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Rfam 10.0 ::
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| Name | Accession | No.seed | Av.len(seed) | Av.%id(seed) | No.full | Av.len(full) | Av.%id(full) | Type | Description |
| 5S_rRNA | RF00001 | 712 | 116 | 59 | 116760 | 114 | 59 | Gene; rRNA; | 5S ribosomal RNA |
| 5_8S_rRNA | RF00002 | 61 | 152 | 70 | 225185 | 153 | 81 | Gene; rRNA; | 5.8S ribosomal RNA |
| U1 | RF00003 | 100 | 162 | 65 | 11210 | 155 | 61 | Gene; snRNA; splicing; | U1 spliceosomal RNA |
| U2 | RF00004 | 211 | 190 | 56 | 7509 | 163 | 51 | Gene; snRNA; splicing; | U2 spliceosomal RNA |
| tRNA | RF00005 | 967 | 73 | 45 | 1101833 | 71 | 54 | Gene; tRNA; | tRNA |
| Vault | RF00006 | 75 | 100 | 58 | 430 | 101 | 61 | Gene; | Vault RNA |
| U12 | RF00007 | 63 | 161 | 62 | 322 | 148 | 65 | Gene; snRNA; splicing; | U12 minor spliceosomal RNA |
| Hammerhead_3 | RF00008 | 84 | 55 | 69 | 1138 | 63 | 67 | Gene; ribozyme; | Hammerhead ribozyme (type III) |
| RNaseP_nuc | RF00009 | 117 | 312 | 48 | 566 | 287 | 40 | Gene; ribozyme; | Nuclear RNase P |
| RNaseP_bact_a | RF00010 | 306 | 380 | 62 | 4081 | 351 | 62 | Gene; ribozyme; | Bacterial RNase P class A |
| RNaseP_bact_b | RF00011 | 114 | 367 | 68 | 538 | 359 | 68 | Gene; ribozyme; | Bacterial RNase P class B |
| U3 | RF00012 | 26 | 219 | 50 | 4544 | 163 | 45 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U3 |
| 6S | RF00013 | 154 | 180 | 45 | 1700 | 176 | 44 | Gene; | 6S / SsrS RNA |
| DsrA | RF00014 | 5 | 85 | 82 | 96 | 85 | 92 | Gene; sRNA; | DsrA RNA |
| U4 | RF00015 | 178 | 144 | 57 | 5596 | 128 | 59 | Gene; snRNA; splicing; | U4 spliceosomal RNA |
| SNORD14 | RF00016 | 18 | 110 | 66 | 999 | 95 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD14 |
| SRP_euk_arch | RF00017 | 102 | 296 | 49 | 13082 | 286 | 51 | Gene; | Eukaryotic type signal recognition particle RNA |
| CsrB | RF00018 | 14 | 345 | 70 | 368 | 268 | 61 | Gene; sRNA; | CsrB/RsmB RNA family |
| Y_RNA | RF00019 | 116 | 99 | 61 | 14651 | 102 | 54 | Gene; | Y RNA |
| U5 | RF00020 | 181 | 117 | 50 | 3444 | 113 | 63 | Gene; snRNA; splicing; | U5 spliceosomal RNA |
| Spot_42 | RF00021 | 19 | 117 | 78 | 235 | 116 | 86 | Gene; sRNA; | Spot 42 RNA |
| GcvB | RF00022 | 26 | 201 | 60 | 223 | 201 | 67 | Gene; | GcvB RNA |
| tmRNA | RF00023 | 222 | 365 | 50 | 3061 | 357 | 48 | Gene; | transfer-messenger RNA |
| Telomerase-vert | RF00024 | 37 | 444 | 58 | 233 | 282 | 55 | Gene; | Vertebrate telomerase RNA |
| Telomerase-cil | RF00025 | 20 | 174 | 52 | 28 | 154 | 50 | Gene; | Ciliate telomerase RNA |
| U6 | RF00026 | 200 | 107 | 72 | 48510 | 103 | 74 | Gene; snRNA; splicing; | U6 spliceosomal RNA |
| let-7 | RF00027 | 57 | 79 | 64 | 796 | 82 | 66 | Gene; miRNA; | let-7 microRNA precursor |
| Intron_gpI | RF00028 | 30 | 322 | 36 | 39049 | 349 | 58 | Intron; | Group I catalytic intron |
| Intron_gpII | RF00029 | 98 | 87 | 54 | 29255 | 76 | 56 | Intron; | Group II catalytic intron |
| RNase_MRP | RF00030 | 67 | 321 | 46 | 496 | 283 | 36 | Gene; ribozyme; | RNase MRP |
| SECIS | RF00031 | 61 | 64 | 43 | 1125 | 64 | 45 | Cis-reg; | Selenocysteine insertion sequence |
| Histone3 | RF00032 | 64 | 26 | 77 | 9816 | 25 | 79 | Cis-reg; | Histone 3' UTR stem-loop |
| MicF | RF00033 | 4 | 92 | 81 | 152 | 91 | 80 | Gene; antisense; | MicF RNA |
| RprA | RF00034 | 14 | 108 | 65 | 198 | 104 | 69 | Gene; sRNA; | RprA RNA |
| OxyS | RF00035 | 5 | 109 | 92 | 115 | 110 | 92 | Gene; sRNA; | OxyS RNA |
| RRE | RF00036 | 65 | 337 | 97 | 22764 | 279 | 87 | Cis-reg; | HIV Rev response element |
| IRE | RF00037 | 39 | 28 | 61 | 2290 | 29 | 72 | Cis-reg; | Iron response element |
| PrfA | RF00038 | 11 | 131 | 87 | 282 | 130 | 99 | Cis-reg; thermoregulator; | PrfA thermoregulator UTR |
| DicF | RF00039 | 5 | 51 | 74 | 141 | 51 | 80 | Gene; antisense; | DicF RNA |
| rne5 | RF00040 | 6 | 345 | 64 | 174 | 315 | 75 | Cis-reg; | RNase E 5' UTR element |
| Entero_OriR | RF00041 | 60 | 121 | 88 | 151 | 118 | 84 | Cis-reg; | Enteroviral 3' UTR element |
| CopA | RF00042 | 37 | 90 | 80 | 153 | 90 | 83 | Gene; antisense; | CopA-like RNA |
| Plasmid_R1162 | RF00043 | 8 | 73 | 79 | 21 | 70 | 79 | Gene; antisense; | R1162-like plasmid antisense RNA |
| Phage_pRNA | RF00044 | 3 | 244 | 98 | 8 | 193 | 79 | Gene; | Bacteriophage pRNA |
| SNORA73 | RF00045 | 53 | 210 | 75 | 802 | 189 | 61 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA73 family |
| snoR30 | RF00046 | 6 | 95 | 88 | 76 | 95 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R30/Z108 |
| mir-2 | RF00047 | 56 | 69 | 68 | 235 | 70 | 67 | Gene; miRNA; | mir-2 microRNA precursor |
| Entero_CRE | RF00048 | 56 | 61 | 82 | 529 | 60 | 82 | Cis-reg; | Enterovirus cis-acting replication element |
| SNORD36 | RF00049 | 61 | 74 | 66 | 435 | 75 | 61 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD36 |
| FMN | RF00050 | 146 | 136 | 72 | 1789 | 139 | 68 | Cis-reg; riboswitch; | FMN riboswitch (RFN element) |
| mir-17 | RF00051 | 54 | 81 | 72 | 316 | 82 | 70 | Gene; miRNA; | mir-17 microRNA precursor family |
| lin-4 | RF00052 | 9 | 69 | 72 | 210 | 69 | 75 | Gene; miRNA; | lin-4 microRNA precursor |
| mir-7 | RF00053 | 60 | 87 | 65 | 212 | 88 | 69 | Gene; miRNA; | mir-7 microRNA precursor |
| SNORD25 | RF00054 | 8 | 80 | 63 | 115 | 78 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD25 |
| SNORD96 | RF00055 | 9 | 87 | 62 | 139 | 86 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD96 family |
| SNORA71 | RF00056 | 40 | 132 | 80 | 402 | 129 | 71 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA71 |
| RyhB | RF00057 | 28 | 65 | 74 | 323 | 65 | 76 | Gene; sRNA; | RyhB RNA |
| HgcF | RF00058 | 4 | 168 | 90 | 8 | 169 | 86 | Gene; | HgcF RNA |
| TPP | RF00059 | 115 | 111 | 56 | 5398 | 107 | 55 | Cis-reg; riboswitch; | TPP riboswitch (THI element) |
| HgcE | RF00060 | 4 | 130 | 82 | 8 | 129 | 78 | Gene; | HgcE RNA |
| IRES_HCV | RF00061 | 79 | 246 | 86 | 6496 | 204 | 92 | Cis-reg; IRES; | Hepatitis C virus internal ribosome entry site |
| HgcC | RF00062 | 5 | 134 | 70 | 71 | 119 | 51 | Gene; | HgcC family RNA |
| SscA | RF00063 | 5 | 96 | 74 | 9 | 96 | 73 | Gene; | SscA RNA |
| HgcG | RF00064 | 4 | 275 | 82 | 9 | 275 | 72 | Gene; | HgcG RNA |
| snoR9 | RF00065 | 5 | 127 | 85 | 8 | 122 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR9 |
| U7 | RF00066 | 56 | 60 | 59 | 5079 | 59 | 64 | Gene; snRNA; | U7 small nuclear RNA |
| SNORD15 | RF00067 | 18 | 124 | 59 | 267 | 118 | 57 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD15 |
| SNORD21 | RF00068 | 5 | 92 | 73 | 91 | 87 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD21 |
| SNORD24 | RF00069 | 14 | 77 | 71 | 307 | 80 | 65 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD24 |
| SNORD29 | RF00070 | 10 | 73 | 76 | 110 | 69 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD29 |
| SNORD73 | RF00071 | 25 | 70 | 77 | 112 | 69 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD73 |
| SNORA75 | RF00072 | 6 | 135 | 74 | 191 | 129 | 66 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA75 |
| mir-156 | RF00073 | 10 | 89 | 72 | 387 | 88 | 71 | Gene; miRNA; | mir-156 microRNA precursor |
| mir-29 | RF00074 | 10 | 67 | 75 | 302 | 67 | 78 | Gene; miRNA; | mir-29 microRNA precursor |
| mir-166 | RF00075 | 30 | 122 | 57 | 369 | 120 | 56 | Gene; miRNA; | mir-166 microRNA precursor |
| mir-181 | RF00076 | 19 | 75 | 82 | 180 | 75 | 82 | Gene; miRNA; | mir-181 microRNA precursor |
| SraB | RF00077 | 5 | 168 | 87 | 102 | 160 | 86 | Gene; sRNA; | SraB RNA |
| SraD | RF00078 | 10 | 75 | 88 | 160 | 75 | 89 | Gene; sRNA; | SraD RNA |
| SraE_OmrA_OmrB | RF00079 | 16 | 88 | 71 | 260 | 86 | 79 | Gene; sRNA; | SraE_OmrA_OmrB family RNA |
| yybP-ykoY | RF00080 | 25 | 123 | 49 | 983 | 122 | 47 | Cis-reg; | yybP-ykoY leader |
| SraH | RF00081 | 9 | 107 | 79 | 161 | 104 | 74 | Gene; sRNA; | SraH RNA |
| SraG | RF00082 | 7 | 172 | 73 | 166 | 171 | 83 | Gene; sRNA; | SraG RNA |
| GlmZ_SraJ | RF00083 | 21 | 211 | 78 | 310 | 198 | 67 | Gene; sRNA; | GlmZ RNA activator of glmS mRNA |
| CsrC | RF00084 | 4 | 253 | 82 | 118 | 250 | 89 | Gene; sRNA; | CsrC RNA family |
| SNORD28 | RF00085 | 20 | 76 | 75 | 90 | 73 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD28 |
| SNORD27 | RF00086 | 11 | 76 | 70 | 168 | 75 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD27 |
| SNORD26 | RF00087 | 17 | 74 | 80 | 62 | 74 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD26 |
| SNORD30 | RF00088 | 20 | 69 | 81 | 83 | 68 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD30 |
| SNORD31 | RF00089 | 26 | 68 | 78 | 194 | 69 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD31 |
| SNORA74 | RF00090 | 23 | 199 | 79 | 274 | 183 | 52 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA74 |
| SNORA62 | RF00091 | 10 | 152 | 82 | 474 | 141 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA62/SNORA6 family |
| SNORA63 | RF00092 | 8 | 128 | 79 | 483 | 121 | 61 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA63 |
| SNORD18 | RF00093 | 16 | 74 | 69 | 355 | 75 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD18 |
| HDV_ribozyme | RF00094 | 33 | 91 | 74 | 538 | 91 | 81 | Gene; ribozyme; | Hepatitis delta virus ribozyme |
| snoPyro_CD | RF00095 | 25 | 56 | 60 | 69 | 56 | 61 | Gene; snRNA; snoRNA; CD-box; | Pyrococcus C/D box small nucleolar RNA |
| U8 | RF00096 | 49 | 135 | 66 | 561 | 128 | 60 | Gene; snRNA; snoRNA; CD-box; | U8 small nucleolar RNA |
| snoR71 | RF00097 | 25 | 107 | 83 | 8199 | 106 | 64 | Gene; snRNA; snoRNA; CD-box; | Plant small nucleolar RNA R71 |
| SNORD22 | RF00099 | 49 | 125 | 81 | 230 | 118 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD22 |
| 7SK | RF00100 | 45 | 322 | 82 | 15656 | 275 | 52 | Gene; | 7SK RNA |
| SraC_RyeA | RF00101 | 13 | 146 | 87 | 187 | 144 | 76 | Gene; sRNA; | SraC/RyeA RNA |
| VA | RF00102 | 54 | 161 | 69 | 438 | 137 | 68 | Gene; | VA RNA |
| mir-1 | RF00103 | 67 | 76 | 68 | 234 | 76 | 68 | Gene; miRNA; | mir-1 microRNA precursor family |
| mir-10 | RF00104 | 11 | 74 | 59 | 406 | 73 | 66 | Gene; miRNA; | mir-10 microRNA precursor family |
| SNORD115 | RF00105 | 32 | 80 | 90 | 2447 | 79 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD115 |
| RNAI | RF00106 | 10 | 102 | 73 | 2383 | 99 | 88 | Gene; antisense; | RNAI |
| FinP | RF00107 | 6 | 77 | 91 | 60 | 77 | 90 | Gene; | FinP |
| SNORD116 | RF00108 | 48 | 93 | 83 | 1434 | 92 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD116 |
| Vimentin3 | RF00109 | 19 | 68 | 75 | 178 | 65 | 83 | Cis-reg; | Vimentin 3' UTR protein-binding region |
| RybB | RF00110 | 8 | 79 | 81 | 161 | 79 | 88 | Gene; sRNA; | RybB RNA |
| RyeB | RF00111 | 18 | 97 | 73 | 245 | 98 | 72 | Gene; sRNA; | RyeB RNA |
| CyaR_RyeE | RF00112 | 18 | 86 | 80 | 161 | 85 | 84 | Gene; sRNA; | CyaR/Rye RNA |
| QUAD | RF00113 | 17 | 147 | 71 | 473 | 147 | 74 | Gene; sRNA; | QUAD RNA |
| S15 | RF00114 | 79 | 116 | 63 | 406 | 116 | 63 | Cis-reg; leader; | Ribosomal S15 leader |
| IS061 | RF00115 | 8 | 180 | 93 | 63 | 175 | 90 | Gene; sRNA; | IS061 RNA |
| C0465 | RF00116 | 8 | 77 | 99 | 55 | 77 | 100 | Gene; sRNA; | C0465 RNA |
| C0719 | RF00117 | 9 | 222 | 98 | 41 | 219 | 96 | Gene; sRNA; | C0719 RNA |
| rydB | RF00118 | 7 | 67 | 93 | 105 | 67 | 96 | Gene; sRNA; | rydB RNA |
| C0299 | RF00119 | 5 | 79 | 97 | 57 | 78 | 97 | Gene; sRNA; | C0299 RNA |
| C0343 | RF00120 | 7 | 75 | 85 | 114 | 74 | 88 | Gene; sRNA; | C0343 RNA |
| MicC | RF00121 | 8 | 122 | 68 | 112 | 118 | 78 | Gene; sRNA; | MicC RNA |
| GadY | RF00122 | 5 | 113 | 99 | 62 | 113 | 99 | Gene; sRNA; | GadY |
| IS102 | RF00124 | 5 | 205 | 90 | 71 | 153 | 63 | Gene; sRNA; | IS102 RNA |
| IS128 | RF00125 | 5 | 210 | 89 | 20 | 206 | 94 | Gene; sRNA; | IS128 RNA |
| ryfA | RF00126 | 10 | 295 | 75 | 107 | 298 | 84 | Gene; sRNA; | ryfA RNA |
| t44 | RF00127 | 20 | 105 | 76 | 344 | 103 | 69 | Gene; sRNA; | t44 RNA |
| GlmY_tke1 | RF00128 | 17 | 157 | 77 | 308 | 151 | 73 | Gene; sRNA; | Glm Y RNA activator of glmS mRNA |
| mir-103 | RF00129 | 28 | 78 | 85 | 175 | 78 | 85 | Gene; miRNA; | mir-103/107 microRNA precursor |
| mir-192 | RF00130 | 41 | 105 | 69 | 88 | 106 | 71 | Gene; miRNA; | mir-192/215 microRNA precursor |
| mir-30 | RF00131 | 36 | 70 | 79 | 170 | 70 | 81 | Gene; miRNA; | mir-30 microRNA precursor |
| snoR24 | RF00132 | 12 | 92 | 80 | 109 | 89 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R24 |
| SNORD33 | RF00133 | 75 | 82 | 63 | 324 | 82 | 60 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z195/SNORD33/SNORD32 family |
| snoZ196 | RF00134 | 23 | 85 | 66 | 203 | 78 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z196/R39/R59 family |
| snoZ223 | RF00135 | 5 | 94 | 86 | 84 | 89 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z223 |
| SNORD81 | RF00136 | 23 | 76 | 80 | 147 | 69 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD81 |
