User:Jennifer Rfm/Sandbox
The $name RNA is the functional product of a gene that is not translated into a protein. Non protein coding RNA molecules usually contain important secondary structure or ligand binding motifs and are involved in many important biological processes in the cell.
The $name RNA is a region in a larger functional RNA molecule and has an important regulatory function. This is termed a cis-regulatory element. Cis-acting regulatory elements usually contain conserved secondary structures or ligand binding motifs. 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. :)
willow work list edited
[edit]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? :)
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 |
| snoRNA U3 | RF00012 | Gene; snRNA; guide; CD-box; | 21 | 227 | 227.2 | 51 | RF00012 |
| 6S 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 |
| snoRNA SNORD14 | RF00016 | Gene; snRNA; guide; CD-box; | 18 | 218 | 108.6 | 64 | RF00016 |
| Eukaryotic type SRP | RF00017 | Gene; | 50 | 433 | 292.5 | 39 | RF00017 |
| CsrB 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 | 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 |
| SECIS_element | 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 |
| snoRNA SNORA73 | RF00045 | Gene; snRNA; guide; HACA-box; | 23 | 71 | 207.7 | 71 | RF00045 |
| snoRNA R30 family | RF00046 | Gene; snRNA; guide; CD-box; | 6 | 30 | 95.6 | 89 | RF00046 |
| mir-2 microRNA | RF00047 | Gene; miRNA; | 9 | 25 | 70.1 | 71 | RF00047 |
| Enterovirus cis-acting replication element | RF00048 | Cis-reg; | 56 | 262 | 61.0 | 81 | RF00048 |
| snoRNA SNORD36 | RF00049 | Gene; snRNA; guide; CD-box; | 20 | 129 | 78.5 | 66 | RF00049 |
| FMN riboswitch | RF00050 | Cis-reg; riboswitch; | 34 | 183 | 144.7 | 65 | RF00050 |
| mir-17 microRNA family | RF00051 | Gene; miRNA; | 54 | 63 | 82.1 | 69 | RF00051 |
| lin-4 microRNA | RF00052 | Gene; miRNA; | 9 | 39 | 70.1 | 73 | RF00052 |
| mir-7 microRNA | RF00053 | Gene; miRNA; | 6 | 29 | 88.2 | 73 | RF00053 |
| snoRNA SNORD25 | RF00054 | Gene; snRNA; guide; CD-box; | 8 | 39 | 81.4 | 65 | RF00054 |
| snoRNA Z37 | RF00055 | Gene; snRNA; guide; CD-box; | 9 | 39 | 90.5 | 65 | RF00055 |
| snoRNA 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 | RF00059 | Cis-reg; riboswitch; | 174 | 496 | 109.2 | 52 | RF00059 |
| HgcE RNA | RF00060 | Gene; | 3 | 5 | 130.0 | 81 | RF00060 |
| HCV IRES | 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 |
| snoRNA snoR9 | RF00065 | Gene; snRNA; guide; CD-box; | 3 | 5 | 127.8 | 84 | RF00065 |
| U7 snRNA | RF00066 | Gene; snRNA; | 24 | 353 | 49.0 | 69 | RF00066 |
| snoRNA SNORD15 | RF00067 | Gene; snRNA; guide; CD-box; | 18 | 49 | 113.1 | 63 | RF00067 |
| snoRNA SNORD21 | RF00068 | Gene; snRNA; guide; CD-box; | 5 | 12 | 89.1 | 66 | RF00068 |
| snoRNA SNORD24 | RF00069 | Gene; snRNA; guide; CD-box; | 14 | 102 | 81.6 | 72 | RF00069 |
| snoRNA SNORD29 | RF00070 | Gene; snRNA; guide; CD-box; | 10 | 19 | 75.1 | 70 | RF00070 |
| snoRNA SNORD73 | RF00071 | Gene; snRNA; guide; CD-box; | 4 | 15 | 68.7 | 84 | RF00071 |
| snoRNA SNORA75 | RF00072 | Gene; snRNA; guide; HACA-box; | 6 | 23 | 130.4 | 73 | RF00072 |
| mir-156 microRNA | RF00073 | Gene; miRNA; | 10 | 47 | 93.5 | 67 | RF00073 |
| mir-29 microRNA | RF00074 | Gene; miRNA; | 10 | 53 | 67.9 | 80 | RF00074 |
| mir-166 microRNA | RF00075 | Gene; miRNA; | 30 | 63 | 123.2 | 57 | RF00075 |
| mir-181 microRNA | 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 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 |
| snoRNA SNORD28 | RF00085 | Gene; snRNA; guide; CD-box; | 4 | 8 | 77.2 | 72 | RF00085 |
| snoRNA SNORD27 | RF00086 | Gene; snRNA; guide; CD-box; | 11 | 28 | 77.9 | 68 | RF00086 |
| snoRNA SNORD26 | RF00087 | Gene; snRNA; guide; CD-box; | 4 | 8 | 74.4 | 82 | RF00087 |
| snoRNA SNORD30 | RF00088 | Gene; snRNA; guide; CD-box; | 3 | 10 | 70.0 | 78 | RF00088 |
| snoRNA SNORD31 | RF00089 | Gene; snRNA; guide; CD-box; | 4 | 12 | 69.0 | 79 | RF00089 |
| snoRNA SNORA74 | RF00090 | Gene; snRNA; guide; HACA-box; | 3 | 9 | 197.8 | 76 | RF00090 |
| snoRNA SNORA62 | RF00091 | Gene; snRNA; guide; HACA-box; | 10 | 26 | 148.2 | 71 | RF00091 |
| snoRNA SNORA63 | RF00092 | Gene; snRNA; guide; HACA-box; | 8 | 37 | 126.3 | 71 | RF00092 |
| snoRNA 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 CD box snoRNA | RF00095 | Gene; snRNA; guide; CD-box; | 38 | 58 | 56.2 | 59 | RF00095 |
