Cis-reg; | 19 | 46 | 66.4 | 64 | RF00555 |
| Ribosomal protein L19 leader | RF00556 | Cis-reg; | 24 | 45 | 40.7 | 53 | RF00556 |
| Ribosomal protein L10 leader | RF00557 | Cis-reg; | 66 | 66 | 141.3 | 48 | RF00557 |
| Ribosomal protein L20 leader | RF00558 | Cis-reg; | 59 | 59 | 126.7 | 55 | RF00558 |
| Ribosomal protein L21 leader | RF00559 | Cis-reg; | 33 | 43 | 77.1 | 56 | RF00559 |
| Small nucleolar RNA SNORA17 | RF00560 | Gene; snRNA; guide; HACA-box; | 38 | 155 | 131.5 | 79 | RF00560 |
| Small nucleolar RNA SNORA40 | RF00561 | Gene; snRNA; guide; HACA-box; | 7 | 23 | 126.2 | 80 | RF00561 |
| Small nucleolar RNA SNORA49 | RF00562 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 134.7 | 92 | RF00562 |
| Small nucleolar RNA SNORA53 | RF00563 | Gene; snRNA; guide; HACA-box; | 4 | 5 | 246.0 | 90 | RF00563 |
| Small Cajal body specific RNA 11 | RF00564 | Gene; snRNA; guide; scaRNA; | 4 | 6 | 137.3 | 79 | RF00564 |
| Small Cajal body specific RNA 25 | RF00565 | Gene; snRNA; guide; scaRNA; | 3 | 9 | 134.6 | 80 | RF00565 |
| Small nucleolar RNA SNORA35 | RF00566 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 125.0 | 91 | RF00566 |
| Small nucleolar RNA SNORD17 | RF00567 | Gene; snRNA; guide; CD-box; | 3 | 3 | 232.0 | 90 | RF00567 |
| Small nucleolar RNA SNORA26 | RF00568 | Gene; snRNA; guide; HACA-box; | 12 | 23 | 121.2 | 73 | RF00568 |
| Small nucleolar RNA SNORD19 | RF00569 | Gene; snRNA; guide; CD-box; | 2 | 4 | 71.0 | 71 | RF00569 |
| Small Nucleolar RNA SNORD64 | RF00570 | Gene; snRNA; guide; CD-box; | 3 | 6 | 63.5 | 93 | RF00570 |
| Small nucleolar RNA SNORD65 | RF00571 | Gene; snRNA; guide; CD-box; | 4 | 6 | 72.2 | 82 | RF00571 |
| Small nucleolar RNA SNORD66 | RF00572 | Gene; snRNA; guide; CD-box; | 4 | 5 | 72.0 | 79 | RF00572 |
| Small nucleolar RNA SNORD67 | RF00573 | Gene; snRNA; guide; CD-box; | 2 | 3 | 106.7 | 98 | RF00573 |
| Small nucleolar RNA SNORD69 | RF00574 | Gene; snRNA; guide; CD-box; | 2 | 3 | 70.7 | 91 | RF00574 |
| Small nucleolar RNA SNORD70 | RF00575 | Gene; snRNA; guide; CD-box; | 4 | 8 | 80.5 | 85 | RF00575 |
| Small nucleolar RNA SNORD71 | RF00576 | Gene; snRNA; guide; HACA-box; | 2 | 3 | 75.3 | 90 | RF00576 |
| Small nucleolar RNA SNORD72 | RF00577 | Gene; snRNA; guide; CD-box; | 3 | 10 | 77.7 | 90 | RF00577 |
| Small nucleolar RNA SNORD89 | RF00578 | Gene; snRNA; guide; CD-box; | 2 | 4 | 105.5 | 93 | RF00578 |
| Small nucleolar RNA SNORD90 | RF00579 | Gene; snRNA; guide; CD-box; | 2 | 3 | 96.0 | 92 | RF00579 |
| Small nucleolar RNA 296A/B | RF00580 | Gene; snRNA; guide; CD-box; | 3 | 6 | 92.5 | 82 | RF00580 |
| Small nucleolar SNORD12/SNORD106 | RF00581 | Gene; snRNA; guide; CD-box; | 8 | 10 | 86.1 | 71 | RF00581 |
| Small Cajal body specific RNA 14 | RF00582 | Gene; snRNA; guide; scaRNA; | 4 | 9 | 129.0 | 69 | RF00582 |
| Small nucleolar RNA SNORD105 | RF00584 | Gene; snRNA; guide; CD-box; | 2 | 5 | 83.8 | 89 | RF00584 |
| Small nucleolar RNA SNORA12 | RF00586 | Gene; snRNA; guide; HACA-box; | 4 | 6 | 151.5 | 84 | RF00586 |
| Small nucleolar RNA SNORD41 | RF00588 | Gene; snRNA; guide; CD-box; | 2 | 3 | 69.7 | 92 | RF00588 |
| Small nucleolar RNA SNORD77 | RF00591 | Gene; snRNA; guide; CD-box; | 5 | 9 | 67.3 | 90 | RF00591 |
| Small nucleolar RNA SNORD78 | RF00592 | Gene; snRNA; guide; CD-box; | 4 | 11 | 65.8 | 90 | RF00592 |
| Small nucleolar RNA U83B | RF00593 | Gene; snRNA; guide; CD-box; | 4 | 9 | 91.4 | 87 | RF00593 |
| Small nucleolar RNA SNORD86 | RF00594 | Gene; snRNA; guide; CD-box; | 6 | 11 | 83.5 | 81 | RF00594 |