| SNORD83 | RF00137 | 7 | 76 | 86 | 200 | 76 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD83 |
| SNORD16 | RF00138 | 5 | 98 | 81 | 94 | 99 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD16 |
| SNORA72 | RF00139 | 29 | 132 | 82 | 391 | 122 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA72 |
| Alpha_RBS | RF00140 | 39 | 107 | 65 | 558 | 91 | 59 | Cis-reg; | Alpha operon ribosome binding site |
| snoZ118 | RF00142 | 7 | 103 | 83 | 87 | 103 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z118/Z121/Z120 |
| mir-6 | RF00143 | 24 | 77 | 68 | 89 | 77 | 66 | Gene; miRNA; | mir-6 microRNA precursor |
| mir-199 | RF00144 | 40 | 99 | 76 | 163 | 99 | 81 | Gene; miRNA; | mir-199 microRNA precursor |
| snoZ105 | RF00145 | 11 | 69 | 63 | 59 | 69 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z105 |
| SNORD34 | RF00147 | 9 | 77 | 70 | 114 | 76 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD34 |
| snoZ103 | RF00149 | 9 | 98 | 78 | 783 | 101 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z103 |
| SNORD42 | RF00150 | 7 | 65 | 75 | 133 | 65 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD42 |
| SNORD58 | RF00151 | 34 | 65 | 80 | 260 | 65 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD58 |
| SNORD79 | RF00152 | 28 | 81 | 75 | 108 | 81 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD79 |
| SNORD62 | RF00153 | 14 | 85 | 87 | 111 | 84 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD62 |
| SNORD63 | RF00154 | 23 | 72 | 79 | 134 | 66 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD63 |
| SNORA66 | RF00155 | 25 | 133 | 82 | 191 | 121 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA66 |
| SNORA70 | RF00156 | 43 | 134 | 79 | 1461 | 127 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA70 |
| SNORD39 | RF00157 | 20 | 79 | 85 | 115 | 77 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD55/SNORD39 |
| SNORD82 | RF00158 | 27 | 69 | 81 | 118 | 68 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD82 |
| snoZ168 | RF00159 | 6 | 82 | 85 | 32 | 81 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z168/Z174 |
| snoZ159 | RF00160 | 10 | 89 | 83 | 103 | 86 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z159/U59 |
| nos_TCE | RF00161 | 9 | 62 | 80 | 46 | 61 | 76 | Cis-reg; | Nanos 3' UTR translation control element |
| SAM | RF00162 | 228 | 109 | 69 | 2910 | 110 | 67 | Cis-reg; riboswitch; | SAM riboswitch (S box leader) |
| Hammerhead_1 | RF00163 | 30 | 59 | 70 | 23865 | 45 | 76 | Gene; ribozyme; | Hammerhead ribozyme (type I) |
| s2m | RF00164 | 38 | 42 | 82 | 438 | 42 | 86 | Cis-reg; | Coronavirus 3' stem-loop II-like motif (s2m) |
| Corona_pk3 | RF00165 | 14 | 62 | 69 | 431 | 62 | 81 | Cis-reg; | Coronavirus 3' UTR pseudoknot |
| PrrB_RsmZ | RF00166 | 24 | 160 | 73 | 72 | 145 | 68 | Gene; sRNA; | PrrB/RsmZ RNA family |
| Purine | RF00167 | 133 | 100 | 56 | 1244 | 100 | 57 | Cis-reg; riboswitch; | Purine riboswitch |
| Lysine | RF00168 | 47 | 183 | 51 | 1126 | 182 | 51 | Cis-reg; riboswitch; | Lysine riboswitch |
| SRP_bact | RF00169 | 463 | 100 | 55 | 3345 | 97 | 53 | Gene; | Bacterial signal recognition particle RNA |
| msr | RF00170 | 10 | 70 | 59 | 41 | 70 | 66 | Gene; | Retron msr RNA |
| Tombus_5 | RF00171 | 9 | 161 | 74 | 51 | 152 | 70 | Cis-reg; | Tombusvirus 5' UTR |
| CAESAR | RF00172 | 9 | 79 | 78 | 105 | 78 | 83 | Cis-reg; | ctgf/hcs24 CAESAR |
| Hairpin | RF00173 | 5 | 51 | 83 | 20 | 49 | 76 | Gene; ribozyme; | Hairpin ribozyme |
| Cobalamin | RF00174 | 431 | 203 | 54 | 3713 | 197 | 48 | Cis-reg; riboswitch; | Cobalamin riboswitch |
| HIV-1_DIS | RF00175 | 70 | 40 | 88 | 2394 | 39 | 93 | Cis-reg; | Human immunodeficiency virus type 1 dimerisation initiation site |
| Tombus_3_IV | RF00176 | 18 | 91 | 94 | 79 | 65 | 96 | Cis-reg; | Tombusvirus 3' UTR region IV |
| SSU_rRNA_5 | RF00177 | 341 | 489 | 50 | 762089 | 488 | 65 | Gene; rRNA; | Small subunit ribosomal RNA, 5' domain |
| mir-24 | RF00178 | 17 | 68 | 82 | 133 | 67 | 84 | Gene; miRNA; | mir-24 microRNA precursor family |
| GAIT | RF00179 | 8 | 70 | 98 | 51 | 71 | 89 | Cis-reg; | GAIT element |
| REN-SRE | RF00180 | 13 | 36 | 89 | 103 | 36 | 80 | Cis-reg; | Renin stability regulatory element (REN-SRE) |
| SNORD113 | RF00181 | 59 | 74 | 67 | 1741 | 75 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD113/SNORD114 family |
| Corona_package | RF00182 | 15 | 129 | 84 | 79 | 128 | 82 | Cis-reg; | Coronavirus packaging signal |
| G-CSF_SLDE | RF00183 | 16 | 93 | 81 | 58 | 93 | 83 | Cis-reg; | G-CSF factor stem-loop destabilising element (SLDE) |
| PVX_3 | RF00184 | 4 | 54 | 98 | 28 | 51 | 95 | Cis-reg; | Potato virus X cis-acting regulatory element |
| Flavi_CRE | RF00185 | 84 | 94 | 66 | 788 | 92 | 74 | Cis-reg; | Flavivirus 3' UTR cis-acting replication element (CRE) |
| SNORD101 | RF00186 | 26 | 73 | 85 | 78 | 72 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD101 |
| SNORD102 | RF00187 | 11 | 71 | 89 | 47 | 72 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD102 |
| SNORD103 | RF00188 | 41 | 80 | 81 | 162 | 79 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD103/SNORD85 |
| SNORD95 | RF00189 | 5 | 67 | 95 | 116 | 62 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD95 |
| SNORA16 | RF00190 | 29 | 135 | 75 | 220 | 129 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA16B/SNORA16A family |
| SNORA57 | RF00191 | 26 | 146 | 81 | 226 | 139 | 66 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA57 |
| BLV_package | RF00192 | 5 | 55 | 100 | 7 | 50 | 95 | Cis-reg; | Bovine leukaemia virus RNA packaging signal |
| CTV_rep_sig | RF00193 | 9 | 273 | 98 | 37 | 263 | 98 | Cis-reg; | Citrus tristeza virus replication signal |
| Rubella_3 | RF00194 | 25 | 66 | 97 | 156 | 51 | 98 | Cis-reg; | Rubella virus 3' cis-acting element |
| RsmY | RF00195 | 11 | 121 | 78 | 44 | 119 | 73 | Gene; sRNA; | RsmY RNA family |
| AMV_RNA1_SL | RF00196 | 6 | 35 | 100 | 12 | 35 | 82 | Cis-reg; | Alfalfa mosaic virus RNA 1 5' UTR stem-loop |
| SL1 | RF00198 | 32 | 103 | 84 | 1431 | 96 | 71 | Gene; | SL1 RNA |
| SL2 | RF00199 | 32 | 110 | 78 | 233 | 108 | 73 | Gene; | SL2 RNA |
| snoZ199 | RF00200 | 17 | 82 | 82 | 72 | 80 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z199 |
| snoZ278 | RF00201 | 7 | 114 | 95 | 89 | 114 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z278 |
| snoR66 | RF00202 | 6 | 74 | 87 | 74 | 73 | 86 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R66 |
| snoR160 | RF00203 | 9 | 79 | 72 | 67 | 72 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R160 |
| snoR12 | RF00204 | 9 | 83 | 79 | 111 | 78 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R12 |
| snoR41 | RF00205 | 7 | 94 | 89 | 35 | 93 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R41 |
| U54 | RF00206 | 22 | 81 | 70 | 85 | 79 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U54 |
| K10_TLS | RF00207 | 5 | 44 | 100 | 12 | 44 | 100 | Cis-reg; | K10 transport/localisation element (TLS) |
| snoR72 | RF00208 | 5 | 87 | 97 | 19 | 80 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R72 |
| IRES_Pesti | RF00209 | 25 | 275 | 89 | 1551 | 239 | 79 | Cis-reg; IRES; | Pestivirus internal ribosome entry site (IRES) |
| IRES_Aptho | RF00210 | 92 | 461 | 84 | 417 | 419 | 65 | Cis-reg; IRES; | Aphthovirus internal ribosome entry site (IRES) |
| SNORD35 | RF00211 | 8 | 88 | 73 | 160 | 86 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD35 |
| SNORD38 | RF00212 | 7 | 68 | 81 | 173 | 69 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD38 |
| snoR38 | RF00213 | 19 | 85 | 57 | 387 | 84 | 56 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R38 |
| Retro_dr1 | RF00214 | 26 | 90 | 90 | 223 | 77 | 68 | Cis-reg; | Retrovirus direct repeat 1 (dr1) |
| Tombus_3_III | RF00215 | 28 | 69 | 81 | 72 | 66 | 81 | Cis-reg; | Tombus virus defective interfering (DI) RNA region 3 |
| IRES_c-myc | RF00216 | 23 | 302 | 98 | 148 | 263 | 81 | Cis-reg; IRES; | c-myc internal ribosome entry site (IRES) |
| SNORD20 | RF00217 | 13 | 79 | 89 | 72 | 75 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD20 |
| SNORD46 | RF00218 | 9 | 89 | 69 | 151 | 92 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD46 |
| Rhino_CRE | RF00220 | 12 | 86 | 85 | 95 | 86 | 74 | Cis-reg; | Human rhinovirus internal cis-acting regulatory element (CRE) |
| SNORD43 | RF00221 | 7 | 76 | 65 | 117 | 71 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD43 |
| IRES_Bag1 | RF00222 | 14 | 368 | 80 | 61 | 318 | 76 | Cis-reg; IRES; | Bag-1 internal ribosome entry site (IRES) |
| IRES_Bip | RF00223 | 9 | 252 | 82 | 88 | 233 | 66 | Cis-reg; IRES; | bip internal ribosome entry site (IRES) |
| IRES_FGF2 | RF00224 | 6 | 493 | 90 | 22 | 445 | 84 | Cis-reg; IRES; | FGF-2 internal ribosome entry site (IRES) |
| IRES_Tobamo | RF00225 | 7 | 151 | 87 | 23 | 148 | 86 | Cis-reg; IRES; | Tobamovirus internal ribosome entry site (IRES) |
| IRES_n-myc | RF00226 | 6 | 323 | 74 | 91 | 267 | 52 | Cis-reg; IRES; | n-myc internal ribosome entry site (IRES) |
| FIE3 | RF00227 | 5 | 67 | 62 | 25 | 66 | 75 | Cis-reg; | FIE3 (ftz instability element 3') element |
| IRES_HepA | RF00228 | 23 | 571 | 97 | 425 | 271 | 74 | Cis-reg; IRES; | Hepatitis A virus internal ribosome entry site (IRES) |
| IRES_Picorna | RF00229 | 92 | 251 | 84 | 2893 | 171 | 80 | Cis-reg; IRES; | Picornavirus internal ribosome entry site (IRES) |
| T-box | RF00230 | 63 | 225 | 48 | 8260 | 215 | 49 | Cis-reg; | T-box leader |
| SCARNA13 | RF00231 | 24 | 274 | 80 | 82 | 265 | 69 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 13 |
| Spi-1 | RF00232 | 5 | 164 | 92 | 41 | 162 | 87 | Cis-reg; | Spi-1 (PU.1) 5' UTR regulatory element |
| Tymo_tRNA-like | RF00233 | 28 | 82 | 72 | 95 | 78 | 65 | Cis-reg; | Tymovirus/Pomovirus tRNA-like 3' UTR element |
| glmS | RF00234 | 17 | 182 | 59 | 411 | 170 | 58 | Cis-reg; riboswitch; | glmS glucosamine-6-phosphate activated ribozyme |
| Plasmid_RNAIII | RF00235 | 7 | 129 | 93 | 13 | 130 | 96 | Gene; | Plasmid RNAIII |
| ctRNA_pGA1 | RF00236 | 15 | 77 | 73 | 34 | 78 | 71 | Gene; antisense; | ctRNA |
| mir-9 | RF00237 | 43 | 61 | 79 | 277 | 61 | 82 | Gene; miRNA; | mir-9/mir-79 microRNA precursor family |
| ctRNA_pND324 | RF00238 | 48 | 85 | 69 | 84 | 84 | 67 | Gene; antisense; | ctRNA |
| mir-124 | RF00239 | 49 | 80 | 74 | 216 | 80 | 79 | Gene; miRNA; | mir-124 microRNA precursor family |
| RNA-OUT | RF00240 | 16 | 70 | 87 | 582 | 69 | 95 | Gene; antisense; | RNA-OUT |
| mir-8 | RF00241 | 9 | 77 | 66 | 204 | 77 | 67 | Gene; miRNA; | mir-8/mir-141/mir-200 microRNA precursor family |
| ctRNA_pT181 | RF00242 | 16 | 96 | 77 | 50 | 90 | 75 | Gene; antisense; | ctRNA |
| traJ_5 | RF00243 | 6 | 108 | 88 | 61 | 107 | 89 | Cis-reg; | traJ 5' UTR |
| mir-26 | RF00244 | 5 | 72 | 75 | 162 | 73 | 76 | Gene; miRNA; | mir-26 microRNA precursor family |
| mir-19 | RF00245 | 36 | 76 | 80 | 216 | 74 | 79 | Gene; miRNA; | mir-19 microRNA precursor family |
| mir-135 | RF00246 | 30 | 90 | 70 | 182 | 90 | 70 | Gene; miRNA; | mir-135 microRNA precursor family |
| mir-160 | RF00247 | 7 | 94 | 68 | 163 | 89 | 66 | Gene; miRNA; | mir-160 microRNA precursor family |
| mir-148 | RF00248 | 5 | 86 | 77 | 151 | 85 | 76 | Gene; miRNA; | mir-148/mir-152 microRNA precursor family |
| mir-46 | RF00249 | 7 | 73 | 83 | 14 | 74 | 73 | Gene; miRNA; | mir-46/mir-47/mir-281 microRNA precursor family |
| mir-TAR | RF00250 | 45 | 60 | 85 | 4071 | 60 | 93 | Gene; miRNA; | Trans-activation response element (TAR) |
| mir-219 | RF00251 | 10 | 71 | 80 | 164 | 72 | 72 | Gene; miRNA; | mir-219 microRNA precursor family |
| Alfamo_CPB | RF00252 | 18 | 182 | 89 | 36 | 133 | 80 | Cis-reg; | Alfalfa mosaic virus coat protein binding (CPB) RNA |
| mir-101 | RF00253 | 24 | 75 | 84 | 118 | 75 | 86 | Gene; miRNA; | mir-101 microRNA precursor family |
| mir-16 | RF00254 | 12 | 80 | 74 | 184 | 79 | 73 | Gene; miRNA; | mir-16 microRNA precursor family |
| mir-218 | RF00255 | 14 | 97 | 77 | 122 | 95 | 78 | Gene; miRNA; | mir-218 microRNA precursor family |
| mir-196 | RF00256 | 14 | 90 | 71 | 216 | 90 | 71 | Gene; miRNA; | mir-196 microRNA precursor family |
| mir-194 | RF00257 | 29 | 84 | 71 | 100 | 85 | 74 | Gene; miRNA; | mir-194 microRNA precursor family |
| mir-130 | RF00258 | 8 | 83 | 87 | 83 | 81 | 74 | Gene; miRNA; | mir-130 microRNA precursor family |
| IFN_gamma | RF00259 | 5 | 168 | 91 | 129 | 93 | 78 | Cis-reg; | Interferon gamma 5' UTR regulatory element |
| HepC_CRE | RF00260 | 52 | 51 | 89 | 1366 | 50 | 91 | Cis-reg; | Hepatitis C virus (HCV) cis-acting replication element (CRE) |
| IRES_L-myc | RF00261 | 11 | 220 | 90 | 86 | 183 | 47 | Cis-reg; IRES; | L-myc internal ribosome entry site (IRES) |
| sar | RF00262 | 6 | 68 | 81 | 41 | 67 | 75 | Gene; antisense; | sar RNA |