| U8 snoRNA | RF00096 | Gene; snRNA; guide; CD-box; | 6 | 38 | 133.8 | 60 | RF00096 |
| Plant snoRNA R71 | RF00097 | Gene; snRNA; guide; CD-box; | 21 | 370 | 106.5 | 77 | RF00097 |
| Snake HACA box snoRNA | RF00098 | Gene; snRNA; guide; HACA-box; | 22 | 55 | 140.3 | 90 | RF00098 |
| snoRNA SNORD22 | RF00099 | Gene; snRNA; guide; CD-box; | 3 | 9 | 125.8 | 84 | RF00099 |
| 7SK RNA | RF00100 | Gene; | 6 | 171 | 317.0 | 72 | RF00100 |
| SraC family RNA | RF00101 | Gene; sRNA; | 4 | 19 | 242.7 | 76 | RF00101 |
| VA RNA | RF00102 | Gene; | 54 | 157 | 158.9 | 70 | RF00102 |
| mir-1 microRNA family | RF00103 | Gene; miRNA; | 7 | 27 | 76.7 | 71 | RF00103 |
| mir-10 microRNA family | RF00104 | Gene; miRNA; | 11 | 73 | 73.8 | 67 | RF00104 |
| snoRNA SNORD115 | RF00105 | Gene; snRNA; guide; CD-box; | 23 | 133 | 81.1 | 90 | RF00105 |
| RNAI | RF00106 | Gene; antisense; | 10 | 138 | 103.5 | 71 | RF00106 |
| FinP antisense RNA | RF00107 | Gene; | 6 | 15 | 77.6 | 91 | RF00107 |
| snoRNA 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 RNA | 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 microRNA family | RF00129 | Gene; miRNA; | 5 | 29 | 78.0 | 85 | RF00129 |
| mir-192 microRNA family | RF00130 | Gene; miRNA; | 4 | 12 | 106.0 | 75 | RF00130 |
| mir-30 microRNA | RF00131 | Gene; miRNA; | 4 | 21 | 70.8 | 82 | RF00131 |
| snoRNA R24 | RF00132 | Gene; snRNA; guide; CD-box; | 12 | 45 | 92.4 | 81 | RF00132 |
| snoRNA SNORD33 family | RF00133 | Gene; snRNA; guide; CD-box; | 17 | 43 | 85.0 | 65 | RF00133 |
| snoRNA Z196 family | RF00134 | Gene; snRNA; guide; CD-box; | 23 | 43 | 84.4 | 64 | RF00134 |
| snoRNA Z223 | RF00135 | Gene; snRNA; guide; CD-box; | 5 | 35 | 90.4 | 82 | RF00135 |
| snoRNA SNORD81 | RF00136 | Gene; snRNA; guide; CD-box; | 3 | 19 | 76.5 | 82 | RF00136 |
| snoRNA SNORD83 | RF00137 | Gene; snRNA; guide; CD-box; | 7 | 56 | 76.9 | 85 | RF00137 |
| snoRNA SNORD16 | RF00138 | Gene; snRNA; guide; CD-box; | 5 | 11 | 98.5 | 81 | RF00138 |
| snoRNA 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 |
| snoRNA Z118 family | RF00142 | Gene; snRNA; guide; CD-box; | 7 | 42 | 103.2 | 81 | RF00142 |
| mir-6 microRNA | RF00143 | Gene; miRNA; | 3 | 9 | 77.0 | 79 | RF00143 |
| mir-199 microRNA | RF00144 | Gene; miRNA; | 3 | 18 | 99.9 | 88 | RF00144 |
| snoRNA Z105 | RF00145 | Gene; snRNA; guide; CD-box; | 5 | 17 | 69.0 | 79 | RF00145 |
| snoRNA SNORD34 | RF00147 | Gene; snRNA; guide; CD-box; | 9 | 34 | 79.4 | 67 | RF00147 |
| snoRNA Z103 | RF00149 | Gene; snRNA; guide; CD-box; | 9 | 42 | 98.3 | 78 | RF00149 |
| snoRNA SNORD42 | RF00150 | Gene; snRNA; guide; CD-box; | 7 | 14 | 64.3 | 76 | RF00150 |
| snoRNA SNORD58 | RF00151 | Gene; snRNA; guide; CD-box; | 3 | 20 | 65.6 | 81 | RF00151 |
| snoRNA SNORD79 | RF00152 | Gene; snRNA; guide; CD-box; | 6 | 9 | 74.4 | 83 | RF00152 |
| snoRNA SNORD62 | RF00153 | Gene; snRNA; guide; CD-box; | 3 | 8 | 85.5 | 94 | RF00153 |
| snoRNA SNORD63 | RF00154 | Gene; snRNA; guide; CD-box; | 2 | 3 | 68.7 | 90 | RF00154 |
| snoRNA SNORA66 | RF00155 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 132.2 | 85 | RF00155 |
| snoRNA SNORA70 | RF00156 | Gene; snRNA; guide; HACA-box; | 13 | 90 | 130.7 | 70 | RF00156 |
| snoRNA SNORD39 | RF00157 | Gene; snRNA; guide; CD-box; | 4 | 15 | 78.3 | 79 | RF00157 |
| snoRNA SNORD82 | RF00158 | Gene; snRNA; guide; CD-box; | 3 | 10 | 69.8 | 88 | RF00158 |
| snoRNA Z168 family | RF00159 | Gene; snRNA; guide; CD-box; | 6 | 18 | 82.2 | 87 | RF00159 |
| snoRNA Z159 family | RF00160 | Gene; snRNA; guide; CD-box; | 10 | 37 | 87.7 | 76 | RF00160 |
| Nanos 3' UTR element | RF00161 | Cis-reg; | 3 | 16 | 63.1 | 90 | RF00161 |
| SAM riboswitch | 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 | RF00164 | Cis-reg; | 38 | 302 | 43.0 | 79 | RF00164 |
| Coronavirus 3' UTR pseudoknot | RF00165 | Cis-reg; | 14 | 85 | 62.5 | 70 | RF00165 |
| PrrB 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 SRP | 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 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 |
| SSU rRNA 5' domain | RF00177 | Gene; rRNA; | 358 | 343 | 487.3 | 48 | RF00177 |
| mir-24 microRNA 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 | RF00180 | Cis-reg; | 13 | 30 | 37.0 | 90 | RF00180 |
| snoRNA SNORD113 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 CRE | RF00185 | Cis-reg; | 84 | 303 | 95.4 | 69 | RF00185 |
| snoRNA SNORD101 | RF00186 | Gene; snRNA; guide; CD-box; | 3 | 6 | 73.2 | 89 | RF00186 |