| SNORA68 | RF00263 | 25 | 132 | 74 | 313 | 123 | 56 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA68 |
| SNORA64 | RF00264 | 9 | 133 | 72 | 186 | 127 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA64/SNORA10 family |
| SNORA69 | RF00265 | 16 | 132 | 82 | 88 | 128 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA69 |
| snoZ17 | RF00266 | 24 | 71 | 79 | 88 | 69 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z17 |
| snoR64 | RF00267 | 14 | 95 | 70 | 46 | 92 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R64/Z200 family |
| snoZ7 | RF00268 | 5 | 78 | 95 | 20 | 74 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoZ7/snoR77 |
| SNORD61 | RF00270 | 35 | 71 | 71 | 122 | 71 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD61 |
| SNORD60 | RF00271 | 22 | 82 | 80 | 114 | 82 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD60 |
| SNORA67 | RF00272 | 10 | 141 | 82 | 233 | 133 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA67 |
| SNORD59 | RF00273 | 24 | 73 | 76 | 176 | 72 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD59 |
| SNORD57 | RF00274 | 23 | 71 | 79 | 90 | 68 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD57 |
| SNORD56 | RF00275 | 7 | 70 | 81 | 181 | 69 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD56 |
| SNORD52 | RF00276 | 20 | 67 | 83 | 105 | 65 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD52 |
| SNORD49 | RF00277 | 26 | 71 | 80 | 126 | 70 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD49 |
| SNORD50 | RF00278 | 24 | 71 | 84 | 151 | 70 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD50 |
| SNORD45 | RF00279 | 11 | 74 | 77 | 235 | 77 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD45 |
| SNORD51 | RF00280 | 13 | 77 | 86 | 79 | 76 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD51 |
| SNORD47 | RF00281 | 19 | 75 | 83 | 91 | 75 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD47 |
| SNORD48 | RF00282 | 7 | 62 | 92 | 70 | 62 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD48 |
| SCARNA18 | RF00283 | 20 | 81 | 87 | 123 | 81 | 78 | Gene; snRNA; snoRNA; scaRNA; | small Cajal body-specific RNA 18 |
| SNORD74 | RF00284 | 22 | 79 | 78 | 170 | 76 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD74 |
| snoZ6 | RF00285 | 7 | 91 | 92 | 91 | 72 | 62 | Gene; snRNA; snoRNA; CD-box; | Z6 small nucleolar RNA |
| SCARNA8 | RF00286 | 22 | 130 | 81 | 104 | 127 | 73 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 8 |
| SNORD44 | RF00287 | 12 | 61 | 83 | 75 | 60 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD44 |
| snoZ30 | RF00288 | 20 | 97 | 84 | 73 | 96 | 81 | Gene; snRNA; snoRNA; CD-box; | Z30 small nucleolar RNA |
| SNORND104 | RF00289 | 18 | 69 | 88 | 61 | 69 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD104 |
| BaMV_CRE | RF00290 | 5 | 140 | 100 | 14 | 140 | 100 | Cis-reg; | Bamboo mosaic potexvirus (BaMV) cis-regulatory element |
| snoR639 | RF00291 | 9 | 139 | 82 | 26 | 139 | 87 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR639/H1 |
| snoTBR5 | RF00292 | 6 | 89 | 85 | 52 | 84 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA TBR5 |
| snoM1 | RF00293 | 7 | 99 | 90 | 17 | 98 | 89 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoM1 |
| snoTBR17 | RF00294 | 5 | 284 | 86 | 53 | 248 | 84 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA TBR17 |
| snoTBR7 | RF00295 | 6 | 75 | 86 | 56 | 72 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA TBR7 |
| snoR16 | RF00296 | 22 | 85 | 76 | 51 | 81 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R16 |
| snoZ221_snoR21b | RF00300 | 12 | 99 | 77 | 40 | 92 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z221/R21b |
| snoZ256 | RF00301 | 5 | 93 | 87 | 20 | 94 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z256 |
| SNORA65 | RF00302 | 8 | 125 | 85 | 152 | 123 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA65 |
| snoR86 | RF00303 | 11 | 124 | 78 | 47 | 124 | 75 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR86 |
| snoZ279_R105_R108 | RF00304 | 20 | 106 | 76 | 40 | 107 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z279/snoR105/snoR108 |
| snoZ248 | RF00305 | 6 | 137 | 98 | 24 | 121 | 91 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z248 |
| snoZ178 | RF00306 | 6 | 152 | 100 | 85 | 125 | 44 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z178 |
| snoR98 | RF00307 | 4 | 108 | 84 | 19 | 101 | 55 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR98 |
| snosnR60_Z15 | RF00309 | 23 | 93 | 63 | 276 | 89 | 60 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR60/Z15/Z230/Z193/J17 |
| snoZ165 | RF00310 | 5 | 90 | 95 | 13 | 88 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z165 |
| snoZ188 | RF00311 | 24 | 118 | 81 | 32 | 114 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z188 |
| snoZ206 | RF00312 | 6 | 130 | 90 | 30 | 116 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z206 |
| snoZ173 | RF00313 | 5 | 106 | 99 | 12 | 88 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z173 |
| snoZ182 | RF00314 | 7 | 89 | 94 | 12 | 88 | 95 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z182 |
| snoJ33 | RF00315 | 5 | 79 | 79 | 40 | 78 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA J33 |
| snoR43 | RF00316 | 16 | 72 | 85 | 28 | 71 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R43 |
| snoZ163 | RF00317 | 7 | 89 | 82 | 30 | 85 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z163/Z177 family |
| snoZ175 | RF00318 | 6 | 75 | 100 | 9 | 73 | 100 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z175 |
| SNORA23 | RF00319 | 5 | 182 | 91 | 100 | 172 | 71 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA23 |
| snoZ185 | RF00320 | 5 | 84 | 95 | 18 | 78 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z185 |
| snoZ247 | RF00321 | 8 | 136 | 81 | 464 | 136 | 54 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z247 |
| SNORA31 | RF00322 | 5 | 125 | 84 | 860 | 122 | 59 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA31 |
| snoR79 | RF00323 | 5 | 64 | 100 | 21 | 56 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R79 |
| snoMBII-202 | RF00324 | 26 | 82 | 71 | 105 | 80 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA MBII-202 |
| SNORD53_SNORD92 | RF00325 | 37 | 79 | 75 | 190 | 80 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD53/SNORD92 |
| snoZ155 | RF00326 | 8 | 77 | 79 | 30 | 77 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z155 |
| snoZ194 | RF00327 | 5 | 106 | 98 | 15 | 103 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z194 |
| snoZ161_228 | RF00328 | 11 | 90 | 67 | 51 | 92 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z161/Z228 |
| snoZ162 | RF00329 | 5 | 88 | 92 | 18 | 90 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z162 |
| snoZ43 | RF00330 | 7 | 99 | 84 | 53 | 96 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z43 |
| snoZ169 | RF00331 | 3 | 69 | 87 | 12 | 67 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z169 |
| snoZ266 | RF00332 | 11 | 91 | 73 | 61 | 90 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z266 |
| snoZ157 | RF00333 | 10 | 97 | 75 | 90 | 96 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z157/R69/R10 |
| SNORA3 | RF00334 | 6 | 128 | 76 | 351 | 125 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA3/SNORA45 family |
| snoZ13_snr52 | RF00335 | 35 | 99 | 71 | 109 | 97 | 61 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z13/snr52 |
| snoJ26 | RF00336 | 5 | 149 | 94 | 33 | 145 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA J26 |
| snoZ112 | RF00337 | 6 | 183 | 94 | 69 | 174 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z112 |
| snoR53 | RF00338 | 5 | 91 | 93 | 19 | 89 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR53 |
| snoR60 | RF00339 | 10 | 73 | 86 | 58 | 72 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR60 |
| SNORA36 | RF00340 | 6 | 128 | 84 | 326 | 122 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA36 family |
| snoZ39 | RF00341 | 5 | 61 | 87 | 72 | 62 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z39 |
| snoZ40 | RF00342 | 5 | 72 | 94 | 84 | 70 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z40 |
| snoZ122 | RF00343 | 9 | 85 | 71 | 92 | 89 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z122 |
| snoZ267 | RF00344 | 5 | 72 | 82 | 29 | 71 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z267 |
| snoR1 | RF00345 | 13 | 93 | 73 | 61 | 89 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR1 |
| snoR9_plant | RF00348 | 7 | 129 | 85 | 53 | 114 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR9 |
| snoR11 | RF00349 | 5 | 91 | 86 | 45 | 90 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R11/Z151 |
| snoZ152 | RF00350 | 9 | 106 | 73 | 37 | 103 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z152/R70/R12/ |
| snoR20 | RF00351 | 4 | 93 | 85 | 7 | 93 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R20 |
| snoR21 | RF00352 | 6 | 82 | 79 | 24 | 77 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R21 |
| snoR31_Z110_Z27 | RF00353 | 8 | 94 | 67 | 68 | 95 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR31/Z110/Z27 |
| snoR28 | RF00355 | 9 | 76 | 83 | 30 | 74 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR28 |
| snoR32_R81 | RF00356 | 6 | 95 | 81 | 16 | 93 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R32/R81/Z41 |
| snoR44_J54 | RF00357 | 29 | 94 | 74 | 93 | 96 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA R44/J54/Z268 family |
| snoZ101 | RF00358 | 14 | 94 | 79 | 49 | 93 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z101 |
| snoZ102_R77 | RF00359 | 9 | 86 | 87 | 44 | 86 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z102/R77 |
| snoZ107_R87 | RF00360 | 9 | 114 | 74 | 78 | 106 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z107/R87 |
| snoZ119 | RF00361 | 6 | 96 | 95 | 18 | 97 | 94 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z119 |
| Pospi_RY | RF00362 | 16 | 79 | 95 | 237 | 78 | 93 | Cis-reg; | Pospiviroid RY motif stem loop |
| mir-BART1 | RF00363 | 5 | 70 | 95 | 18 | 70 | 98 | Gene; miRNA; | mir-BART1 microRNA precursor family |
| mir-BART2 | RF00364 | 8 | 61 | 96 | 18 | 59 | 96 | Gene; miRNA; | mir-BART2 microRNA precursor family |
| mir-BHRF1-1 | RF00365 | 5 | 66 | 98 | 10 | 66 | 99 | Gene; miRNA; | mir-BHRF1-1 microRNA precursor family |
| mir-BHRF1-2 | RF00366 | 5 | 65 | 85 | 13 | 65 | 93 | Gene; miRNA; | mir-BHRF1-2 microRNA precursor family |
| mir-BHRF1-3 | RF00367 | 5 | 65 | 100 | 10 | 65 | 100 | Gene; miRNA; | mir-BHRF1-3 microRNA precursor family |
| sroB | RF00368 | 11 | 78 | 76 | 151 | 80 | 82 | Gene; sRNA; | sroB RNA |
| sroC | RF00369 | 6 | 160 | 77 | 138 | 159 | 78 | Gene; sRNA; | sroC RNA |
| sroD | RF00370 | 5 | 86 | 87 | 124 | 83 | 91 | Gene; sRNA; | sroD RNA |
| sroE | RF00371 | 4 | 88 | 83 | 113 | 89 | 91 | Gene; sRNA; | sroE RNA |
| sroH | RF00372 | 6 | 157 | 86 | 45 | 160 | 96 | Gene; sRNA; | sroH RNA |
| RNaseP_arch | RF00373 | 72 | 312 | 56 | 322 | 304 | 51 | Gene; ribozyme; | Archaeal RNase P |
| Gammaretro_CES | RF00374 | 23 | 100 | 91 | 1308 | 100 | 76 | Cis-reg; | Gammaretrovirus core encapsidation signal |
| HIV_PBS | RF00375 | 130 | 99 | 93 | 3082 | 90 | 83 | Cis-reg; | HIV primer binding site (PBS) |
| HIV_GSL3 | RF00376 | 72 | 83 | 82 | 17893 | 80 | 88 | Cis-reg; | HIV gag stem loop 3 (GSL3) |
| snoU6-53 | RF00377 | 25 | 107 | 77 | 111 | 105 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U6-53/MBII-28 |
| Qrr | RF00378 | 31 | 106 | 78 | 204 | 105 | 79 | Gene; sRNA; | Qrr RNA |
| ydaO-yuaA | RF00379 | 106 | 143 | 62 | 885 | 157 | 60 | Cis-reg; | ydaO/yuaA leader |
| ykoK | RF00380 | 96 | 168 | 63 | 600 | 168 | 64 | Cis-reg; | ykoK leader |
| Antizyme_FSE | RF00381 | 13 | 57 | 86 | 223 | 57 | 87 | Cis-reg; frameshift_element; | Antizyme RNA frameshifting stimulation element |
| DnaX | RF00382 | 5 | 65 | 88 | 151 | 64 | 87 | Cis-reg; frameshift_element; | DnaX ribosomal frameshifting element |
| IS1222_FSE | RF00383 | 5 | 118 | 94 | 61 | 115 | 94 | Cis-reg; frameshift_element; | Insertion sequence IS1222 ribosomal frameshifting element |
| Pox_AX_element | RF00384 | 10 | 62 | 95 | 94 | 62 | 96 | Cis-reg; | Poxvirus AX element late mRNA cis-regulatory element |
| IBV_D-RNA | RF00385 | 10 | 41 | 95 | 113 | 40 | 96 | Cis-reg; | Infectious bronchitis virus D-RNA |
| Entero_5_CRE | RF00386 | 160 | 89 | 86 | 732 | 80 | 77 | Cis-reg; | Enterovirus 5' cloverleaf cis-acting replication element |
| IRES_FGF1 | RF00387 | 6 | 165 | 88 | 53 | 158 | 75 | Cis-reg; IRES; | FGF-1 internal ribosome entry site (IRES) |
| QaRNA | RF00388 | 6 | 103 | 70 | 19 | 97 | 82 | Gene; antisense; | Qa RNA |
| satBaMV_CRE | RF00389 | 42 | 158 | 95 | 74 | 157 | 95 | Cis-reg; | Bamboo mosaic virus satellite RNA cis-regulatory element |
| UPSK | RF00390 | 6 | 23 | 95 | 28 | 23 | 96 | Cis-reg; | UPSK RNA |
| RtT | RF00391 | 58 | 129 | 71 | 1240 | 127 | 57 | Cis-reg; | RtT RNA |
| SNORA5 | RF00392 | 6 | 134 | 77 | 285 | 127 | 66 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA5 |
| SNORA8 | RF00393 | 5 | 139 | 89 | 190 | 132 | 76 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA8 |
| SNORA4 | RF00394 | 7 | 140 | 75 | 171 | 134 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA4 |
| SNORA13 | RF00396 | 48 | 133 | 68 | 160 | 128 | 59 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA13 |
| SNORA14 | RF00397 | 16 | 134 | 79 | 105 | 128 | 72 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA14 |
| SNORA15 | RF00398 | 20 | 135 | 83 | 198 | 122 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA15 |
| SNORA24 | RF00399 | 5 | 129 | 89 | 182 | 125 | 75 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA24 |
| SNORA28 | RF00400 | 25 | 125 | 80 | 176 | 120 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA28 |
| SNORA20 | RF00401 | 17 | 129 | 85 | 182 | 127 | 73 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA20 |
| SNORA25 | RF00402 | 27 | 127 | 77 | 541 | 121 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA25 |
| SNORA41 | RF00403 | 29 | 132 | 79 | 126 | 127 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA41 |
| SNORA46 | RF00404 | 21 | 136 | 83 | 90 | 134 | 76 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA46 |
| SNORA44 | RF00405 | 25 | 129 | 83 | 339 | 124 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA44 |
| SNORA42 | RF00406 | 21 | 134 | 81 | 795 | 127 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA42/SNORA80 family |
| SNORA50 | RF00407 | 14 | 135 | 73 | 153 | 134 | 65 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA50 |
| SNORA1 | RF00408 | 28 | 133 | 78 | 268 | 127 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA1 |
| SNORA7 | RF00409 | 27 | 139 | 81 | 25640 | 131 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA7 |
| SNORA2 | RF00410 | 18 | 135 | 74 | 1231 | 134 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA2/SNORA34 family |
| SNORA9 | RF00411 | 36 | 132 | 78 | 303 | 128 | 72 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA9 |
| SNORA21 | RF00412 | 5 | 133 | 89 | 192 | 127 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA21 |
| SNORA19 | RF00413 | 31 | 127 | 80 | 371 | 121 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA19 |
| SNORA22 | RF00414 | 30 | 133 | 79 | 155 | 130 | 76 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA22 |
| SNORA30 | RF00415 | 11 | 129 | 73 | 195 | 127 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA30/SNORA37 family |
| SNORA43 | RF00416 | 22 | 134 | 74 | 185 | 132 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA43 |
| SNORA56 | RF00417 | 13 | 129 | 83 | 63 | 125 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA56 |
| SNORA58 | RF00418 | 19 | 135 | 82 | 94 | 134 | 78 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA58 |
| SNORA52 | RF00419 | 20 | 133 | 72 | 107 | 125 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA52 |
| SNORA61 | RF00420 | 23 | 129 | 75 | 1234 | 120 | 57 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA61 |
| SNORA32 | RF00421 | 9 | 121 | 84 | 333 | 110 | 66 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA32 |
| SCARNA24 | RF00422 | 21 | 130 | 81 | 153 | 126 | 78 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 24 |
| SCARNA4 | RF00423 | 23 | 128 | 85 | 119 | 126 | 75 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 4 |
| SCARNA16 | RF00424 | 37 | 184 | 77 | 161 | 171 | 72 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 16 |
| SNORA18 | RF00425 | 29 | 131 | 77 | 416 | 125 | 65 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA18 |
| SCARNA15 | RF00426 | 18 | 128 | 78 | 170 | 125 | 64 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 15 |
| SCARNA23 | RF00427 | 18 | 125 | 82 | 68 | 121 | 73 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 23 |
| SNORA38 | RF00428 | 25 | 131 | 86 | 303 | 128 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA38 |
| SNORA29 | RF00429 | 23 | 138 | 79 | 214 | 136 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA29 |
| SNORA54 | RF00430 | 5 | 127 | 60 | 113 | 123 | 60 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA54 |
| SNORA55 | RF00431 | 25 | 134 | 86 | 127 | 128 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA55 |
| SNORA51 | RF00432 | 9 | 132 | 82 | 608 | 126 | 71 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA51 |
| Hsp90_CRE | RF00433 | 6 | 151 | 95 | 27 | 141 | 80 | Cis-reg; thermoregulator; | Hsp90 cis-regulatory element |
| BTE | RF00434 | 17 | 101 | 74 | 99 | 105 | 78 | Cis-reg; | Luteovirus cap-independent translation element (BTE) |
| ROSE | RF00435 | 13 | 101 | 61 | 71 | 92 | 57 | Cis-reg; thermoregulator; | Repression of heat shock gene expression (ROSE) element |
| UnaL2 | RF00436 | 30 | 54 | 78 | 16952 | 53 | 76 | Cis-reg; | UnaL2 LINE 3' element |
| HLE | RF00437 | 5 | 129 | 83 | 36 | 128 | 76 | Cis-reg; | Hairy RNA localisation element (HLE) |
| SNORA33 | RF00438 | 26 | 129 | 80 | 292 | 122 | 65 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA33 |
| SNORD87 | RF00439 | 9 | 82 | 89 | 60 | 84 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD87 |
| SNORD37 | RF00440 | 7 | 63 | 79 | 239 | 68 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD37 |
| snoZ242 | RF00441 | 5 | 197 | 89 | 18 | 187 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z242 |
| ykkC-yxkD | RF00442 | 109 | 107 | 65 | 303 | 105 | 62 | Cis-reg; | ykkC-yxkD leader |
| SNORA27 | RF00443 | 22 | 127 | 84 | 203 | 120 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA27 |
| PrrF | RF00444 | 17 | 148 | 81 | 56 | 138 | 77 | Gene; sRNA; | PrrF RNA |
| mir-399 | RF00445 | 13 | 113 | 60 | 134 | 111 | 53 | Gene; miRNA; | mir-399 microRNA precursor family |
| mir-133 | RF00446 | 46 | 87 | 67 | 215 | 87 | 74 | Gene; miRNA; | mir-133 microRNA precursor family |
| IRES_Kv1_4 | RF00447 | 6 | 256 | 88 | 47 | 252 | 85 | Cis-reg; IRES; | Voltage-gated potassium-channel Kv1.4 IRES |
| IRES_EBNA | RF00448 | 6 | 211 | 84 | 14 | 211 | 76 | Cis-reg; IRES; | Epstein-Barr virus nuclear antigen (EBNA) IRES |
| IRES_HIF1 | RF00449 | 16 | 277 | 77 | 58 | 255 | 74 | Cis-reg; IRES; | HIF-1 alpha IRES |
| mir-395 | RF00451 | 21 | 102 | 63 | 571 | 98 | 63 | Gene; miRNA; | mir-395 microRNA precursor family |
| mir-172 | RF00452 | 11 | 121 | 58 | 303 | 125 | 62 | Gene; miRNA; | mir-172 microRNA precursor family |
| Cardiovirus_CRE | RF00453 | 4 | 33 | 85 | 7 | 33 | 87 | Cis-reg; | Cardiovirus cis-acting replication element (CRE) |
| p27_CRE | RF00454 | 11 | 58 | 94 | 34 | 58 | 93 | Cis-reg; | p27 cis-regulatory element |
| mir-15 | RF00455 | 14 | 85 | 71 | 143 | 85 | 74 | Gene; miRNA; | mir-15 microRNA precursor family |
| mir-34 | RF00456 | 18 | 87 | 72 | 156 | 85 | 66 | Gene; miRNA; | mir-34 microRNA precursor family |
| IRES_mnt | RF00457 | 21 | 200 | 93 | 48 | 197 | 92 | Cis-reg; IRES; | Mnt IRES |
| IRES_Cripavirus | RF00458 | 7 | 198 | 53 | 16 | 198 | 57 | Cis-reg; IRES; | Cripavirus internal ribosome entry site (IRES) |
| MPMV_package | RF00459 | 9 | 277 | 72 | 556 | 273 | 50 | Cis-reg; | Mason-Pfizer monkey virus packaging signal |
| U1A_PIE | RF00460 | 35 | 74 | 77 | 145 | 73 | 81 | Cis-reg; | U1A polyadenylation inhibition element (PIE) |
| IRES_VEGF_A | RF00461 | 7 | 303 | 91 | 44 | 299 | 93 | Cis-reg; IRES; | Vascular endothelial growth factor (VEGF) IRES A |
| IRES_APC | RF00462 | 6 | 53 | 90 | 53 | 41 | 82 | Cis-reg; IRES; | APC internal ribosome entry site (IRES) |
| ApoB_5_CRE | RF00463 | 5 | 126 | 92 | 23 | 124 | 96 | Cis-reg; | Apolipoprotein B (apoB) 5' UTR cis-regulatory element |
| mir-92 | RF00464 | 43 | 79 | 76 | 173 | 78 | 68 | Gene; miRNA; | mir-92 microRNA precursor family |
| JEV_hairpin | RF00465 | 20 | 59 | 88 | 393 | 59 | 87 | Cis-reg; | Japanese encephalitis virus (JEV) hairpin structure |
| RSV_PBS | RF00467 | 23 | 75 | 92 | 163 | 69 | 70 | Cis-reg; | Rous sarcoma virus (RSV) primer binding site (PBS) |
| HCV_SLVII | RF00468 | 110 | 65 | 75 | 2063 | 65 | 81 | Cis-reg; | Hepatitis C virus stem-loop VII |
| HCV_SLIV | RF00469 | 110 | 36 | 89 | 1366 | 37 | 91 | Cis-reg; | Hepatitis C stem-loop IV |
| Toga_5_CRE | RF00470 | 33 | 266 | 80 | 135 | 248 | 72 | Cis-reg; | Togavirus 5' plus strand cis-regulatory element |
| snosnR48 | RF00471 | 6 | 108 | 74 | 38 | 108 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR48 |
| snosnR55 | RF00472 | 6 | 89 | 75 | 41 | 89 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR55/Z10 |
| snosnR54 | RF00473 | 9 | 85 | 74 | 126 | 83 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR54 |
| snosnR57 | RF00474 | 6 | 90 | 75 | 36 | 89 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR57 |
| snosnR69 | RF00475 | 6 | 97 | 63 | 40 | 97 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR69 |
| snosnR61 | RF00476 | 56 | 83 | 68 | 221 | 80 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR61/Z1/Z11 |
| snosnR66 | RF00477 | 5 | 100 | 75 | 36 | 101 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR66 |
| SCARNA6 | RF00478 | 17 | 263 | 74 | 154 | 256 | 55 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 6 |
| snosnR71 | RF00479 | 7 | 92 | 76 | 68 | 92 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR71 |
| HIV_FE | RF00480 | 145 | 51 | 81 | 11088 | 51 | 90 | Cis-reg; frameshift_element; | HIV Ribosomal frameshift signal |
| HCV_X3 | RF00481 | 22 | 99 | 97 | 156 | 99 | 98 | Cis-reg; | Hepatitis C virus 3'X element |
| snoF1_F2 | RF00482 | 8 | 139 | 88 | 44 | 139 | 72 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA F1/F2/snoR5a |
| IRES_IGF2 | RF00483 | 9 | 120 | 95 | 72 | 117 | 91 | Cis-reg; IRES; | Insulin-like growth factor II IRES |
| IRES_Cx32 | RF00484 | 6 | 144 | 93 | 48 | 144 | 94 | Cis-reg; IRES; | Connexin-32 internal ribosome entry site (IRES) |
| K_chan_RES | RF00485 | 85 | 114 | 70 | 2252 | 113 | 61 | Cis-reg; | Potassium channel RNA editing signal |
| mir-129 | RF00486 | 6 | 90 | 83 | 110 | 90 | 81 | Gene; miRNA; | mir-129 microRNA precursor family |
| IRES_Cx43 | RF00487 | 14 | 198 | 87 | 140 | 195 | 71 | Cis-reg; IRES; | Connexin-43 internal ribosome entry site (IRES) |
| U1_yeast | RF00488 | 5 | 566 | 60 | 27 | 557 | 65 | Gene; snRNA; splicing; | Yeast U1 spliceosomal RNA |
| ctRNA_p42d | RF00489 | 10 | 45 | 85 | 106 | 45 | 87 | Gene; antisense; | ctRNA |
| S-element | RF00490 | 29 | 67 | 74 | 138 | 66 | 72 | Cis-reg; | S-element |
| SVLPA | RF00491 | 6 | 53 | 95 | 125 | 54 | 99 | Cis-reg; | Simian virus 40 late polyadenylation signal (SVLPA) |
| SCARNA17 | RF00492 | 6 | 141 | 78 | 119 | 136 | 70 | Gene; snRNA; snoRNA; scaRNA; | small Cajal body-specific RNA 17 |
| snoU2-30 | RF00493 | 21 | 69 | 88 | 158 | 70 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U2-30 |
| snoU2_19 | RF00494 | 28 | 80 | 80 | 182 | 78 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U2-19 |
| IRES_Hsp70 | RF00495 | 14 | 211 | 81 | 100 | 211 | 79 | Cis-reg; IRES; | Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) |
| Corona_SL-III | RF00496 | 5 | 42 | 95 | 36 | 42 | 98 | Cis-reg; | Coronavirus SL-III cis-acting replication element (CRE) |
| EAV_LTH | RF00498 | 6 | 45 | 100 | 19 | 45 | 99 | Cis-reg; | Equine arteritis virus leader TRS hairpin (LTH) |
| Parecho_CRE | RF00499 | 5 | 111 | 87 | 17 | 95 | 85 | Cis-reg; | Human parechovirus 1 (HPeV1) cis regulatory element (CRE) |
| TCV_H5 | RF00500 | 5 | 45 | 100 | 6 | 41 | 98 | Cis-reg; | Turnip crinkle virus (TCV) repressor of minus strand synthesis H5 |
| Rota_CRE | RF00501 | 14 | 67 | 86 | 109 | 63 | 87 | Cis-reg; | Rotavirus cis-acting replication element (CRE) |
| TCV_Pr | RF00502 | 4 | 33 | 92 | 4 | 33 | 92 | Cis-reg; | Turnip crinkle virus (TCV) core promoter hairpin (Pr) |
| RNAIII | RF00503 | 11 | 490 | 86 | 80 | 486 | 90 | Gene; | RNAIII |
| Glycine | RF00504 | 44 | 100 | 55 | 4223 | 85 | 62 | Cis-reg; riboswitch; | Glycine riboswitch |
| RydC | RF00505 | 5 | 64 | 88 | 96 | 64 | 91 | Gene; sRNA; | RydC RNA |
| Thr_leader | RF00506 | 27 | 120 | 79 | 258 | 116 | 72 | Cis-reg; leader; | Threonine operon leader |
| Corona_FSE | RF00507 | 23 | 82 | 66 | 359 | 82 | 70 | Cis-reg; frameshift_element; | Coronavirus frameshifting stimulation element |
| snosnR64 | RF00509 | 10 | 103 | 84 | 28 | 102 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR64 |
| Tombus_IRE | RF00510 | 22 | 88 | 85 | 44 | 89 | 86 | Cis-reg; | Tombusvirus internal replication element (IRE) |
| IRES_KSHV | RF00511 | 5 | 248 | 99 | 5 | 248 | 99 | Cis-reg; IRES; | Kaposi's sarcoma-associated herpesvirus internal ribosome entry site (IRES) |
| Leu_leader | RF00512 | 6 | 146 | 63 | 170 | 145 | 74 | Cis-reg; leader; | Leucine operon leader |