| snoRNA SNORD102 | RF00187 | Gene; snRNA; guide; CD-box; | 2 | 4 | 71.8 | 94 | RF00187 |
| snoRNA SNORD103 | RF00188 | Gene; snRNA; guide; CD-box; | 3 | 5 | 89.8 | 96 | RF00188 |
| snoRNA SNORD95 | RF00189 | Gene; snRNA; guide; CD-box; | 5 | 12 | 68.3 | 80 | RF00189 |
| U98 snoRNA | RF00190 | Gene; snRNA; guide; HACA-box; | 3 | 14 | 133.3 | 78 | RF00190 |
| snoRNA 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 |
| snoRNA Z199 | RF00200 | Gene; snRNA; guide; CD-box; | 17 | 38 | 83.1 | 79 | RF00200 |
| snoRNA Z278 | RF00201 | Gene; snRNA; guide; CD-box; | 7 | 19 | 114.7 | 94 | RF00201 |
| snoRNA R66 | RF00202 | Gene; snRNA; guide; CD-box; | 6 | 35 | 73.2 | 89 | RF00202 |
| snoRNA R160 | RF00203 | Gene; snRNA; guide; CD-box; | 9 | 21 | 78.4 | 76 | RF00203 |
| snoRNA R12 | RF00204 | Gene; snRNA; guide; CD-box; | 9 | 66 | 80.8 | 82 | RF00204 |
| snoRNA R41 | RF00205 | Gene; snRNA; guide; CD-box; | 7 | 15 | 95.4 | 85 | RF00205 |
| snoRNA SNORD54 | RF00206 | Gene; snRNA; guide; CD-box; | 22 | 45 | 80.2 | 70 | RF00206 |
| K10 RNA element | RF00207 | Cis-reg; | 3 | 6 | 44.0 | 100 | RF00207 |
| snoRNA R72 | RF00208 | Gene; snRNA; guide; CD-box; | 4 | 10 | 87.0 | 98 | RF00208 |
| Pestivirus IRES | RF00209 | Cis-reg; IRES; | 25 | 997 | 249.1 | 80 | RF00209 |
| Aphthovirus IRES | RF00210 | Cis-reg; IRES; | 92 | 188 | 461.5 | 73 | RF00210 |
| snoRNA SNORD35 | RF00211 | Gene; snRNA; guide; CD-box; | 8 | 17 | 88.1 | 76 | RF00211 |
| snoRNA SNORD38 | RF00212 | Gene; snRNA; guide; CD-box; | 7 | 23 | 69.0 | 76 | RF00212 |
| snoRNA R38 | RF00213 | Gene; snRNA; guide; CD-box; | 19 | 50 | 84.4 | 58 | RF00213 |
| Retrovirus direct repeat RNA | RF00214 | Cis-reg; | 26 | 124 | 89.2 | 86 | RF00214 |
| Tombus virus defective interfering RNA region 3 | RF00215 | Cis-reg; | 28 | 66 | 69.6 | 79 | RF00215 |
| c-myc IRES | RF00216 | Cis-reg; IRES; | 23 | 54 | 296.5 | 79 | RF00216 |
| snoRNA SNORD20 | RF00217 | Gene; snRNA; guide; CD-box; | 4 | 6 | 80.2 | 100 | RF00217 |
| snoRNA SNORD46 | RF00218 | Gene; snRNA; guide; CD-box; | 9 | 27 | 87.9 | 70 | RF00218 |
| snoRNA SNORD32 | RF00219 | Gene; snRNA; guide; CD-box; | 4 | 21 | 82.0 | 90 | RF00219 |
| Human rhinovirus CRE | RF00220 | Cis-reg; | 12 | 60 | 85.5 | 72 | RF00220 |
| snoRNA SNORD43 | RF00221 | Gene; snRNA; guide; CD-box; | 7 | 19 | 85.7 | 61 | RF00221 |
| Bag-1 IRES | RF00222 | Cis-reg; IRES; | 4 | 15 | 349.8 | 86 | RF00222 |
| bip IRES | RF00223 | Cis-reg; IRES; | 4 | 10 | 236.4 | 74 | RF00223 |
| FGF-2 IRES | RF00224 | Cis-reg; IRES; | 3 | 9 | 435.2 | 95 | RF00224 |
| Tobamovirus IRES | RF00225 | Cis-reg; IRES; | 7 | 11 | 152.1 | 86 | RF00225 |
| n-myc IRES | RF00226 | Cis-reg; IRES; | 6 | 29 | 269.7 | 57 | RF00226 |
| FIE3 RNA element | RF00227 | Cis-reg; | 5 | 10 | 65.0 | 77 | RF00227 |
| Hepatitis A virus IRES | RF00228 | Cis-reg; IRES; | 23 | 137 | 389.0 | 95 | RF00228 |
| Picornavirus IRES | RF00229 | Cis-reg; IRES; | 208 | 1512 | 205.1 | 80 | RF00229 |
| T-box leader | RF00230 | Cis-reg; | 103 | 716 | 226.8 | 46 | RF00230 |
| scaRNA 13 | RF00231 | Gene; snRNA; guide; scaRNA; | 3 | 7 | 273.4 | 86 | RF00231 |
| Spi-1 5' UTR regulatory element | RF00232 | Cis-reg; | 5 | 10 | 165.2 | 89 | RF00232 |
| Tymovirus 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 microRNA family | RF00237 | Gene; miRNA; | 5 | 34 | 61.3 | 85 | RF00237 |
| ctRNA | RF00238 | Gene; antisense; | 48 | 52 | 85.3 | 71 | RF00238 |
| mir-124 microRNA family | RF00239 | Gene; miRNA; | 6 | 25 | 80.6 | 85 | RF00239 |
| RNA-OUT | RF00240 | Gene; | 4 | 172 | 70.0 | 96 | RF00240 |
| mir-8 microRNA 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 family | RF00244 | Gene; miRNA; | 5 | 24 | 73.5 | 80 | RF00244 |
| mir-19 microRNA family | RF00245 | Gene; miRNA; | 3 | 43 | 75.4 | 82 | RF00245 |
| mir-135 microRNA family | RF00246 | Gene; miRNA; | 5 | 22 | 90.2 | 75 | RF00246 |
| mir-160 microRNA family | RF00247 | Gene; miRNA; | 7 | 33 | 94.5 | 65 | RF00247 |
| mir-148 microRNA family | RF00248 | Gene; miRNA; | 5 | 9 | 86.2 | 71 | RF00248 |
| mir-46 microRNA 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 family | RF00251 | Gene; miRNA; | 7 | 31 | 72.3 | 79 | RF00251 |
| Alfalfa mosaic virus coat protein binding RNA | RF00252 | Cis-reg; | 18 | 23 | 159.4 | 90 | RF00252 |
| mir-101 microRNA family | RF00253 | Gene; miRNA; | 4 | 20 | 75.0 | 89 | RF00253 |
| mir-16 microRNA family | RF00254 | Gene; miRNA; | 12 | 37 | 80.4 | 76 | RF00254 |