| Trp_leader | RF00513 | 24 | 100 | 60 | 240 | 98 | 65 | Cis-reg; leader; | Tryptophan operon leader |
| His_leader | RF00514 | 36 | 128 | 64 | 303 | 126 | 70 | Cis-reg; leader; | Histidine operon leader |
| PyrR | RF00515 | 56 | 121 | 45 | 795 | 105 | 49 | Cis-reg; | PyrR binding site |
| ylbH | RF00516 | 3 | 118 | 62 | 119 | 119 | 87 | Cis-reg; | ylbH leader |
| serC | RF00517 | 70 | 52 | 78 | 220 | 52 | 77 | Cis-reg; | serC leader |
| speF | RF00518 | 6 | 327 | 71 | 86 | 332 | 70 | Cis-reg; | speF leader |
| suhB | RF00519 | 99 | 76 | 53 | 333 | 75 | 51 | Gene; sRNA; | suhB |
| ybhL | RF00520 | 8 | 73 | 80 | 55 | 75 | 82 | Cis-reg; | ybhL leader |
| SAM_alpha | RF00521 | 40 | 79 | 71 | 227 | 78 | 68 | Cis-reg; riboswitch; | SAM riboswitch (alpha-proteobacteria) |
| PreQ1 | RF00522 | 42 | 45 | 67 | 415 | 45 | 69 | Cis-reg; riboswitch; | PreQ1 riboswitch |
| Prion_pknot | RF00523 | 157 | 41 | 89 | 5282 | 41 | 91 | Cis-reg; | Prion pseudoknot |
| R2_retro_el | RF00524 | 15 | 215 | 66 | 732 | 134 | 62 | Cis-reg; | R2 RNA element |
| Flavivirus_DB | RF00525 | 111 | 72 | 74 | 4972 | 71 | 78 | Cis-reg; | Flavivirus DB element |
| snoMe28S-U3344 | RF00526 | 8 | 83 | 79 | 44 | 81 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-U3344 |
| snoMe28S-G3255 | RF00527 | 10 | 82 | 76 | 49 | 82 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Gm3255 |
| snoMe28S-Gm1083 | RF00528 | 11 | 89 | 87 | 110 | 89 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Gm1083 |
| snoMe28S-Am2589 | RF00529 | 16 | 108 | 69 | 59 | 107 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Am2589 |
| snoMe28S-Cm2645 | RF00530 | 20 | 75 | 80 | 108 | 72 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Cm2645 |
| snoMe28S-Gm3113 | RF00531 | 15 | 83 | 76 | 44 | 83 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Gm3113 |
| snoMe18S-Um1356 | RF00532 | 22 | 86 | 72 | 123 | 85 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me18S-Um1356 |
| snoMe18S-Gm1358 | RF00533 | 13 | 75 | 79 | 55 | 74 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me18S-Gm1358 |
| SgrS | RF00534 | 9 | 229 | 48 | 129 | 224 | 74 | Gene; antisense; | SgrS RNA |
| snoMe28S-Am982 | RF00535 | 13 | 78 | 75 | 100 | 71 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Am982 |
| snoMe28S-Cm3227 | RF00536 | 13 | 81 | 91 | 62 | 81 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Cm3227 |
| snoMe28S-Am2634 | RF00537 | 18 | 93 | 71 | 101 | 90 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Am2634 |
| snoCD11 | RF00538 | 26 | 74 | 79 | 81 | 71 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA CD11 |
| snoMe28S-Cm788 | RF00539 | 5 | 72 | 90 | 31 | 72 | 84 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Me28S-Cm788 |
| snopsi18S-1854 | RF00540 | 16 | 155 | 80 | 54 | 154 | 80 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi18S-1854 |
| snopsi28S-2876 | RF00541 | 8 | 145 | 81 | 23 | 145 | 87 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi28S-2876 |
| snopsi28S-1192 | RF00542 | 15 | 140 | 82 | 78 | 136 | 81 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi28S-1192 |
| snopsi18S-1377 | RF00543 | 15 | 139 | 73 | 103 | 138 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi18S-1377 |
| snopsi28S-3327 | RF00544 | 14 | 143 | 80 | 58 | 139 | 73 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi28S-3327 |
| snopsi18S-841 | RF00545 | 24 | 140 | 69 | 73 | 137 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi18S-841/snoR66 |
| snopsi28S-3316 | RF00546 | 33 | 132 | 72 | 91 | 131 | 75 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA psi28S-3316 |
| IRES_TrkB | RF00547 | 15 | 343 | 78 | 57 | 305 | 71 | Cis-reg; IRES; | TrkB IRES |
| U11 | RF00548 | 68 | 154 | 58 | 426 | 138 | 63 | Gene; snRNA; splicing; | U11 spliceosomal RNA |
| IRES_c-sis | RF00549 | 10 | 602 | 95 | 48 | 550 | 89 | Cis-reg; IRES; | c-sis internal ribosome entry site (IRES) |
| HepE_CRE | RF00550 | 46 | 147 | 85 | 187 | 147 | 85 | Cis-reg; | Hepatitis E virus cis-reactive element |
| bicoid_3 | RF00551 | 15 | 549 | 75 | 83 | 488 | 85 | Cis-reg; | Bicoid 3'-UTR regulatory element |
| rncO | RF00552 | 18 | 204 | 84 | 173 | 192 | 81 | Cis-reg; | rncO |
| SCARNA1 | RF00553 | 30 | 163 | 72 | 100 | 148 | 71 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 1 |
| SNORA48 | RF00554 | 24 | 135 | 80 | 591 | 138 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA48 |
| L13_leader | RF00555 | 26 | 67 | 66 | 209 | 67 | 68 | Cis-reg; leader; | Ribosomal protein L13 leader |
| L19_leader | RF00556 | 16 | 40 | 58 | 201 | 41 | 61 | Cis-reg; leader; | Ribosomal protein L19 leader |
| L10_leader | RF00557 | 106 | 140 | 47 | 492 | 137 | 48 | Cis-reg; leader; | Ribosomal protein L10 leader |
| L20_leader | RF00558 | 43 | 126 | 53 | 373 | 126 | 54 | Cis-reg; leader; | Ribosomal protein L20 leader |
| L21_leader | RF00559 | 38 | 79 | 57 | 305 | 80 | 62 | Cis-reg; leader; | Ribosomal protein L21 leader |
| SNORA17 | RF00560 | 53 | 132 | 81 | 3916 | 125 | 65 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA17 |
| SNORA40 | RF00561 | 28 | 127 | 84 | 670 | 118 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA40 |
| SNORA49 | RF00562 | 21 | 132 | 82 | 65 | 130 | 76 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA49 |
| SNORA53 | RF00563 | 28 | 240 | 79 | 98 | 216 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA53 |
| SCARNA11 | RF00564 | 24 | 138 | 81 | 160 | 128 | 64 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 11 |
| SCARNA3 | RF00565 | 23 | 137 | 77 | 89 | 128 | 74 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 3 |
| SNORA35 | RF00566 | 31 | 128 | 66 | 106 | 128 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA35 |
| SNORD17 | RF00567 | 19 | 236 | 78 | 50 | 235 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD17 |
| SNORA26 | RF00568 | 76 | 121 | 79 | 399 | 120 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA26 |
| SNORD19 | RF00569 | 22 | 76 | 85 | 63 | 72 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD19 |
| SNORD64 | RF00570 | 17 | 65 | 79 | 55 | 66 | 79 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD64 |
| SNORD65 | RF00571 | 24 | 72 | 83 | 142 | 72 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD65 |
| SNORD66 | RF00572 | 18 | 76 | 84 | 83 | 75 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD66 |
| SNORD67 | RF00573 | 15 | 111 | 79 | 77 | 107 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD67 |
| SNORD69 | RF00574 | 11 | 77 | 88 | 47 | 75 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD69 |
| SNORD70 | RF00575 | 21 | 87 | 79 | 131 | 85 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD70 |
| SNORD71 | RF00576 | 17 | 85 | 85 | 47 | 84 | 84 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORD71 |
| SNORD72 | RF00577 | 16 | 80 | 85 | 66 | 79 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD72 |
| SNORD89 | RF00578 | 18 | 113 | 89 | 72 | 110 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD89 |
| SNORD90 | RF00579 | 18 | 110 | 86 | 51 | 108 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD90 |
| SNORD91 | RF00580 | 24 | 93 | 80 | 95 | 93 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD91 family |
| SNORD12 | RF00581 | 8 | 88 | 70 | 189 | 89 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar SNORD12/SNORD106 |
| SCARNA14 | RF00582 | 22 | 135 | 77 | 100 | 129 | 74 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 14 |
| SNORD105 | RF00584 | 15 | 85 | 84 | 44 | 84 | 83 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD105 |
| SNORA12 | RF00586 | 22 | 147 | 79 | 106 | 143 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA12 |
| SNORD41 | RF00588 | 20 | 70 | 77 | 67 | 70 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD41 |
| SNORD77 | RF00591 | 21 | 67 | 81 | 222 | 68 | 65 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD77 |
| SNORD78 | RF00592 | 18 | 65 | 84 | 108 | 63 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD78 |
| snoU83B | RF00593 | 21 | 93 | 83 | 125 | 89 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U83B |
| SNORD86 | RF00594 | 6 | 85 | 79 | 96 | 83 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD86 |
| SNORA76 | RF00598 | 22 | 131 | 87 | 243 | 125 | 58 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA76 |
| SNORA77 | RF00599 | 19 | 124 | 77 | 138 | 123 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA77 |
| SNORA79 | RF00600 | 25 | 144 | 78 | 148 | 142 | 70 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA79 |
| SCARNA20 | RF00601 | 5 | 130 | 82 | 189 | 126 | 66 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 20 |
| SCARNA21 | RF00602 | 24 | 139 | 78 | 109 | 139 | 72 | Gene; snRNA; snoRNA; scaRNA; | Small Cajal body specific RNA 21 |
| SNORD23 | RF00603 | 15 | 108 | 87 | 69 | 107 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD23 |
| SNORD88 | RF00604 | 35 | 91 | 79 | 193 | 89 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD88 |
| SNORD93 | RF00606 | 15 | 72 | 91 | 67 | 74 | 87 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD93 |
| SNORD98 | RF00607 | 9 | 65 | 80 | 61 | 62 | 86 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD98 |
| SNORD99 | RF00608 | 23 | 73 | 80 | 57 | 72 | 82 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD99 |
| SNORD100 | RF00609 | 25 | 80 | 77 | 88 | 77 | 73 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD100 |
| SNORD110 | RF00610 | 16 | 69 | 86 | 59 | 71 | 71 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD110 |
| SNORD111 | RF00611 | 5 | 81 | 72 | 131 | 82 | 67 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD111 |
| SNORD75 | RF00612 | 5 | 65 | 78 | 100 | 62 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD75 |
| SNORD94 | RF00613 | 18 | 137 | 81 | 71 | 131 | 73 | Gene; snRNA; snoRNA; CD-box; | Small Nucleolar RNA SNORD94 |
| SNORA11 | RF00614 | 35 | 128 | 84 | 524 | 124 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA11 |
| LhrA | RF00615 | 10 | 268 | 99 | 27 | 265 | 97 | Gene; sRNA; | Listeria Hfq binding LhrA |
| LhrC | RF00616 | 12 | 112 | 90 | 77 | 106 | 89 | Gene; sRNA; | Listeria Hfq binding LhrC |
| cHP | RF00617 | 59 | 45 | 72 | 2787 | 45 | 81 | Cis-reg; | flavivirus capsid hairpin cHP |
| U4atac | RF00618 | 59 | 135 | 59 | 419 | 122 | 66 | Gene; snRNA; splicing; | U4atac minor spliceosomal RNA |
| U6atac | RF00619 | 61 | 121 | 71 | 1625 | 117 | 65 | Gene; snRNA; splicing; | U6atac minor spliceosomal RNA |
| HCV_ARF_SL | RF00620 | 36 | 153 | 90 | 5837 | 149 | 93 | Cis-reg; | Hepatitis C alternative reading frame stem-loop |
| CoTC_ribozyme | RF00621 | 10 | 187 | 88 | 38 | 186 | 75 | Gene; ribozyme; | Beta-globin co-transcriptional cleavage ribozyme |
| CPEB3_ribozyme | RF00622 | 11 | 76 | 85 | 102 | 74 | 78 | Gene; ribozyme; | Mammalian CPEB3 ribozyme |
| P1 | RF00623 | 11 | 180 | 69 | 32 | 173 | 60 | Gene; | Pseudomonas sRNA P1 |
| P9 | RF00624 | 12 | 75 | 79 | 67 | 80 | 78 | Gene; | Pseudomonas sRNA P9 |
| P11 | RF00625 | 10 | 136 | 74 | 23 | 137 | 72 | Gene; | Pseudomonas sRNA P11 |
| Gurken | RF00626 | 3 | 69 | 99 | 4 | 71 | 85 | Cis-reg; | Gurken localisation signal |
| P15 | RF00627 | 14 | 120 | 81 | 31 | 119 | 79 | Gene; | Pseudomonas sRNA P15 |
| P16 | RF00628 | 15 | 194 | 73 | 29 | 193 | 72 | Gene; | Pseudomonas sRNA P16 |
| P24 | RF00629 | 13 | 254 | 72 | 31 | 236 | 71 | Gene; | Pseudomonas sRNA P24 |
| P26 | RF00630 | 27 | 63 | 73 | 237 | 61 | 79 | Gene; | Pseudomonas sRNA P26 |
| sxy | RF00632 | 2 | 104 | 97 | 16 | 104 | 98 | Cis-reg; | sxy 5' UTR element |
| SAM-IV | RF00634 | 40 | 115 | 73 | 267 | 115 | 70 | Cis-reg; riboswitch; | S-adenosyl methionine (SAM) riboswitch, |
| HAR1F | RF00635 | 17 | 131 | 93 | 48 | 126 | 89 | Gene; | Human accelerated region 1F |
| NRON | RF00636 | 24 | 368 | 91 | 46 | 364 | 91 | Gene; | ncRNA Repressor of NFAT (nuclear factor of activated T cells) |
| mir-276 | RF00637 | 16 | 93 | 74 | 60 | 93 | 79 | Gene; miRNA; | microRNA mir-276 |
| MIR159 | RF00638 | 67 | 195 | 53 | 368 | 199 | 51 | Gene; miRNA; | microRNA MIR159 |
| mir-515 | RF00639 | 41 | 87 | 79 | 697 | 86 | 80 | Gene; miRNA; | microRNA mir-515 |
| MIR167_1 | RF00640 | 19 | 158 | 53 | 297 | 160 | 54 | Gene; miRNA; | microRNA MIR167_1 |
| mir-154 | RF00641 | 107 | 79 | 57 | 1459 | 79 | 58 | Gene; miRNA; | microRNA mir-154 |
| mir-23 | RF00642 | 24 | 75 | 70 | 135 | 74 | 76 | Gene; miRNA; | microRNA mir-23 |
| MIR171_1 | RF00643 | 45 | 106 | 56 | 274 | 105 | 60 | Gene; miRNA; | microRNA MIR171_1 |
| mir-27 | RF00644 | 32 | 82 | 68 | 132 | 82 | 74 | Gene; miRNA; | microRNA mir-27 |
| MIR169_2 | RF00645 | 87 | 128 | 52 | 317 | 127 | 48 | Gene; miRNA; | microRNA MIR169_2 |
| mir-204 | RF00646 | 31 | 101 | 71 | 129 | 102 | 76 | Gene; miRNA; | microRNA mir-204 |
| MIR164 | RF00647 | 31 | 115 | 62 | 206 | 132 | 63 | Gene; miRNA; | microRNA MIR164 |