| mir-218 microRNA family | RF00255 | Gene; miRNA; | 3 | 23 | 96.1 | 80 | RF00255 |
| mir-196 microRNA family | RF00256 | Gene; miRNA; | 14 | 45 | 91.1 | 73 | RF00256 |
| mir-194 microRNA family | RF00257 | Gene; miRNA; | 4 | 13 | 85.0 | 79 | RF00257 |
| mir-130 microRNA 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 CRE | RF00260 | Cis-reg; | 52 | 348 | 51.0 | 87 | RF00260 |
| L-myc IRES | RF00261 | Cis-reg; IRES; | 3 | 5 | 220.2 | 94 | RF00261 |
| sar RNA | RF00262 | Gene; antisense; | 4 | 7 | 65.9 | 87 | RF00262 |
| snoRNA SNORA68 | RF00263 | Gene; snRNA; guide; HACA-box; | 4 | 12 | 127.4 | 76 | RF00263 |
| snoRNA SNORA64 family | RF00264 | Gene; snRNA; guide; HACA-box; | 9 | 17 | 132.4 | 70 | RF00264 |
| snoRNA SNORA69 | RF00265 | Gene; snRNA; guide; HACA-box; | 3 | 9 | 132.1 | 76 | RF00265 |
| snoRNA Z17 | RF00266 | Gene; snRNA; guide; CD-box; | 4 | 8 | 71.8 | 79 | RF00266 |
| snoRNA R64 family | RF00267 | Gene; snRNA; guide; CD-box; | 11 | 24 | 94.2 | 70 | RF00267 |
| snoRNA snoZ7 | RF00268 | Gene; snRNA; guide; CD-box; | 3 | 9 | 80.2 | 82 | RF00268 |
| snoRNA SNORD61 | RF00270 | Gene; snRNA; guide; CD-box; | 3 | 6 | 71.3 | 87 | RF00270 |
| snoRNA SNORD60 | RF00271 | Gene; snRNA; guide; CD-box; | 3 | 9 | 81.7 | 87 | RF00271 |
| snoRNA SNORA67 | RF00272 | Gene; snRNA; guide; HACA-box; | 10 | 21 | 139.9 | 73 | RF00272 |
| snoRNA SNORD59 | RF00273 | Gene; snRNA; guide; CD-box; | 4 | 11 | 72.1 | 83 | RF00273 |
| snoRNA SNORD57 | RF00274 | Gene; snRNA; guide; CD-box; | 3 | 5 | 69.6 | 88 | RF00274 |
| snoRNA SNORD56 | RF00275 | Gene; snRNA; guide; CD-box; | 7 | 14 | 70.8 | 84 | RF00275 |
| snoRNA SNORD52 | RF00276 | Gene; snRNA; guide; CD-box; | 4 | 19 | 66.4 | 80 | RF00276 |
| snoRNA SNORD49 | RF00277 | Gene; snRNA; guide; CD-box; | 4 | 10 | 68.6 | 73 | RF00277 |
| snoRNA SNORD50 | RF00278 | Gene; snRNA; guide; CD-box; | 6 | 12 | 70.8 | 83 | RF00278 |
| snoRNA SNORD45 | RF00279 | Gene; snRNA; guide; CD-box; | 11 | 18 | 75.7 | 80 | RF00279 |
| snoRNA SNORD51 | RF00280 | Gene; snRNA; guide; CD-box; | 3 | 4 | 75.0 | 88 | RF00280 |
| snoRNA SNORD47 | RF00281 | Gene; snRNA; guide; CD-box; | 3 | 11 | 74.9 | 88 | RF00281 |
| snoRNA SNORD48 | RF00282 | Gene; snRNA; guide; CD-box; | 3 | 13 | 63.2 | 92 | RF00282 |
| scaRNA 18 | RF00283 | Gene; snRNA; guide; scaRNA; | 4 | 18 | 80.3 | 86 | RF00283 |
| Z18 snoRNA | RF00284 | Gene; snRNA; guide; CD-box; | 4 | 19 | 76.2 | 76 | RF00284 |
| Z6 snoRNA | RF00285 | Gene; snRNA; guide; CD-box; | 3 | 18 | 86.0 | 77 | RF00285 |
| scaRNA 8 | RF00286 | Gene; snRNA; guide; scaRNA; | 3 | 5 | 128.4 | 81 | RF00286 |
| snoRNA SNORD44 | RF00287 | Gene; snRNA; guide; CD-box; | 3 | 5 | 60.6 | 92 | RF00287 |
| Z30 snoRNA | RF00288 | Gene; snRNA; guide; CD-box; | 4 | 12 | 97.4 | 83 | RF00288 |
| Z12 snoRNA | RF00289 | Gene; snRNA; guide; CD-box; | 3 | 5 | 70.0 | 87 | RF00289 |
| Bamboo mosaic potexvirus cis-regulatory element | RF00290 | Cis-reg; | 4 | 14 | 140.0 | 100 | RF00290 |
| snoRNA snoR639 | RF00291 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 138.0 | 100 | RF00291 |
| snoRNA TBR5 | RF00292 | Gene; snRNA; guide; CD-box; | 3 | 5 | 90.0 | 80 | RF00292 |
| snoRNA snoM1 | RF00293 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 99.6 | 91 | RF00293 |
| snoRNA TBR17 | RF00294 | Gene; snRNA; guide; CD-box; | 5 | 8 | 270.5 | 74 | RF00294 |
| snoRNA TBR7 | RF00295 | Gene; snRNA; guide; CD-box; | 6 | 9 | 74.8 | 80 | RF00295 |
| snoRNA R16 | RF00296 | Gene; snRNA; guide; CD-box; | 17 | 18 | 84.8 | 77 | RF00296 |
| snoRNA Z221 | RF00300 | Gene; snRNA; guide; CD-box; | 3 | 7 | 112.4 | 96 | RF00300 |
| snoRNA Z256 | RF00301 | Gene; snRNA; guide; CD-box; | 5 | 10 | 94.4 | 75 | RF00301 |
| snoRNA SNORA65 | RF00302 | Gene; snRNA; guide; HACA-box; | 8 | 9 | 123.9 | 81 | RF00302 |
| snoRNA snoR86 | RF00303 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 125.3 | 87 | RF00303 |
| snoRNA Z279 | RF00304 | Gene; snRNA; guide; CD-box; | 3 | 7 | 111.1 | 94 | RF00304 |
| snoRNA Z248 | RF00305 | Gene; snRNA; guide; CD-box; | 4 | 10 | 137.0 | 98 | RF00305 |
| snoRNA Z178 | RF00306 | Gene; snRNA; guide; CD-box; | 4 | 6 | 152.0 | 100 | RF00306 |
| snoRNA snoR98 | RF00307 | Gene; snRNA; guide; HACA-box; | 4 | 5 | 110.4 | 87 | RF00307 |
| snoRNA snR60 family | RF00309 | Gene; snRNA; guide; CD-box; | 23 | 43 | 93.4 | 64 | RF00309 |
| snoRNA Z165 | RF00310 | Gene; snRNA; guide; CD-box; | 3 | 8 | 90.9 | 95 | RF00310 |
| snoRNA Z188 | RF00311 | Gene; snRNA; guide; CD-box; | 7 | 20 | 119.7 | 78 | RF00311 |
| snoRNA Z206 | RF00312 | Gene; snRNA; guide; CD-box; | 3 | 12 | 130.3 | 89 | RF00312 |
| snoRNA Z173 | RF00313 | Gene; snRNA; guide; CD-box; | 3 | 5 | 106.6 | 100 | RF00313 |
| snoRNA Z182 | RF00314 | Gene; snRNA; guide; CD-box; | 4 | 9 | 88.7 | 96 | RF00314 |
| snoRNA J33 | RF00315 | Gene; snRNA; guide; CD-box; | 3 | 24 | 80.9 | 67 | RF00315 |
| snoRNA R43 | RF00316 | Gene; snRNA; guide; CD-box; | 16 | 20 | 73.1 | 83 | RF00316 |
| snoRNA Z163 family | RF00317 | Gene; snRNA; guide; CD-box; | 7 | 15 | 88.5 | 85 | RF00317 |
| snoRNA Z175 | RF00318 | Gene; snRNA; guide; CD-box; | 3 | 5 | 81.0 | 99 | RF00318 |
| snoRNA MBI-1 | RF00319 | Gene; snRNA; guide; HACA-box; | 5 | 7 | 182.4 | 83 | RF00319 |
| snoRNA Z185 | RF00320 | Gene; snRNA; guide; CD-box; | 2 | 8 | 84.2 | 92 | RF00320 |
| snoRNA Z247 | RF00321 | Gene; snRNA; guide; CD-box; | 8 | 32 | 137.3 | 71 | RF00321 |
| snoRNA MBI-161 | RF00322 | Gene; snRNA; guide; HACA-box; | 5 | 8 | 127.1 | 88 | RF00322 |
| snoRNA R79 | RF00323 | Gene; snRNA; guide; CD-box; | 4 | 9 | 63.1 | 96 | RF00323 |
| snoRNA MBII-202 | RF00324 | Gene; snRNA; guide; CD-box; | 5 | 11 | 78.0 | 80 | RF00324 |
| snoRNA SNORD53 | RF00325 | Gene; snRNA; guide; CD-box; | 3 | 8 | 76.2 | 82 | RF00325 |
| snoRNA Z155 | RF00326 | Gene; snRNA; guide; CD-box; | 8 | 14 | 78.0 | 81 | RF00326 |
| snoRNA Z194 | RF00327 | Gene; snRNA; guide; CD-box; | 3 | 7 | 106.3 | 99 | RF00327 |
| snoRNA Z161 family | RF00328 | Gene; snRNA; guide; CD-box; | 7 | 15 | 92.2 | 82 | RF00328 |
| snoRNA Z162 | RF00329 | Gene; snRNA; guide; CD-box; | 3 | 7 | 88.1 | 90 | RF00329 |
| snoRNA Z43 | RF00330 | Gene; snRNA; guide; CD-box; | 4 | 13 | 99.2 | 82 | RF00330 |
| snoRNA Z169 | RF00331 | Gene; snRNA; guide; CD-box; | 3 | 8 | 66.8 | 90 | RF00331 |
| snoRNA Z266 | RF00332 | Gene; snRNA; guide; CD-box; | 4 | 22 | 87.0 | 81 | RF00332 |
| snoRNA Z157 family | RF00333 | Gene; snRNA; guide; CD-box; | 10 | 26 | 97.4 | 73 | RF00333 |
| snoRNA MBI-28 | RF00334 | Gene; snRNA; guide; HACA-box; | 3 | 18 | 115.6 | 77 | RF00334 |
| snoRNA Z13 family | RF00335 | Gene; snRNA; guide; CD-box; | 4 | 10 | 95.9 | 74 | RF00335 |
| snoRNA J26 | RF00336 | Gene; snRNA; guide; CD-box; | 5 | 18 | 146.4 | 91 | RF00336 |
| snoRNA Z112 | RF00337 | Gene; snRNA; guide; CD-box; | 3 | 29 | 182.7 | 92 | RF00337 |
| snoRNA snR53 | RF00338 | Gene; snRNA; guide; CD-box; | 3 | 3 | 89.7 | 94 | RF00338 |
| snoRNA snoR60 | RF00339 | Gene; snRNA; guide; CD-box; | 3 | 26 | 73.8 | 84 | RF00339 |
| snoRNA snoMBI-87 | RF00340 | Gene; snRNA; guide; HACA-box; | 6 | 25 | 131.4 | 79 | RF00340 |
| snoRNA Z39 | RF00341 | Gene; snRNA; guide; CD-box; | 5 | 8 | 61.6 | 88 | RF00341 |
| snoRNA Z40 | RF00342 | Gene; snRNA; guide; CD-box; | 5 | 11 | 73.0 | 89 | RF00342 |
| snoRNA Z122 | RF00343 | Gene; snRNA; guide; CD-box; | 3 | 16 | 84.9 | 75 | RF00343 |
| snoRNA Z267 | RF00344 | Gene; snRNA; guide; CD-box; | 5 | 12 | 73.1 | 78 | RF00344 |
| snoRNA snoR1 | RF00345 | Gene; snRNA; guide; CD-box; | 7 | 20 | 95.1 | 80 | RF00345 |
| snoRNA Z50 | RF00347 | Gene; snRNA; guide; CD-box; | 3 | 4 | 65.8 | 93 | RF00347 |
| snoRNA snoR9 | RF00348 | Gene; snRNA; guide; CD-box; | 7 | 32 | 126.0 | 76 | RF00348 |
| snoRNA R11 family | RF00349 | Gene; snRNA; guide; CD-box; | 5 | 19 | 91.9 | 84 | RF00349 |
| snoRNA Z152 family | RF00350 | Gene; snRNA; guide; CD-box; | 4 | 12 | 98.8 | 80 | RF00350 |
| snoRNA R20 | RF00351 | Gene; snRNA; guide; CD-box; | 3 | 4 | 91.0 | 93 | RF00351 |
| snoRNA R21 | RF00352 | Gene; snRNA; guide; CD-box; | 4 | 8 | 82.0 | 88 | RF00352 |
| snoRNA snoR31 family | RF00353 | Gene; snRNA; guide; CD-box; | 8 | 35 | 95.3 | 87 | RF00353 |
| snoRNA snoR28 | RF00355 | Gene; snRNA; guide; CD-box; | 4 | 11 | 74.0 | 94 | RF00355 |
| snoRNA R32 family | RF00356 | Gene; snRNA; guide; CD-box; | 6 | 8 | 95.6 | 84 | RF00356 |
| snoRNA R44 family | RF00357 | Gene; snRNA; guide; CD-box; | 19 | 39 | 97.6 | 70 | RF00357 |
| snoRNA Z101 | RF00358 | Gene; snRNA; guide; CD-box; | 3 | 18 | 94.4 | 71 | RF00358 |
| snoRNA Z102 family | RF00359 | Gene; snRNA; guide; CD-box; | 4 | 11 | 86.5 | 89 | RF00359 |
| snoRNA Z107 family | RF00360 | Gene; snRNA; guide; CD-box; | 6 | 38 | 112.8 | 81 | RF00360 |
| snoRNA 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 family | RF00363 | Gene; miRNA; | 3 | 4 | 70.0 | 93 | RF00363 |