| MIR396 | RF00648 | 26 | 136 | 53 | 158 | 137 | 57 | Gene; miRNA; | microRNA MIR396 |
| mir-128 | RF00649 | 15 | 83 | 76 | 115 | 83 | 86 | Gene; miRNA; | microRNA mir-128 |
| mir-153 | RF00650 | 18 | 86 | 77 | 105 | 86 | 85 | Gene; miRNA; | microRNA mir-153 |
| mir-221 | RF00651 | 44 | 69 | 73 | 135 | 69 | 76 | Gene; miRNA; | microRNA mir-221 |
| MIR478 | RF00652 | 17 | 76 | 88 | 394 | 86 | 83 | Gene; miRNA; | microRNA MIR478 |
| mir-22 | RF00653 | 13 | 87 | 75 | 80 | 85 | 86 | Gene; miRNA; | microRNA mir-22 |
| mir-216 | RF00654 | 36 | 88 | 61 | 118 | 88 | 66 | Gene; miRNA; | microRNA mir-216 |
| mir-28 | RF00655 | 25 | 85 | 79 | 605 | 89 | 63 | Gene; miRNA; | microRNA mir-28 |
| mir-205 | RF00656 | 26 | 101 | 72 | 72 | 101 | 77 | Gene; miRNA; | microRNA mir-205 |
| mir-184 | RF00657 | 33 | 83 | 70 | 106 | 83 | 71 | Gene; miRNA; | microRNA mir-184 |
| mir-21 | RF00658 | 10 | 72 | 77 | 68 | 72 | 91 | Gene; miRNA; | microRNA mir-21 |
| mir-365 | RF00659 | 9 | 89 | 80 | 106 | 92 | 87 | Gene; miRNA; | microRNA mir-365 |
| mir-214 | RF00660 | 8 | 107 | 77 | 65 | 108 | 89 | Gene; miRNA; | microRNA mir-214 |
| mir-31 | RF00661 | 38 | 85 | 59 | 176 | 86 | 59 | Gene; miRNA; | microRNA mir-31 |
| mir-132 | RF00662 | 20 | 89 | 65 | 91 | 87 | 69 | Gene; miRNA; | microRNA mir-132 |
| mir-183 | RF00663 | 13 | 98 | 76 | 74 | 100 | 85 | Gene; miRNA; | microRNA mir-183 |
| mir-223 | RF00664 | 15 | 109 | 74 | 59 | 110 | 85 | Gene; miRNA; | microRNA mir-223 |
| mir-290 | RF00665 | 27 | 81 | 67 | 205 | 81 | 65 | Gene; miRNA; | microRNA mir-290 |
| mir-32 | RF00666 | 7 | 70 | 89 | 53 | 69 | 96 | Gene; miRNA; | microRNA mir-32 |
| mir-33 | RF00667 | 45 | 68 | 69 | 130 | 68 | 71 | Gene; miRNA; | microRNA mir-33 |
| mir-302 | RF00668 | 47 | 68 | 72 | 192 | 67 | 75 | Gene; miRNA; | microRNA mir-302 |
| mir-96 | RF00669 | 27 | 78 | 90 | 68 | 78 | 91 | Gene; miRNA; | microRNA mir-96 |
| mir-105 | RF00670 | 20 | 80 | 67 | 206 | 80 | 66 | Gene; miRNA; | microRNA mir-105 |
| mir-138 | RF00671 | 25 | 78 | 78 | 106 | 79 | 75 | Gene; miRNA; | microRNA mir-138 |
| mir-190 | RF00672 | 28 | 87 | 65 | 149 | 86 | 75 | Gene; miRNA; | microRNA mir-190 |
| mir-217 | RF00673 | 25 | 105 | 78 | 61 | 105 | 81 | Gene; miRNA; | microRNA mir-217 |
| mir-187 | RF00674 | 19 | 102 | 78 | 49 | 103 | 84 | Gene; miRNA; | microRNA mir-187 |
| mir-145 | RF00675 | 10 | 88 | 78 | 60 | 87 | 85 | Gene; miRNA; | microRNA mir-145 |
| mir-127 | RF00676 | 2 | 98 | 97 | 52 | 97 | 99 | Gene; miRNA; | microRNA mir-127 |
| MIR168 | RF00677 | 10 | 129 | 62 | 113 | 130 | 74 | Gene; miRNA; | microRNA MIR168 |
| mir-140 | RF00678 | 10 | 98 | 86 | 54 | 98 | 94 | Gene; miRNA; | microRNA mir-140 |
| mir-210 | RF00679 | 26 | 95 | 64 | 77 | 95 | 67 | Gene; miRNA; | microRNA mir-210 |
| mir-224 | RF00680 | 5 | 80 | 87 | 53 | 81 | 96 | Gene; miRNA; | microRNA mir-224 |
| mir-198 | RF00681 | 3 | 62 | 88 | 28 | 61 | 94 | Gene; miRNA; | microRNA mir-198 |
| mir-144 | RF00682 | 15 | 85 | 84 | 59 | 85 | 90 | Gene; miRNA; | microRNA mir-144 |
| mir-143 | RF00683 | 17 | 105 | 78 | 56 | 105 | 85 | Gene; miRNA; | microRNA mir-143 |
| mir-122 | RF00684 | 29 | 74 | 94 | 58 | 74 | 95 | Gene; miRNA; | mir-122 microRNA precursor |
| mir-36 | RF00685 | 38 | 99 | 55 | 131 | 100 | 54 | Gene; miRNA; | microRNA mir-36 |
| mir-338 | RF00686 | 21 | 81 | 73 | 60 | 80 | 73 | Gene; miRNA; | microRNA mir-338 |
| mir-136 | RF00687 | 2 | 82 | 95 | 44 | 82 | 99 | Gene; miRNA; | microRNA mir-136 |
| MIR394 | RF00688 | 13 | 111 | 66 | 75 | 115 | 73 | Gene; miRNA; | microRNA MIR394 |
| MIR390 | RF00689 | 12 | 120 | 71 | 70 | 104 | 86 | Gene; miRNA; | microRNA MIR390 |
| MIR408 | RF00690 | 6 | 131 | 71 | 24 | 154 | 68 | Gene; miRNA; | microRNA MIR408 |
| mir-146 | RF00691 | 33 | 90 | 64 | 98 | 89 | 69 | Gene; miRNA; | microRNA mir-146 |
| MIR171_2 | RF00692 | 7 | 109 | 71 | 25 | 106 | 69 | Gene; miRNA; | microRNA MIR171_2 |
| mir-147 | RF00693 | 70 | 69 | 67 | 230 | 69 | 72 | Gene; miRNA; | microRNA mir-147 |
| mir-137 | RF00694 | 28 | 100 | 62 | 106 | 100 | 68 | Gene; miRNA; | microRNA mir-137 |
| MIR398 | RF00695 | 14 | 106 | 58 | 124 | 109 | 61 | Gene; miRNA; | microRNA MIR398 |
| mir-203 | RF00696 | 10 | 79 | 80 | 50 | 79 | 73 | Gene; miRNA; | microRNA mir-203 |
| mir-186 | RF00697 | 19 | 90 | 72 | 208 | 90 | 66 | Gene; miRNA; | microRNA mir-186 |
| mir-489 | RF00698 | 19 | 92 | 79 | 54 | 91 | 83 | Gene; miRNA; | microRNA mir-489 |
| mir-134 | RF00699 | 5 | 72 | 89 | 41 | 72 | 95 | Gene; miRNA; | microRNA mir-134 |
| mir-375 | RF00700 | 9 | 68 | 83 | 52 | 68 | 92 | Gene; miRNA; | microRNA mir-375 |
| mir-126 | RF00701 | 10 | 73 | 85 | 53 | 73 | 89 | Gene; miRNA; | microRNA mir-126 |
| mir-182 | RF00702 | 15 | 85 | 85 | 54 | 84 | 89 | Gene; miRNA; | microRNA mir-182 |
| mir-139 | RF00703 | 5 | 68 | 81 | 46 | 68 | 91 | Gene; miRNA; | microRNA mir-139 |
| MIR397 | RF00704 | 7 | 113 | 62 | 31 | 111 | 59 | Gene; miRNA; | microRNA MIR397 |
| mir-202 | RF00705 | 13 | 87 | 81 | 41 | 87 | 84 | Gene; miRNA; | microRNA mir-202 |
| mir-263 | RF00706 | 23 | 91 | 59 | 69 | 90 | 62 | Gene; miRNA; | microRNA mir-263 |
| mir-197 | RF00707 | 2 | 72 | 89 | 39 | 74 | 94 | Gene; miRNA; | microRNA mir-197 |
| mir-450 | RF00708 | 21 | 91 | 74 | 120 | 91 | 79 | Gene; miRNA; | microRNA mir-450 |
| mir-455 | RF00709 | 4 | 85 | 93 | 53 | 85 | 97 | Gene; miRNA; | microRNA mir-455 |
| mir-44 | RF00710 | 6 | 93 | 75 | 14 | 93 | 72 | Gene; miRNA; | microRNA mir-44 |
| mir-449 | RF00711 | 57 | 91 | 58 | 177 | 91 | 58 | Gene; miRNA; | microRNA mir-449 |
| mir-460 | RF00712 | 8 | 76 | 78 | 19 | 75 | 74 | Gene; miRNA; | microRNA mir-460 |
| mir-239 | RF00713 | 9 | 101 | 58 | 14 | 102 | 55 | Gene; miRNA; | microRNA mir-239 |
| MIR535 | RF00714 | 5 | 98 | 71 | 38 | 101 | 79 | Gene; miRNA; | microRNA MIR535 |
| mir-383 | RF00715 | 5 | 73 | 92 | 45 | 73 | 96 | Gene; miRNA; | microRNA mir-383 |
| mir-3 | RF00716 | 11 | 72 | 69 | 48 | 70 | 70 | Gene; miRNA; | microRNA mir-3 |
| mir-315 | RF00717 | 16 | 82 | 75 | 31 | 82 | 71 | Gene; miRNA; | microRNA mir-315 |
| mir-431 | RF00718 | 6 | 113 | 89 | 42 | 113 | 95 | Gene; miRNA; | microRNA mir-431 |
| mir-326 | RF00719 | 6 | 94 | 92 | 36 | 94 | 93 | Gene; miRNA; | microRNA mir-326 |
| mir-317 | RF00720 | 13 | 90 | 72 | 37 | 91 | 74 | Gene; miRNA; | microRNA mir-317 |
| MIR475 | RF00721 | 4 | 115 | 88 | 36 | 118 | 72 | Gene; miRNA; | microRNA MIR475 |
| mir-451 | RF00722 | 17 | 72 | 77 | 55 | 72 | 84 | Gene; miRNA; | microRNA mir-451 |
| mir-448 | RF00723 | 17 | 111 | 75 | 88 | 110 | 70 | Gene; miRNA; | microRNA mir-448 |
| mir-282 | RF00724 | 14 | 94 | 65 | 34 | 94 | 73 | Gene; miRNA; | microRNA mir-282 |
| mir-iab-4 | RF00725 | 7 | 84 | 85 | 35 | 84 | 87 | Gene; miRNA; | microRNA mir-iab-4 |
| mir-87 | RF00726 | 11 | 98 | 67 | 42 | 96 | 59 | Gene; miRNA; | microRNA mir-87 |
| bantam | RF00727 | 10 | 91 | 68 | 43 | 91 | 74 | Gene; miRNA; | microRNA bantam |
| mir-81 | RF00728 | 9 | 100 | 65 | 23 | 97 | 61 | Gene; miRNA; | microRNA mir-81 |
| mir-278 | RF00729 | 11 | 99 | 74 | 32 | 98 | 78 | Gene; miRNA; | microRNA mir-278 |
| mir-277 | RF00730 | 11 | 104 | 68 | 34 | 101 | 74 | Gene; miRNA; | microRNA mir-277 |
| mir-155 | RF00731 | 17 | 64 | 76 | 66 | 65 | 85 | Gene; miRNA; | microRNA mir-155 |
| mir-305 | RF00732 | 13 | 87 | 74 | 30 | 88 | 78 | Gene; miRNA; | microRNA mir-305 |
| mir-296 | RF00733 | 12 | 78 | 84 | 36 | 79 | 89 | Gene; miRNA; | microRNA mir-296 |
| mir-52 | RF00734 | 5 | 98 | 84 | 7 | 98 | 85 | Gene; miRNA; | microRNA mir-52 |
| mir-367 | RF00735 | 13 | 67 | 88 | 49 | 67 | 92 | Gene; miRNA; | microRNA mir-367 |
| mir-320 | RF00736 | 57 | 81 | 69 | 307 | 81 | 68 | Gene; miRNA; | microRNA mir-320 |
| mir-322 | RF00737 | 10 | 83 | 89 | 34 | 83 | 90 | Gene; miRNA; | microRNA mir-322 |
| MIR476 | RF00739 | 2 | 93 | 89 | 8 | 92 | 78 | Gene; miRNA; | microRNA MIR476 |
| mir-370 | RF00740 | 6 | 77 | 90 | 36 | 78 | 91 | Gene; miRNA; | microRNA mir-370 |
| mir-378 | RF00741 | 8 | 65 | 99 | 35 | 66 | 97 | Gene; miRNA; | microRNA mir-378 |
| MIR162_2 | RF00742 | 10 | 93 | 78 | 71 | 98 | 78 | Gene; miRNA; | microRNA MIR162_2 |
| mir-308 | RF00743 | 11 | 63 | 87 | 25 | 63 | 88 | Gene; miRNA; | microRNA mir-308 |
| mir-361 | RF00744 | 4 | 70 | 93 | 40 | 71 | 96 | Gene; miRNA; | microRNA mir-361 |
| mir-499 | RF00745 | 18 | 89 | 79 | 54 | 89 | 86 | Gene; miRNA; | microRNA mir-499 |
| mir-454 | RF00746 | 16 | 115 | 62 | 46 | 113 | 74 | Gene; miRNA; | microRNA mir-454 |
| mir-283 | RF00747 | 13 | 93 | 59 | 29 | 95 | 70 | Gene; miRNA; | microRNA mir-283 |
| mir-433 | RF00748 | 4 | 93 | 94 | 43 | 93 | 97 | Gene; miRNA; | microRNA mir-433 |
| mir-208 | RF00749 | 16 | 78 | 71 | 99 | 79 | 75 | Gene; miRNA; | microRNA mir-208 |
| mir-458 | RF00750 | 7 | 77 | 80 | 11 | 77 | 81 | Gene; miRNA; | microRNA mir-458 |
| mir-12 | RF00751 | 8 | 71 | 74 | 23 | 73 | 85 | Gene; miRNA; | microRNA mir-12 |
| mir-14 | RF00752 | 6 | 65 | 79 | 30 | 63 | 90 | Gene; miRNA; | microRNA mir-14 |
| mir-503 | RF00753 | 13 | 70 | 89 | 33 | 70 | 90 | Gene; miRNA; | microRNA mir-503 |
| mir-279 | RF00754 | 11 | 91 | 64 | 37 | 90 | 71 | Gene; miRNA; | microRNA mir-279 |
| mir-542 | RF00755 | 3 | 84 | 88 | 34 | 85 | 96 | Gene; miRNA; | microRNA mir-542 |
| mir-299 | RF00756 | 6 | 63 | 88 | 43 | 62 | 90 | Gene; miRNA; | microRNA mir-299 |
| mir-275 | RF00757 | 14 | 92 | 69 | 32 | 91 | 72 | Gene; miRNA; | microRNA mir-275 |
| mir-346 | RF00758 | 3 | 94 | 73 | 42 | 96 | 91 | Gene; miRNA; | microRNA mir-346 |
| mir-342 | RF00760 | 10 | 98 | 88 | 37 | 98 | 89 | Gene; miRNA; | microRNA mir-342 |
| mir-340 | RF00761 | 44 | 94 | 58 | 665 | 95 | 53 | Gene; miRNA; | microRNA mir-340 |
| mir-412 | RF00762 | 11 | 90 | 88 | 36 | 90 | 92 | Gene; miRNA; | microRNA mir-412 |
| mir-339 | RF00763 | 16 | 95 | 78 | 39 | 94 | 81 | Gene; miRNA; | microRNA mir-339 |
| mir-191 | RF00764 | 4 | 91 | 89 | 39 | 90 | 96 | Gene; miRNA; | microRNA mir-191 |
| mir-337 | RF00765 | 6 | 96 | 85 | 29 | 95 | 91 | Gene; miRNA; | microRNA mir-337 |
| mir-335 | RF00766 | 8 | 94 | 93 | 39 | 94 | 95 | Gene; miRNA; | microRNA mir-335 |
| mir-150 | RF00767 | 15 | 84 | 83 | 46 | 85 | 80 | Gene; miRNA; | microRNA mir-150 |
| MIR405 | RF00768 | 13 | 122 | 77 | 70 | 120 | 91 | Gene; miRNA; | microRNA MIR405 |
| mir-331 | RF00769 | 3 | 94 | 94 | 39 | 94 | 97 | Gene; miRNA; | microRNA mir-331 |
| mir-330 | RF00770 | 6 | 97 | 91 | 34 | 97 | 96 | Gene; miRNA; | microRNA mir-330 |
| mir-185 | RF00771 | 4 | 80 | 93 | 44 | 80 | 97 | Gene; miRNA; | microRNA mir-185 |
| mir-328 | RF00772 | 13 | 83 | 82 | 40 | 83 | 87 | Gene; miRNA; | microRNA mir-328 |
| mir-298 | RF00773 | 4 | 86 | 72 | 21 | 86 | 83 | Gene; miRNA; | microRNA mir-298 |
| mir-360 | RF00774 | 4 | 112 | 69 | 5 | 110 | 67 | Gene; miRNA; | microRNA mir-360 |
| mir-432 | RF00775 | 6 | 92 | 75 | 81 | 85 | 79 | Gene; miRNA; | microRNA mir-432 |
| mir-540 | RF00776 | 3 | 82 | 78 | 13 | 77 | 73 | Gene; miRNA; | microRNA mir-540 |
| mir-541 | RF00777 | 9 | 90 | 82 | 35 | 89 | 87 | Gene; miRNA; | microRNA mir-541 |
| MIR473 | RF00778 | 6 | 91 | 59 | 20 | 96 | 54 | Gene; miRNA; | microRNA MIR473 |
| MIR474 | RF00779 | 11 | 101 | 56 | 608 | 88 | 48 | Gene; miRNA; | microRNA MIR474 |
| MIR477 | RF00780 | 3 | 90 | 68 | 30 | 96 | 71 | Gene; miRNA; | microRNA MIR477 |
| mir-505 | RF00781 | 3 | 84 | 93 | 37 | 83 | 97 | Gene; miRNA; | microRNA mir-505 |
| MIR480 | RF00782 | 69 | 138 | 68 | 732 | 125 | 52 | Gene; miRNA; | microRNA MIR480 |
| mir-484 | RF00783 | 14 | 66 | 85 | 40 | 66 | 89 | Gene; miRNA; | microRNA mir-484 |
| mir-486 | RF00784 | 11 | 67 | 88 | 30 | 68 | 92 | Gene; miRNA; | microRNA mir-486 |
| mir-90 | RF00785 | 5 | 96 | 76 | 6 | 96 | 74 | Gene; miRNA; | microRNA mir-90 |
| mir-289 | RF00786 | 3 | 90 | 84 | 17 | 93 | 89 | Gene; miRNA; | microRNA mir-289 |
| mir-288 | RF00787 | 7 | 97 | 91 | 20 | 97 | 94 | Gene; miRNA; | microRNA mir-288 |
| mir-287 | RF00788 | 9 | 90 | 81 | 24 | 84 | 78 | Gene; miRNA; | microRNA mir-287 |
| mir-286 | RF00789 | 14 | 96 | 68 | 33 | 96 | 74 | Gene; miRNA; | microRNA mir-286 |
| mir-358 | RF00790 | 3 | 112 | 70 | 4 | 112 | 76 | Gene; miRNA; | microRNA mir-358 |
| mir-357 | RF00791 | 5 | 106 | 69 | 7 | 107 | 70 | Gene; miRNA; | microRNA mir-357 |
| mir-490 | RF00792 | 16 | 128 | 83 | 49 | 126 | 89 | Gene; miRNA; | microRNA mir-490 |
| mir-497 | RF00793 | 6 | 112 | 88 | 42 | 112 | 95 | Gene; miRNA; | microRNA mir-497 |
| mir-42 | RF00794 | 4 | 99 | 81 | 6 | 98 | 78 | Gene; miRNA; | microRNA mir-42 |
| mir-43 | RF00795 | 4 | 102 | 75 | 6 | 102 | 72 | Gene; miRNA; | microRNA mir-43 |
| mir-48 | RF00796 | 4 | 107 | 70 | 6 | 104 | 74 | Gene; miRNA; | microRNA mir-48 |
| mir-355 | RF00797 | 4 | 116 | 71 | 5 | 116 | 68 | Gene; miRNA; | microRNA mir-355 |
| mir-49 | RF00798 | 4 | 97 | 76 | 5 | 97 | 73 | Gene; miRNA; | microRNA mir-49 |
| mir-354 | RF00799 | 4 | 112 | 92 | 5 | 110 | 88 | Gene; miRNA; | microRNA mir-354 |
| mir-353 | RF00800 | 4 | 114 | 77 | 9 | 114 | 78 | Gene; miRNA; | microRNA mir-353 |
| mir-280 | RF00801 | 8 | 94 | 84 | 19 | 94 | 89 | Gene; miRNA; | microRNA mir-280 |
| mir-207 | RF00802 | 7 | 78 | 85 | 30 | 78 | 82 | Gene; miRNA; | microRNA mir-207 |
| mir-425 | RF00803 | 5 | 84 | 72 | 43 | 85 | 92 | Gene; miRNA; | microRNA mir-425 |
| mir-240 | RF00804 | 3 | 113 | 68 | 4 | 112 | 64 | Gene; miRNA; | microRNA mir-240 |
| mir-351 | RF00805 | 2 | 98 | 92 | 5 | 98 | 95 | Gene; miRNA; | microRNA mir-351 |
| mir-350 | RF00806 | 10 | 96 | 88 | 43 | 95 | 90 | Gene; miRNA; | microRNA mir-350 |
| mir-314 | RF00807 | 6 | 88 | 83 | 20 | 89 | 91 | Gene; miRNA; | microRNA mir-314 |
| mir-86 | RF00808 | 5 | 96 | 79 | 11 | 94 | 64 | Gene; miRNA; | microRNA mir-86 |
| mir-241 | RF00809 | 4 | 96 | 75 | 6 | 96 | 75 | Gene; miRNA; | microRNA mir-241 |
| mir-85 | RF00810 | 4 | 105 | 69 | 5 | 106 | 68 | Gene; miRNA; | microRNA mir-85 |
| mir-84 | RF00811 | 4 | 110 | 72 | 5 | 114 | 64 | Gene; miRNA; | microRNA mir-84 |
| mir-83 | RF00812 | 4 | 110 | 86 | 6 | 110 | 86 | Gene; miRNA; | microRNA mir-83 |
| mir-11 | RF00813 | 14 | 78 | 70 | 33 | 76 | 75 | Gene; miRNA; | microRNA mir-11 |
| mir-316 | RF00814 | 4 | 88 | 91 | 24 | 88 | 90 | Gene; miRNA; | microRNA mir-316 |
| mir-244 | RF00815 | 4 | 102 | 76 | 5 | 102 | 72 | Gene; miRNA; | microRNA mir-244 |
| mir-245 | RF00816 | 5 | 93 | 61 | 54 | 90 | 81 | Gene; miRNA; | microRNA mir-245 |
| mir-80 | RF00817 | 4 | 101 | 91 | 5 | 101 | 87 | Gene; miRNA; | microRNA mir-80 |
| mir-318 | RF00818 | 5 | 68 | 85 | 20 | 68 | 91 | Gene; miRNA; | microRNA mir-318 |
| mir-246 | RF00819 | 4 | 108 | 65 | 5 | 108 | 69 | Gene; miRNA; | microRNA mir-246 |
| mir-248 | RF00820 | 4 | 104 | 72 | 6 | 104 | 72 | Gene; miRNA; | microRNA mir-248 |
| mir-249 | RF00821 | 4 | 110 | 73 | 5 | 110 | 68 | Gene; miRNA; | microRNA mir-249 |
| mir-274 | RF00822 | 7 | 105 | 78 | 21 | 100 | 84 | Gene; miRNA; | microRNA mir-274 |
| lsy-6 | RF00823 | 4 | 73 | 78 | 6 | 74 | 75 | Gene; miRNA; | microRNA lsy-6 |
| mir-50 | RF00824 | 5 | 97 | 71 | 6 | 98 | 69 | Gene; miRNA; | microRNA mir-50 |
| mir-344 | RF00825 | 32 | 93 | 66 | 315 | 94 | 65 | Gene; miRNA; | microRNA mir-344 |
| mir-55 | RF00826 | 3 | 97 | 76 | 5 | 98 | 69 | Gene; miRNA; | microRNA mir-55 |
| mir-77 | RF00827 | 5 | 98 | 76 | 7 | 99 | 72 | Gene; miRNA; | microRNA mir-77 |
| mir-75 | RF00828 | 4 | 98 | 70 | 5 | 97 | 66 | Gene; miRNA; | microRNA mir-75 |
| mir-149 | RF00829 | 3 | 89 | 92 | 25 | 88 | 95 | Gene; miRNA; | microRNA mir-149 |
| mir-74 | RF00830 | 6 | 95 | 67 | 10 | 96 | 64 | Gene; miRNA; | microRNA mir-74 |
| mir-73 | RF00831 | 7 | 100 | 70 | 9 | 101 | 66 | Gene; miRNA; | microRNA mir-73 |
| mir-71 | RF00832 | 15 | 58 | 70 | 30 | 63 | 70 | Gene; miRNA; | microRNA mir-71 |
| mir-70 | RF00833 | 4 | 118 | 56 | 5 | 119 | 60 | Gene; miRNA; | microRNA mir-70 |
| mir-268 | RF00834 | 4 | 89 | 78 | 8 | 85 | 73 | Gene; miRNA; | microRNA mir-268 |
| mir-58 | RF00835 | 4 | 98 | 88 | 7 | 98 | 84 | Gene; miRNA; | microRNA mir-58 |
| mir-250 | RF00836 | 4 | 80 | 84 | 6 | 79 | 84 | Gene; miRNA; | microRNA mir-250 |
| mir-251 | RF00837 | 4 | 96 | 78 | 5 | 98 | 77 | Gene; miRNA; | microRNA mir-251 |
| mir-252 | RF00838 | 6 | 79 | 71 | 11 | 79 | 66 | Gene; miRNA; | microRNA mir-252 |
| mir-452 | RF00839 | 4 | 85 | 88 | 45 | 84 | 95 | Gene; miRNA; | microRNA mir-452 |
| mir-374 | RF00840 | 14 | 70 | 79 | 64 | 71 | 83 | Gene; miRNA; | microRNA mir-374 |
| mir-384 | RF00841 | 17 | 92 | 70 | 257 | 92 | 61 | Gene; miRNA; | microRNA mir-384 |
| MIR403 | RF00842 | 11 | 106 | 68 | 46 | 113 | 73 | Gene; miRNA; | microRNA MIR403 |
| mir-228 | RF00843 | 4 | 97 | 88 | 7 | 98 | 80 | Gene; miRNA; | microRNA mir-228 |
| mir-67 | RF00844 | 16 | 65 | 79 | 45 | 66 | 84 | Gene; miRNA; | microRNA mir-67 |
| MIR158 | RF00845 | 2 | 100 | 91 | 4 | 104 | 76 | Gene; miRNA; | microRNA MIR158 |
| mir-64 | RF00846 | 4 | 106 | 61 | 24 | 110 | 69 | Gene; miRNA; | microRNA mir-64 |
| mir-62 | RF00847 | 4 | 60 | 93 | 5 | 60 | 93 | Gene; miRNA; | microRNA mir-62 |
| mir-61 | RF00848 | 4 | 86 | 75 | 6 | 88 | 75 | Gene; miRNA; | microRNA mir-61 |
| mir-60 | RF00849 | 4 | 72 | 89 | 7 | 71 | 88 | Gene; miRNA; | microRNA mir-60 |
| mir-259 | RF00850 | 4 | 102 | 79 | 7 | 93 | 79 | Gene; miRNA; | microRNA mir-259 |
| mir-230 | RF00851 | 2 | 97 | 72 | 5 | 96 | 72 | Gene; miRNA; | microRNA mir-230 |
| mir-231 | RF00852 | 4 | 80 | 85 | 7 | 81 | 77 | Gene; miRNA; | microRNA mir-231 |
| mir-304 | RF00853 | 5 | 88 | 92 | 18 | 88 | 95 | Gene; miRNA; | microRNA mir-304 |
| mir-5 | RF00854 | 6 | 71 | 90 | 22 | 70 | 92 | Gene; miRNA; | microRNA mir-5 |
| mir-254 | RF00855 | 4 | 109 | 75 | 5 | 110 | 73 | Gene; miRNA; | microRNA mir-254 |
| mir-232 | RF00856 | 3 | 97 | 79 | 6 | 98 | 80 | Gene; miRNA; | microRNA mir-232 |
| mir-233 | RF00857 | 4 | 98 | 82 | 5 | 97 | 76 | Gene; miRNA; | microRNA mir-233 |
| mir-306 | RF00858 | 7 | 86 | 69 | 19 | 84 | 78 | Gene; miRNA; | microRNA mir-306 |
| mir-234 | RF00859 | 4 | 100 | 69 | 6 | 98 | 60 | Gene; miRNA; | microRNA mir-234 |
| mir-488 | RF00861 | 5 | 82 | 93 | 37 | 82 | 92 | Gene; miRNA; | microRNA mir-488 |
| mir-491 | RF00862 | 5 | 83 | 88 | 41 | 82 | 95 | Gene; miRNA; | microRNA mir-491 |
| mir-BART17 | RF00863 | 2 | 103 | 72 | 17 | 102 | 97 | Gene; miRNA; | microRNA mir-BART17 |
| mir-BART20 | RF00864 | 2 | 80 | 81 | 9 | 80 | 96 | Gene; miRNA; | microRNA mir-BART20 |
| MIR169_5 | RF00865 | 6 | 133 | 66 | 146 | 147 | 52 | Gene; miRNA; | microRNA MIR169_5 |
| mir-BART3 | RF00866 | 2 | 75 | 81 | 35 | 75 | 90 | Gene; miRNA; | microRNA mir-BART3 |
| mir-BART5 | RF00867 | 2 | 89 | 84 | 18 | 89 | 95 | Gene; miRNA; | microRNA mir-BART5 |
| mir-BART15 | RF00868 | 2 | 78 | 80 | 18 | 78 | 97 | Gene; miRNA; | microRNA mir-BART15 |
| mir-BART7 | RF00869 | 2 | 85 | 83 | 15 | 85 | 98 | Gene; miRNA; | microRNA mir-BART7 |
| mir-423 | RF00870 | 5 | 80 | 86 | 39 | 80 | 98 | Gene; miRNA; | microRNA mir-423 |
| mir-689 | RF00871 | 20 | 109 | 85 | 491 | 104 | 80 | Gene; miRNA; | microRNA mir-689 |
| mir-652 | RF00872 | 17 | 96 | 75 | 448 | 96 | 64 | Gene; miRNA; | microRNA mir-652 |
| mir-550 | RF00873 | 3 | 97 | 96 | 35 | 96 | 94 | Gene; miRNA; | microRNA mir-550 |
| mir-BART12 | RF00874 | 2 | 95 | 72 | 15 | 95 | 96 | Gene; miRNA; | microRNA mir-BART12 |
| mir-692 | RF00875 | 13 | 81 | 76 | 1914 | 80 | 65 | Gene; miRNA; | microRNA mir-692 |
| mir-684 | RF00876 | 30 | 88 | 86 | 1607 | 86 | 70 | Gene; miRNA; | microRNA mir-684 |
| mir-592 | RF00877 | 5 | 87 | 90 | 52 | 87 | 98 | Gene; miRNA; | microRNA mir-592 |
| mir-456 | RF00878 | 7 | 106 | 71 | 10 | 105 | 73 | Gene; miRNA; | microRNA mir-456 |
| mir-615 | RF00879 | 6 | 96 | 96 | 40 | 94 | 96 | Gene; miRNA; | microRNA mir-615 |
| MIR811 | RF00882 | 5 | 189 | 82 | 519 | 186 | 68 | Gene; miRNA; | microRNA MIR811 |
| MIR820 | RF00883 | 2 | 181 | 94 | 33 | 179 | 60 | Gene; miRNA; | microRNA MIR820 |
| MIR815 | RF00884 | 3 | 80 | 80 | 72 | 81 | 66 | Gene; miRNA; | microRNA MIR815 |
| MIR821 | RF00885 | 5 | 274 | 88 | 2316 | 270 | 71 | Gene; miRNA; | microRNA MIR821 |
| MIR807 | RF00886 | 34 | 175 | 85 | 422 | 172 | 83 | Gene; miRNA; | microRNA MIR807 |
| mir-802 | RF00887 | 15 | 94 | 87 | 53 | 93 | 87 | Gene; miRNA; | microRNA mir-802 |
| mir-770 | RF00888 | 4 | 97 | 77 | 24 | 95 | 86 | Gene; miRNA; | microRNA mir-770 |
| mir-668 | RF00890 | 8 | 63 | 87 | 33 | 64 | 92 | Gene; miRNA; | microRNA mir-668 |
| mir-671 | RF00891 | 3 | 75 | 99 | 55 | 75 | 98 | Gene; miRNA; | microRNA mir-671 |
| mir-551 | RF00892 | 25 | 85 | 74 | 79 | 85 | 75 | Gene; miRNA; | microRNA mir-551 |
| MIR854 | RF00893 | 3 | 221 | 98 | 141 | 217 | 82 | Gene; miRNA; | microRNA MIR854 |
| mir-790 | RF00894 | 4 | 70 | 84 | 8 | 71 | 79 | Gene; miRNA; | microRNA mir-790 |
| mir-786 | RF00895 | 2 | 90 | 62 | 2 | 90 | 62 | Gene; miRNA; | microRNA mir-786 |
| mir-787 | RF00896 | 3 | 90 | 59 | 3 | 90 | 59 | Gene; miRNA; | microRNA mir-787 |
| mir-675 | RF00897 | 11 | 72 | 87 | 54 | 72 | 93 | Gene; miRNA; | microRNA mir-675 |
| mir-242 | RF00898 | 4 | 70 | 79 | 5 | 70 | 79 | Gene; miRNA; | microRNA mir-242 |
| mir-235 | RF00899 | 4 | 72 | 81 | 8 | 71 | 80 | Gene; miRNA; | microRNA mir-235 |
| mir-255 | RF00900 | 4 | 107 | 66 | 6 | 111 | 72 | Gene; miRNA; | microRNA mir-255 |
| MIR845_1 | RF00901 | 2 | 88 | 80 | 4 | 88 | 87 | Gene; miRNA; | microRNA MIR845_1 |
| mir-791 | RF00902 | 3 | 86 | 74 | 5 | 85 | 70 | Gene; miRNA; | microRNA mir-791 |
| mir-359 | RF00903 | 4 | 90 | 72 | 5 | 90 | 65 | Gene; miRNA; | microRNA mir-359 |
| mir-392 | RF00904 | 3 | 71 | 72 | 3 | 71 | 72 | Gene; miRNA; | microRNA mir-392 |
| mir-789 | RF00905 | 3 | 96 | 68 | 7 | 92 | 55 | Gene; miRNA; | microRNA mir-789 |
| MIR1122 | RF00906 | 34 | 108 | 60 | 5191 | 125 | 48 | Gene; miRNA; | microRNA MIR1122 |
| mir-941 | RF00907 | 2 | 89 | 94 | 120 | 81 | 72 | Gene; miRNA; | microRNA mir-941 |
| MIR529 | RF00908 | 3 | 131 | 77 | 14 | 130 | 83 | Gene; miRNA; | microRNA MIR529 |
| mir-883 | RF00909 | 3 | 77 | 85 | 14 | 76 | 77 | Gene; miRNA; | microRNA mir-883 |
| mir-873 | RF00910 | 3 | 77 | 97 | 39 | 77 | 98 | Gene; miRNA; | microRNA mir-873 |
| mir-672 | RF00911 | 9 | 100 | 81 | 26 | 99 | 89 | Gene; miRNA; | microRNA mir-672 |
| mir-877 | RF00912 | 14 | 86 | 82 | 60 | 85 | 89 | Gene; miRNA; | microRNA mir-877 |
| mir-674 | RF00914 | 2 | 100 | 99 | 5 | 100 | 99 | Gene; miRNA; | microRNA mir-674 |
| mir-760 | RF00915 | 8 | 79 | 90 | 29 | 79 | 97 | Gene; miRNA; | microRNA mir-760 |
| mir-708 | RF00917 | 24 | 83 | 78 | 422 | 83 | 65 | Gene; miRNA; | microRNA mir-708 |
| mir-872 | RF00918 | 7 | 80 | 85 | 23 | 80 | 84 | Gene; miRNA; | microRNA mir-872 |
| mir-874 | RF00919 | 4 | 77 | 99 | 42 | 77 | 98 | Gene; miRNA; | microRNA mir-874 |
| MIR444 | RF00920 | 4 | 148 | 75 | 24 | 142 | 53 | Gene; miRNA; | microRNA MIR444 |
| mir-665 | RF00921 | 8 | 91 | 89 | 30 | 89 | 89 | Gene; miRNA; | microRNA mir-665 |
| mir-673 | RF00922 | 2 | 76 | 98 | 6 | 76 | 99 | Gene; miRNA; | microRNA mir-673 |
| MIR1027 | RF00925 | 2 | 142 | 100 | 3 | 142 | 98 | Gene; miRNA; | microRNA MIR1027 |
| MIR1151 | RF00926 | 2 | 144 | 90 | 2 | 144 | 90 | Gene; miRNA; | microRNA MIR1151 |
| mir-582 | RF00927 | 9 | 98 | 91 | 38 | 98 | 93 | Gene; miRNA; | microRNA mir-582 |
| mir-590 | RF00928 | 12 | 96 | 75 | 88 | 98 | 69 | Gene; miRNA; | microRNA mir-590 |
| mir-574 | RF00929 | 3 | 77 | 94 | 16 | 76 | 90 | Gene; miRNA; | microRNA mir-574 |
| mir-879 | RF00931 | 2 | 76 | 95 | 42 | 72 | 64 | Gene; miRNA; | microRNA mir-879 |
| mir-471 | RF00932 | 2 | 78 | 98 | 6 | 78 | 99 | Gene; miRNA; | microRNA mir-471 |
| mir-875 | RF00933 | 10 | 76 | 91 | 59 | 67 | 89 | Gene; miRNA; | microRNA mir-875 |
| mir-463 | RF00934 | 2 | 81 | 91 | 15 | 76 | 74 | Gene; miRNA; | microRNA mir-463 |
| mir-876 | RF00935 | 4 | 81 | 89 | 44 | 81 | 94 | Gene; miRNA; | microRNA mir-876 |
| mir-744 | RF00936 | 5 | 100 | 94 | 40 | 100 | 97 | Gene; miRNA; | microRNA mir-744 |
| mir-653 | RF00937 | 15 | 97 | 82 | 45 | 97 | 86 | Gene; miRNA; | microRNA mir-653 |
| mir-504 | RF00939 | 6 | 83 | 94 | 37 | 83 | 96 | Gene; miRNA; | microRNA mir-504 |
| mir-327 | RF00940 | 2 | 61 | 87 | 32 | 61 | 79 | Gene; miRNA; | microRNA mir-327 |
| mir-434 | RF00941 | 2 | 94 | 92 | 47 | 78 | 66 | Gene; miRNA; | microRNA mir-434 |
| mir-1224 | RF00942 | 11 | 85 | 89 | 38 | 85 | 88 | Gene; miRNA; | microRNA mir-1224 |
| MIR824 | RF00943 | 2 | 644 | 55 | 50 | 607 | 93 | Gene; miRNA; | microRNA MIR824 |
| mir-1226 | RF00945 | 3 | 75 | 86 | 19 | 75 | 83 | Gene; miRNA; | microRNA mir-1226 |
| mir-1225 | RF00946 | 8 | 92 | 95 | 37 | 92 | 96 | Gene; miRNA; | microRNA mir-1225 |
| mir-929 | RF00947 | 16 | 94 | 73 | 38 | 95 | 76 | Gene; miRNA; | microRNA mir-929 |
| mir-996 | RF00948 | 6 | 98 | 72 | 32 | 96 | 75 | Gene; miRNA; | microRNA mir-996 |
| mir-983 | RF00949 | 3 | 98 | 73 | 15 | 97 | 82 | Gene; miRNA; | microRNA mir-983 |
| mir-927 | RF00950 | 15 | 76 | 77 | 32 | 77 | 81 | Gene; miRNA; | microRNA mir-927 |
| mir-1302 | RF00951 | 36 | 51 | 78 | 37205 | 51 | 71 | Gene; miRNA; | microRNA mir-1302 |
| mir-650 | RF00952 | 13 | 94 | 84 | 788 | 93 | 77 | Gene; miRNA; | microRNA mir-650 |
| mir-1497 | RF00953 | 2 | 73 | 81 | 3 | 73 | 87 | Gene; miRNA; | microRNA mir-1497 |
| MIR1446 | RF00954 | 5 | 104 | 84 | 12 | 103 | 62 | Gene; miRNA; | microRNA MIR1446 |
| mir-1829 | RF00955 | 3 | 60 | 90 | 6 | 60 | 83 | Gene; miRNA; | microRNA mir-1829 |
| MIR1444 | RF00956 | 3 | 85 | 80 | 8 | 85 | 87 | Gene; miRNA; | microRNA MIR1444 |
| mir-663 | RF00957 | 14 | 89 | 77 | 466 | 89 | 81 | Gene; miRNA; | microRNA mir-663 |
| mir-498 | RF00958 | 6 | 121 | 65 | 24 | 122 | 74 | Gene; miRNA; | microRNA mir-498 |