| mir-BART2 microRNA family | RF00364 | Gene; miRNA; | 8 | 14 | 60.4 | 93 | RF00364 |
| mir-BHRF1-1 microRNA family | RF00365 | Gene; miRNA; | 3 | 6 | 66.0 | 97 | RF00365 |
| mir-BHRF1-2 microRNA family | RF00366 | Gene; miRNA; | 4 | 9 | 65.0 | 90 | RF00366 |
| mir-BHRF1-3 microRNA 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 | RF00375 | Cis-reg; | 388 | 1609 | 94.8 | 79 | RF00375 |
| HIV gag stem loop 3 | RF00376 | Cis-reg; | 1403 | 6923 | 81.1 | 87 | RF00376 |
| snoRNA U6-53 family | RF00377 | Gene; snRNA; guide; CD-box; | 4 | 8 | 106.9 | 83 | RF00377 |
| Qrr RNA | RF00378 | Gene; sRNA; | 6 | 25 | 103.0 | 79 | RF00378 |
| ydaO leader | RF00379 | Cis-reg; | 25 | 80 | 155.4 | 55 | RF00379 |
| ykoK leader | RF00380 | Cis-reg; | 36 | 57 | 168.1 | 61 | RF00380 |
| Antizyme RNA frameshifting 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 CRE | RF00386 | Cis-reg; | 160 | 287 | 88.1 | 84 | RF00386 |
| FGF-1 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 |
| snoRNA SNORA5 | RF00392 | Gene; snRNA; guide; HACA-box; | 6 | 12 | 131.1 | 74 | RF00392 |
| snoRNA SNORA8 | RF00393 | Gene; snRNA; guide; HACA-box; | 5 | 14 | 135.1 | 85 | RF00393 |
| snoRNA SNORA4 | RF00394 | Gene; snRNA; guide; HACA-box; | 7 | 13 | 138.9 | 76 | RF00394 |
| snoRNA SNORA13 | RF00396 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 132.5 | 87 | RF00396 |
| snoRNA SNORA14 | RF00397 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 134.7 | 92 | RF00397 |
| snoRNA SNORA15 | RF00398 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 128.2 | 84 | RF00398 |
| snoRNA SNORA24 | RF00399 | Gene; snRNA; guide; HACA-box; | 5 | 17 | 125.5 | 74 | RF00399 |
| snoRNA SNORA28 | RF00400 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 124.7 | 95 | RF00400 |
| snoRNA SNORA20 | RF00401 | Gene; snRNA; guide; HACA-box; | 17 | 34 | 128.7 | 88 | RF00401 |
| snoRNA SNORA25 | RF00402 | Gene; snRNA; guide; HACA-box; | 9 | 29 | 128.1 | 74 | RF00402 |
| snoRNA SNORA41 | RF00403 | Gene; snRNA; guide; HACA-box; | 6 | 8 | 129.0 | 88 | RF00403 |
| snoRNA SNORA46 | RF00404 | Gene; snRNA; guide; HACA-box; | 3 | 8 | 125.4 | 81 | RF00404 |
| snoRNA SNORA44 | RF00405 | Gene; snRNA; guide; HACA-box; | 6 | 17 | 127.5 | 81 | RF00405 |
| snoRNA SNORA42 | RF00406 | Gene; snRNA; guide; HACA-box; | 4 | 44 | 131.1 | 79 | RF00406 |
| snoRNA SNORA50 | RF00407 | Gene; snRNA; guide; HACA-box; | 3 | 4 | 135.5 | 98 | RF00407 |
| snoRNA SNORA1 | RF00408 | Gene; snRNA; guide; HACA-box; | 6 | 11 | 132.8 | 87 | RF00408 |
| snoRNA SNORA7 | RF00409 | Gene; snRNA; guide; HACA-box; | 8 | 45 | 137.8 | 69 | RF00409 |
| snoRNA SNORA2 | RF00410 | Gene; snRNA; guide; HACA-box; | 18 | 27 | 134.0 | 72 | RF00410 |
| snoRNA SNORA9 | RF00411 | Gene; snRNA; guide; HACA-box; | 6 | 14 | 130.4 | 87 | RF00411 |
| snoRNA SNORA21 | RF00412 | Gene; snRNA; guide; HACA-box; | 5 | 13 | 133.5 | 86 | RF00412 |
| snoRNA SNORA19 | RF00413 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 121.3 | 91 | RF00413 |
| snoRNA SNORA22 | RF00414 | Gene; snRNA; guide; HACA-box; | 5 | 6 | 135.0 | 91 | RF00414 |
| snoRNA SNORA30 | RF00415 | Gene; snRNA; guide; HACA-box; | 11 | 14 | 129.1 | 70 | RF00415 |
| snoRNA SNORA43 | RF00416 | Gene; snRNA; guide; HACA-box; | 7 | 20 | 135.1 | 71 | RF00416 |
| snoRNA SNORA56 | RF00417 | Gene; snRNA; guide; HACA-box; | 4 | 7 | 129.9 | 97 | RF00417 |
| snoRNA SNORA58 | RF00418 | Gene; snRNA; guide; HACA-box; | 4 | 7 | 134.9 | 85 | RF00418 |
| snoRNA SNORA52 | RF00419 | Gene; snRNA; guide; HACA-box; | 4 | 9 | 135.1 | 74 | RF00419 |
| snoRNA SNORA61 | RF00420 | Gene; snRNA; guide; HACA-box; | 4 | 15 | 128.7 | 77 | RF00420 |
| snoRNA SNORA32 | RF00421 | Gene; snRNA; guide; HACA-box; | 9 | 33 | 116.7 | 78 | RF00421 |
| scaRNA 24 | RF00422 | Gene; snRNA; guide; scaRNA; | 3 | 7 | 133.1 | 84 | RF00422 |
| scaRNA 4 | RF00423 | Gene; snRNA; guide; scaRNA; | 3 | 12 | 127.2 | 88 | RF00423 |
| scaRNA 16 | RF00424 | Gene; snRNA; guide; scaRNA; | 6 | 9 | 182.8 | 80 | RF00424 |
| snoRNA SNORA18 | RF00425 | Gene; snRNA; guide; HACA-box; | 6 | 19 | 126.4 | 79 | RF00425 |
| scaRNA 15 | RF00426 | Gene; snRNA; guide; scaRNA; | 3 | 8 | 124.2 | 96 | RF00426 |
| scaRNA 23 | RF00427 | Gene; snRNA; guide; scaRNA; | 3 | 4 | 126.0 | 92 | RF00427 |
| snoRNA SNORA38 | RF00428 | Gene; snRNA; guide; HACA-box; | 5 | 26 | 132.2 | 84 | RF00428 |
| snoRNA SNORA29 | RF00429 | Gene; snRNA; guide; HACA-box; | 3 | 10 | 137.3 | 82 | RF00429 |
| snoRNA SNORA54 | RF00430 | Gene; snRNA; guide; HACA-box; | 5 | 10 | 126.0 | 72 | RF00430 |
| snoRNA SNORA55 | RF00431 | Gene; snRNA; guide; HACA-box; | 3 | 14 | 126.6 | 84 | RF00431 |
| snoRNA 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 | RF00434 | Cis-reg; | 17 | 32 | 101.2 | 73 | RF00434 |
| ROSE RNA 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 | RF00437 | Cis-reg; | 4 | 20 | 130.5 | 89 | RF00437 |
| snoRNA SNORA33 | RF00438 | Gene; snRNA; guide; HACA-box; | 5 | 11 | 125.8 | 77 | RF00438 |
| snoRNA SNORD87 | RF00439 | Gene; snRNA; guide; CD-box; | 4 | 7 | 81.9 | 93 | RF00439 |
| snoRNA SNORD37 | RF00440 | Gene; snRNA; guide; CD-box; | 7 | 11 | 64.5 | 78 | RF00440 |
| snoRNA 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 |
| snoRNA 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 family | RF00445 | Gene; miRNA; | 13 | 41 | 113.7 | 57 | RF00445 |
| mir-133 microRNA 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 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 |
| snoRNA R105 family | RF00450 | Gene; snRNA; guide; CD-box; | 7 | 7 | 103.3 | 77 | RF00450 |
| mir-395 microRNA family | RF00451 | Gene; miRNA; | 21 | 107 | 99.7 | 64 | RF00451 |
| mir-172 microRNA family | RF00452 | Gene; miRNA; | 8 | 19 | 113.5 | 65 | RF00452 |
| Cardiovirus 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 family | RF00455 | Gene; miRNA; | 4 | 29 | 85.4 | 80 | RF00455 |
| mir-34 microRNA family | RF00456 | Gene; miRNA; | 18 | 20 | 87.2 | 70 | RF00456 |
| Mnt IRES | RF00457 | Cis-reg; IRES; | 4 | 7 | 203.1 | 97 | RF00457 |
| Cripavirus 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 | RF00460 | Cis-reg; | 8 | 27 | 74.0 | 80 | RF00460 |
| Vascular endothelial growth factor IRES A | RF00461 | Cis-reg; IRES; | 7 | 13 | 305.5 | 92 | RF00461 |
| APC IRES | RF00462 | Cis-reg; IRES; | 6 | 8 | 53.0 | 85 | RF00462 |
| Apolipoprotein B 5' UTR cis-regulatory element | RF00463 | Cis-reg; | 3 | 12 | 118.9 | 94 | RF00463 |
| mir-92 microRNA family | RF00464 | Gene; miRNA; | 33 | 45 | 79.2 | 62 | RF00464 |
| Japanese encephalitis virus hairpin structure | RF00465 | Cis-reg; | 20 | 213 | 59.5 | 84 | RF00465 |
| Rous sarcoma virus primer binding site | 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 |
| snoRNA snR48 | RF00471 | Gene; snRNA; guide; CD-box; | 6 | 8 | 109.4 | 78 | RF00471 |
| snoRNA snR55 family | RF00472 | Gene; snRNA; guide; CD-box; | 6 | 9 | 88.4 | 74 | RF00472 |
| snoRNA snR54 | RF00473 | Gene; snRNA; guide; CD-box; | 9 | 16 | 81.8 | 76 | RF00473 |
| snoRNA snR57 | RF00474 | Gene; snRNA; guide; CD-box; | 6 | 8 | 91.6 | 75 | RF00474 |
| snoRNA snR69 | RF00475 | Gene; snRNA; guide; CD-box; | 7 | 14 | 95.6 | 61 | RF00475 |
| snoRNA snR61 family | RF00476 | Gene; snRNA; guide; CD-box; | 17 | 20 | 82.3 | 69 | RF00476 |
| snoRNA snR66 | RF00477 | Gene; snRNA; guide; CD-box; | 5 | 9 | 100.7 | 82 | RF00477 |
| scaRNA 6 | RF00478 | Gene; snRNA; guide; scaRNA; | 4 | 9 | 265.7 | 63 | RF00478 |
| snoRNA 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 |
| snoRNA F1 family | 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 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 family | RF00486 | Gene; miRNA; | 6 | 10 | 91.1 | 82 | RF00486 |
| Connexin-43 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 |
| scaRNA 17 | RF00492 | Gene; snRNA; guide; scaRNA; | 6 | 16 | 141.8 | 81 | RF00492 |
| snoRNA U2-30 | RF00493 | Gene; snRNA; guide; CD-box; | 3 | 7 | 69.3 | 86 | RF00493 |
| snoRNA U2-19 | RF00494 | Gene; snRNA; guide; CD-box; | 4 | 7 | 78.9 | 87 | RF00494 |
| Heat shock protein 70 IRES | RF00495 | Cis-reg; IRES; | 14 | 38 | 209.7 | 81 | RF00495 |
| Coronavirus SL-III CRE | RF00496 | Cis-reg; | 5 | 13 | 42.0 | 96 | RF00496 |
| Equine arteritis virus leader TRS hairpin | RF00498 | Cis-reg; | 4 | 12 | 45.0 | 99 | RF00498 |
| Human parechovirus 1 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 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 |
| snoRNA 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 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 |
| snoRNA Me28S-U3344 | RF00526 | Gene; snRNA; guide; CD-box; | 3 | 6 | 81.3 | 88 | RF00526 |
| snoRNA Me28S-Gm3255 | RF00527 | Gene; snRNA; guide; CD-box; | 4 | 14 | 83.5 | 86 | RF00527 |
| snoRNA Me28S-Gm1083 | RF00528 | Gene; snRNA; guide; CD-box; | 4 | 30 | 87.5 | 91 | RF00528 |
| snoRNA Me28S-Am2589 | RF00529 | Gene; snRNA; guide; CD-box; | 3 | 9 | 108.0 | 74 | RF00529 |
| snoRNA Me28S-Cm2645 | RF00530 | Gene; snRNA; guide; CD-box; | 6 | 19 | 75.0 | 92 | RF00530 |
| snoRNA Me28S-Gm3113 | RF00531 | Gene; snRNA; guide; CD-box; | 3 | 6 | 83.2 | 84 | RF00531 |
| snoRNA Me18S-Um1356 | RF00532 | Gene; snRNA; guide; CD-box; | 3 | 15 | 84.8 | 92 | RF00532 |
| snoRNA 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 |
| snoRNA Me28S-Am982 | RF00535 | Gene; snRNA; guide; CD-box; | 4 | 14 | 79.3 | 86 | RF00535 |
| snoRNA Me28S-Cm3227 | RF00536 | Gene; snRNA; guide; CD-box; | 4 | 12 | 81.7 | 94 | RF00536 |
| snoRNA Me28S-Am2634 | RF00537 | Gene; snRNA; guide; CD-box; | 9 | 24 | 90.2 | 83 | RF00537 |
| snoRNA CD11 | RF00538 | Gene; snRNA; guide; CD-box; | 6 | 9 | 70.7 | 91 | RF00538 |
| snoRNA Me28S-Cm788 | RF00539 | Gene; snRNA; guide; CD-box; | 3 | 6 | 72.5 | 93 | RF00539 |
| snoRNA psi18S-1854 | RF00540 | Gene; snRNA; guide; HACA-box; | 6 | 15 | 150.6 | 87 | RF00540 |
| snoRNA psi28S-2876 | RF00541 | Gene; snRNA; guide; HACA-box; | 3 | 6 | 143.3 | 93 | RF00541 |
| snoRNA psi28S-1192 | RF00542 | Gene; snRNA; guide; HACA-box; | 5 | 19 | 138.6 | 87 | RF00542 |
| snoRNA psi18S-1377 | RF00543 | Gene; snRNA; guide; HACA-box; | 5 | 16 | 132.8 | 78 | RF00543 |
| snoRNA psi28S-3327 | RF00544 | Gene; snRNA; guide; HACA-box; | 3 | 10 | 142.4 | 81 | RF00544 |
| snoRNA psi18S-841 family | RF00545 | Gene; snRNA; guide; HACA-box; | 3 | 7 | 139.7 | 76 | RF00545 |
| snoRNA 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 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 RNA | RF00552 | Cis-reg; | 6 | 24 | 204.1 | 80 | RF00552 |
| scaRNA 1 | RF00553 | Gene; snRNA; guide; scaRNA; | 3 | 3 | 165.7 | 92 | RF00553 |
| snoRNA 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 |
| snoRNA SNORA17 | RF00560 | Gene; snRNA; guide; HACA-box; | 38 | 155 | 131.5 | 79 | RF00560 |
| snoRNA SNORA40 | RF00561 | Gene; snRNA; guide; HACA-box; | 7 | 23 | 126.2 | 80 | RF00561 |
| snoRNA SNORA49 | RF00562 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 134.7 | 92 | RF00562 |
| snoRNA SNORA53 | RF00563 | Gene; snRNA; guide; HACA-box; | 4 | 5 | 246.0 | 90 | RF00563 |
| scaRNA 11 | RF00564 | Gene; snRNA; guide; scaRNA; | 4 | 6 | 137.3 | 79 | RF00564 |
| scaRNA 25 | RF00565 | Gene; snRNA; guide; scaRNA; | 3 | 9 | 134.6 | 80 | RF00565 |
| snoRNA SNORA35 | RF00566 | Gene; snRNA; guide; HACA-box; | 3 | 3 | 125.0 | 91 | RF00566 |
| snoRNA SNORD17 | RF00567 | Gene; snRNA; guide; CD-box; | 3 | 3 | 232.0 | 90 | RF00567 |
| snoRNA SNORA26 | RF00568 | Gene; snRNA; guide; HACA-box; | 12 | 23 | 121.2 | 73 | RF00568 |
| snoRNA SNORD19 | RF00569 | Gene; snRNA; guide; CD-box; | 2 | 4 | 71.0 | 71 | RF00569 |
| snoRNA SNORD64 | RF00570 | Gene; snRNA; guide; CD-box; | 3 | 6 | 63.5 | 93 | RF00570 |
| snoRNA SNORD65 | RF00571 | Gene; snRNA; guide; CD-box; | 4 | 6 | 72.2 | 82 | RF00571 |
| snoRNA SNORD66 | RF00572 | Gene; snRNA; guide; CD-box; | 4 | 5 | 72.0 | 79 | RF00572 |
| snoRNA SNORD67 | RF00573 | Gene; snRNA; guide; CD-box; | 2 | 3 | 106.7 | 98 | RF00573 |
| snoRNA SNORD69 | RF00574 | Gene; snRNA; guide; CD-box; | 2 | 3 | 70.7 | 91 | RF00574 |
| snoRNA SNORD70 | RF00575 | Gene; snRNA; guide; CD-box; | 4 | 8 | 80.5 | 85 | RF00575 |
| snoRNA SNORD71 | RF00576 | Gene; snRNA; guide; HACA-box; | 2 | 3 | 75.3 | 90 | RF00576 |
| snoRNA SNORD72 | RF00577 | Gene; snRNA; guide; CD-box; | 3 | 10 | 77.7 | 90 | RF00577 |
| snoRNA SNORD89 | RF00578 | Gene; snRNA; guide; CD-box; | 2 | 4 | 105.5 | 93 | RF00578 |
| snoRNA SNORD90 | RF00579 | Gene; snRNA; guide; CD-box; | 2 | 3 | 96.0 | 92 | RF00579 |
| snoRNA 296A/B | RF00580 | Gene; snRNA; guide; CD-box; | 3 | 6 | 92.5 | 82 | RF00580 |
| snoRNA SNORD12 family | RF00581 | Gene; snRNA; guide; CD-box; | 8 | 10 | 86.1 | 71 | RF00581 |
| scaRNA 14 | RF00582 | Gene; snRNA; guide; scaRNA; | 4 | 9 | 129.0 | 69 | RF00582 |
| snoRNA SNORD105 | RF00584 | Gene; snRNA; guide; CD-box; | 2 | 5 | 83.8 | 89 | RF00584 |
| snoRNA SNORA12 | RF00586 | Gene; snRNA; guide; HACA-box; | 4 | 6 | 151.5 | 84 | RF00586 |
| snoRNA SNORD41 | RF00588 | Gene; snRNA; guide; CD-box; | 2 | 3 | 69.7 | 92 | RF00588 |
| snoRNA SNORD77 | RF00591 | Gene; snRNA; guide; CD-box; | 5 | 9 | 67.3 | 90 | RF00591 |
| snoRNA SNORD78 | RF00592 | Gene; snRNA; guide; CD-box; | 4 | 11 | 65.8 | 90 | RF00592 |
| snoRNA U83B | RF00593 | Gene; snRNA; guide; CD-box; | 4 | 9 | 91.4 | 87 | RF00593 |
| snoRNA SNORD86 | RF00594 | Gene; snRNA; guide; CD-box; | 6 | 11 | 83.5 | 81 | RF00594 |