| mir-612 | RF00959 | 6 | 100 | 77 | 31 | 98 | 82 | Gene; miRNA; | microRNA mir-612 |
| mir-661 | RF00960 | 4 | 98 | 80 | 15 | 92 | 83 | Gene; miRNA; | microRNA mir-661 |
| mir-581 | RF00961 | 2 | 96 | 94 | 23 | 85 | 56 | Gene; miRNA; | microRNA mir-581 |
| mir-586 | RF00962 | 2 | 98 | 93 | 13 | 96 | 79 | Gene; miRNA; | microRNA mir-586 |
| mir-642 | RF00963 | 2 | 97 | 95 | 10 | 95 | 95 | Gene; miRNA; | microRNA mir-642 |
| mir-938 | RF00964 | 2 | 83 | 87 | 11 | 83 | 97 | Gene; miRNA; | microRNA mir-938 |
| mir-549 | RF00965 | 2 | 95 | 99 | 10 | 96 | 98 | Gene; miRNA; | microRNA mir-549 |
| mir-676 | RF00966 | 10 | 88 | 88 | 35 | 86 | 85 | Gene; miRNA; | microRNA mir-676 |
| mir-281 | RF00967 | 2 | 82 | 76 | 5 | 81 | 64 | Gene; miRNA; | microRNA mir-281 |
| mir-626 | RF00968 | 8 | 96 | 63 | 51 | 80 | 55 | Gene; miRNA; | microRNA mir-626 |
| mir-556 | RF00969 | 2 | 95 | 89 | 13 | 92 | 84 | Gene; miRNA; | microRNA mir-556 |
| mir-648 | RF00970 | 2 | 94 | 93 | 15 | 94 | 95 | Gene; miRNA; | microRNA mir-648 |
| mir-578 | RF00971 | 3 | 93 | 95 | 19 | 86 | 53 | Gene; miRNA; | microRNA mir-578 |
| mir-651 | RF00972 | 5 | 95 | 78 | 20 | 96 | 79 | Gene; miRNA; | microRNA mir-651 |
| mir-597 | RF00973 | 4 | 97 | 82 | 22 | 97 | 75 | Gene; miRNA; | microRNA mir-597 |
| mir-607 | RF00974 | 3 | 97 | 95 | 11 | 98 | 87 | Gene; miRNA; | microRNA mir-607 |
| MIR845_2 | RF00975 | 2 | 131 | 93 | 193 | 130 | 82 | Gene; miRNA; | microRNA MIR845_2 |
| mir-583 | RF00976 | 2 | 75 | 96 | 10 | 75 | 99 | Gene; miRNA; | microRNA mir-583 |
| mir-600 | RF00977 | 4 | 81 | 83 | 20 | 80 | 92 | Gene; miRNA; | microRNA mir-600 |
| mir-638 | RF00978 | 2 | 100 | 97 | 25 | 99 | 91 | Gene; miRNA; | microRNA mir-638 |
| mir-553 | RF00979 | 3 | 66 | 77 | 14 | 56 | 84 | Gene; miRNA; | microRNA mir-553 |
| mir-643 | RF00980 | 2 | 97 | 91 | 12 | 92 | 91 | Gene; miRNA; | microRNA mir-643 |
| mir-939 | RF00981 | 3 | 82 | 99 | 13 | 82 | 94 | Gene; miRNA; | microRNA mir-939 |
| mir-200 | RF00982 | 2 | 85 | 63 | 3 | 85 | 73 | Gene; miRNA; | microRNA mir-200 |
| mir-662 | RF00983 | 14 | 94 | 87 | 36 | 94 | 84 | Gene; miRNA; | microRNA mir-662 |
| mir-576 | RF00984 | 2 | 98 | 92 | 14 | 99 | 72 | Gene; miRNA; | microRNA mir-576 |
| mir-640 | RF00985 | 3 | 95 | 97 | 58 | 95 | 70 | Gene; miRNA; | microRNA mir-640 |
| mir-920 | RF00986 | 6 | 75 | 75 | 19 | 74 | 82 | Gene; miRNA; | microRNA mir-920 |
| mir-589 | RF00987 | 2 | 99 | 96 | 16 | 98 | 90 | Gene; miRNA; | microRNA mir-589 |
| mir-657 | RF00988 | 2 | 98 | 89 | 13 | 97 | 96 | Gene; miRNA; | microRNA mir-657 |
| mir-492 | RF00989 | 16 | 115 | 84 | 1419 | 114 | 62 | Gene; miRNA; | microRNA mir-492 |
| mir-552 | RF00990 | 3 | 95 | 94 | 24 | 94 | 79 | Gene; miRNA; | microRNA mir-552 |
| mir-599 | RF00991 | 11 | 94 | 85 | 45 | 93 | 88 | Gene; miRNA; | microRNA mir-599 |
| mir-593 | RF00992 | 3 | 101 | 80 | 20 | 102 | 87 | Gene; miRNA; | microRNA mir-593 |
| mir-1473 | RF00993 | 2 | 81 | 80 | 3 | 80 | 86 | Gene; miRNA; | microRNA mir-1473 |
| mir-1255 | RF00994 | 12 | 66 | 80 | 38391 | 65 | 80 | Gene; miRNA; | microRNA mir-1255 |
| mir-616 | RF00995 | 3 | 94 | 81 | 30 | 93 | 83 | Gene; miRNA; | microRNA mir-616 |
| mir-631 | RF00996 | 10 | 74 | 76 | 30 | 72 | 86 | Gene; miRNA; | microRNA mir-631 |
| mir-942 | RF00997 | 2 | 86 | 97 | 12 | 86 | 99 | Gene; miRNA; | microRNA mir-942 |
| mir-562 | RF00998 | 19 | 96 | 68 | 25821 | 102 | 71 | Gene; miRNA; | microRNA mir-562 |
| mir-924 | RF00999 | 4 | 53 | 84 | 85 | 51 | 78 | Gene; miRNA; | microRNA mir-924 |
| mir-580 | RF01000 | 2 | 97 | 95 | 11 | 97 | 98 | Gene; miRNA; | microRNA mir-580 |
| mir-609 | RF01001 | 2 | 94 | 96 | 13 | 94 | 98 | Gene; miRNA; | microRNA mir-609 |
| mir-936 | RF01002 | 4 | 97 | 78 | 30 | 97 | 73 | Gene; miRNA; | microRNA mir-936 |
| mir-563 | RF01003 | 7 | 79 | 74 | 26 | 79 | 79 | Gene; miRNA; | microRNA mir-563 |
| mir-557 | RF01004 | 2 | 71 | 92 | 16 | 72 | 75 | Gene; miRNA; | microRNA mir-557 |
| MIR530 | RF01005 | 3 | 164 | 72 | 39 | 135 | 48 | Gene; miRNA; | microRNA MIR530 |
| mir-601 | RF01006 | 3 | 79 | 96 | 15 | 78 | 84 | Gene; miRNA; | microRNA mir-601 |
| mir-624 | RF01007 | 2 | 97 | 97 | 13 | 98 | 87 | Gene; miRNA; | microRNA mir-624 |
| mir-636 | RF01008 | 5 | 96 | 80 | 20 | 98 | 89 | Gene; miRNA; | microRNA mir-636 |
| mir-M7 | RF01009 | 2 | 73 | 73 | 50 | 75 | 86 | Gene; miRNA; | microRNA mir-M7 |
| mir-632 | RF01010 | 16 | 94 | 83 | 41 | 93 | 84 | Gene; miRNA; | microRNA mir-632 |
| mir-605 | RF01011 | 2 | 83 | 95 | 11 | 84 | 98 | Gene; miRNA; | microRNA mir-605 |
| mir-628 | RF01012 | 9 | 94 | 79 | 44 | 95 | 91 | Gene; miRNA; | microRNA mir-628 |
| mir-577 | RF01013 | 2 | 96 | 95 | 12 | 96 | 98 | Gene; miRNA; | microRNA mir-577 |
| mir-1306 | RF01014 | 8 | 74 | 91 | 72 | 74 | 96 | Gene; miRNA; | microRNA mir-1306 |
| mir-885 | RF01015 | 4 | 73 | 80 | 240 | 78 | 75 | Gene; miRNA; | microRNA mir-885 |
| mir-584 | RF01016 | 16 | 102 | 63 | 1696 | 117 | 54 | Gene; miRNA; | microRNA mir-584 |
| mir-625 | RF01017 | 2 | 84 | 90 | 7 | 78 | 97 | Gene; miRNA; | microRNA mir-625 |
| mir-569 | RF01018 | 12 | 95 | 85 | 43 | 94 | 86 | Gene; miRNA; | microRNA mir-569 |
| mir-922 | RF01019 | 13 | 79 | 80 | 34 | 80 | 79 | Gene; miRNA; | microRNA mir-922 |
| mir-572 | RF01020 | 3 | 57 | 91 | 27 | 55 | 94 | Gene; miRNA; | microRNA mir-572 |
| mir-558 | RF01021 | 3 | 93 | 97 | 16 | 94 | 83 | Gene; miRNA; | microRNA mir-558 |
| mir-611 | RF01022 | 8 | 67 | 77 | 33 | 67 | 79 | Gene; miRNA; | microRNA mir-611 |
| mir-940 | RF01023 | 8 | 93 | 92 | 27 | 93 | 93 | Gene; miRNA; | microRNA mir-940 |
| mir-944 | RF01024 | 2 | 88 | 93 | 14 | 85 | 76 | Gene; miRNA; | microRNA mir-944 |
| mir-934 | RF01025 | 2 | 83 | 93 | 12 | 80 | 99 | Gene; miRNA; | microRNA mir-934 |
| MIR828 | RF01026 | 5 | 91 | 65 | 18 | 101 | 55 | Gene; miRNA; | microRNA MIR828 |
| mir-765 | RF01027 | 2 | 114 | 92 | 16 | 110 | 91 | Gene; miRNA; | microRNA mir-765 |
| mir-633 | RF01028 | 3 | 97 | 74 | 827 | 76 | 58 | Gene; miRNA; | microRNA mir-633 |
| mir-649 | RF01029 | 7 | 102 | 66 | 7891 | 103 | 54 | Gene; miRNA; | microRNA mir-649 |
| mir-422 | RF01030 | 3 | 88 | 78 | 23 | 90 | 68 | Gene; miRNA; | microRNA mir-422 |
| mir-639 | RF01031 | 6 | 97 | 80 | 24 | 97 | 85 | Gene; miRNA; | microRNA mir-639 |
| mir-554 | RF01032 | 4 | 96 | 79 | 32 | 94 | 70 | Gene; miRNA; | microRNA mir-554 |
| mir-767 | RF01033 | 14 | 109 | 83 | 37 | 109 | 86 | Gene; miRNA; | microRNA mir-767 |
| mir-618 | RF01034 | 5 | 101 | 94 | 19 | 101 | 79 | Gene; miRNA; | microRNA mir-618 |
| mir-887 | RF01035 | 3 | 79 | 82 | 18 | 78 | 87 | Gene; miRNA; | microRNA mir-887 |
| mir-567 | RF01036 | 9 | 94 | 71 | 25 | 94 | 69 | Gene; miRNA; | microRNA mir-567 |
| mir-644 | RF01037 | 3 | 93 | 91 | 274 | 99 | 61 | Gene; miRNA; | microRNA mir-644 |
| mir-1307 | RF01038 | 7 | 100 | 95 | 29 | 99 | 95 | Gene; miRNA; | microRNA mir-1307 |
| mir-937 | RF01039 | 8 | 85 | 78 | 31 | 85 | 80 | Gene; miRNA; | microRNA mir-937 |
| mir-573 | RF01040 | 2 | 99 | 94 | 16 | 98 | 82 | Gene; miRNA; | microRNA mir-573 |
| mir-604 | RF01041 | 2 | 94 | 97 | 12 | 94 | 98 | Gene; miRNA; | microRNA mir-604 |
| mir-891 | RF01042 | 7 | 78 | 87 | 92 | 78 | 74 | Gene; miRNA; | microRNA mir-891 |
| MIR1023 | RF01043 | 4 | 162 | 59 | 5 | 161 | 55 | Gene; miRNA; | microRNA MIR1023 |
| mir-345 | RF01044 | 10 | 96 | 86 | 44 | 97 | 84 | Gene; miRNA; | microRNA mir-345 |
| mir-544 | RF01045 | 26 | 96 | 70 | 25455 | 103 | 62 | Gene; miRNA; | microRNA mir-544 |
| WLE3 | RF01046 | 10 | 43 | 86 | 37 | 43 | 87 | Cis-reg; | Wingless localisation element 3 (WLE3) |
| HBV | RF01047 | 6 | 60 | 93 | 6910 | 60 | 98 | Cis-reg; | HBV RNA encapsidation signal epsilon |
| Sacc_telomerase | RF01050 | 13 | 1189 | 71 | 62 | 1087 | 78 | Gene; | Saccharomyces telomerase |
| GEMM_RNA_motif | RF01051 | 162 | 86 | 64 | 1049 | 86 | 60 | Cis-reg; | GEMM cis-regulatory element |
| Arthropod_7SK | RF01052 | 19 | 397 | 64 | 47 | 332 | 59 | Gene; | Arthropod 7SK RNA |
| Deinococcus_Y_RNA | RF01053 | 2 | 126 | 100 | 2 | 126 | 100 | Gene; | Deinococcus radiodurans Y RNA |
| preQ1-II | RF01054 | 14 | 104 | 68 | 71 | 105 | 70 | Cis-reg; riboswitch; | preQ1-II (pre queuosine) riboswitch |
| MOCO_RNA_motif | RF01055 | 179 | 141 | 59 | 424 | 138 | 58 | Cis-reg; riboswitch; | Moco (molybdenum cofactor) riboswitch |
| Mg_sensor | RF01056 | 4 | 114 | 78 | 109 | 114 | 87 | Cis-reg; riboswitch; | Magnesium Sensor |
| SAH_riboswitch | RF01057 | 52 | 84 | 63 | 225 | 80 | 61 | Cis-reg; riboswitch; | S-adenosyl-L-homocysteine riboswitch |
| MIR806 | RF01058 | 8 | 241 | 87 | 17853 | 239 | 76 | Gene; miRNA; | microRNA MIR806 |
| mir-598 | RF01059 | 30 | 95 | 65 | 4656 | 91 | 54 | Gene; miRNA; | microRNA mir-598 |
| mir-548 | RF01061 | 54 | 83 | 76 | 51442 | 80 | 64 | Gene; miRNA; | microRNA mir-548 |
| MIR812 | RF01062 | 9 | 170 | 74 | 29421 | 171 | 68 | Gene; miRNA; | microRNA MIR812 |
| mir-324 | RF01063 | 27 | 85 | 62 | 2955 | 78 | 51 | Gene; miRNA; | microRNA mir-324 |
| mir-253 | RF01064 | 4 | 100 | 81 | 6 | 100 | 78 | Gene; miRNA; | microRNA mir-253 |
| 23S-methyl | RF01065 | 19 | 100 | 59 | 118 | 100 | 63 | Cis-reg; | 23S methyl RNA motif |
| 6C | RF01066 | 20 | 75 | 73 | 65 | 76 | 82 | Cis-reg; | 6C RNA |
| ATPC | RF01067 | 92 | 91 | 73 | 144 | 89 | 77 | Gene; | ATPC RNA motif |
| mini-ykkC | RF01068 | 73 | 47 | 61 | 388 | 47 | 66 | Cis-reg; | mini-ykkC RNA motif |
| purD | RF01069 | 21 | 126 | 56 | 69 | 126 | 58 | Cis-reg; | purD RNA motif |
| sucA | RF01070 | 35 | 83 | 72 | 114 | 82 | 81 | Cis-reg; | SucA RNA motif |
| OLE | RF01071 | 20 | 604 | 65 | 51 | 590 | 65 | Gene; | Ornate Large Extremophilic RNA |
| TMV_UPD-PK3 | RF01072 | 27 | 30 | 79 | 294 | 28 | 88 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| GP_knot1 | RF01073 | 9 | 61 | 82 | 7012 | 62 | 77 | Cis-reg; | Gag/pol translational readthrough site |
| RF_site1 | RF01074 | 4 | 40 | 84 | 12 | 40 | 87 | Cis-reg; | Putative RNA-dependent RNA polymerase ribosomal frameshift site |
| TLS-PK1 | RF01075 | 2 | 96 | 90 | 23 | 95 | 98 | Cis-reg; | Pseudoknot of tRNA-like structure |
| RF_site2 | RF01076 | 2 | 72 | 93 | 137 | 71 | 96 | Cis-reg; | Polymerase ribosomal frameshift site |
| TLS-PK2 | RF01077 | 4 | 66 | 87 | 44 | 66 | 92 | Cis-reg; | Pseudoknot of tRNA-like structure |
| PK-PYVV | RF01078 | 3 | 57 | 86 | 5 | 57 | 90 | Cis-reg; | 3'-terminal pseudoknot in PYVV |
| RF_site3 | RF01079 | 2 | 39 | 97 | 18 | 39 | 99 | Cis-reg; | Putative RNA-dependent RNA polymerase ribosomal frameshift site |
| UPD-PKib | RF01080 | 4 | 32 | 86 | 16 | 31 | 89 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV1_UPD-PKe | RF01081 | 3 | 26 | 87 | 14 | 26 | 95 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV1_UPD-PKh | RF01082 | 2 | 25 | 89 | 11 | 25 | 95 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| UPD-PK2 | RF01083 | 4 | 21 | 94 | 22 | 21 | 99 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| TLS-PK3 | RF01084 | 8 | 128 | 59 | 294 | 125 | 72 | Cis-reg; | Pseudoknot of tRNA-like structure |
| TLS-PK4 | RF01085 | 2 | 117 | 90 | 8 | 116 | 95 | Cis-reg; | Pseudoknot of tRNA-like structure |
| LR-PK1 | RF01086 | 15 | 344 | 77 | 1108 | 276 | 57 | Cis-reg; | Long range pseudoknot |
| PK-repZ | RF01087 | 6 | 149 | 91 | 37 | 142 | 89 | Cis-reg; | Pseudoknot of the regulatory region of the repZ gene |
| TLS-PK5 | RF01088 | 3 | 67 | 82 | 19 | 67 | 92 | Cis-reg; | Pseudoknot of tRNA-like structure |
| PK-repBA | RF01089 | 7 | 123 | 65 | 31 | 115 | 60 | Cis-reg; | Pseudoknot of the regulatory region of the repBA gene |
| RF_site4 | RF01090 | 7 | 66 | 89 | 52 | 65 | 97 | Cis-reg; | Edr gene ribosomal frameshift signal |
| PK-SPCSV | RF01091 | 2 | 61 | 100 | 2 | 61 | 100 | Cis-reg; | 3'-terminal pseudoknot in SPCSV |
| GP_knot2 | RF01092 | 2 | 61 | 100 | 13 | 61 | 90 | Cis-reg; | Gag/pol translational readthrough site |
| RF_site5 | RF01093 | 12 | 60 | 80 | 76 | 60 | 81 | Cis-reg; | Ma3 gene ribosomal frameshift signal |
| RF_site6 | RF01094 | 2 | 118 | 87 | 2 | 118 | 87 | Cis-reg; | Polymerase ribosomal frameshift site |
| PK-CuYV_BPYV | RF01095 | 2 | 56 | 100 | 4 | 56 | 100 | Cis-reg; | 3'-terminal pseudoknot of CuYV/BPYV |
| PK-HAV | RF01096 | 2 | 55 | 93 | 47 | 54 | 90 | Cis-reg; | 3'-terminal pseudoknot of HepA virus |
| RF_site8 | RF01097 | 4 | 52 | 94 | 744 | 51 | 87 | Cis-reg; | Gag/pro ribosomal frameshift site |
| RF_site9 | RF01098 | 2 | 49 | 95 | 29 | 48 | 90 | Cis-reg; | Gag/pro ribosomal frameshift site |
| PK-IAV | RF01099 | 32 | 48 | 88 | 8075 | 48 | 95 | Cis-reg; | Pseudoknot of influenza A virus gene |
| PK-BYV | RF01100 | 2 | 40 | 100 | 4 | 40 | 96 | Cis-reg; | 3'-terminal pseudoknot in BYV |
| TLS-PK6 | RF01101 | 3 | 40 | 91 | 32 | 39 | 96 | Cis-reg; | Pseudoknot of tRNA-like structure |
| PK1-TEV_CVMV | RF01102 | 2 | 36 | 81 | 8 | 36 | 83 | Cis-reg; | 5'-leader pseudoknot of TEV/CVMV |
| UPD-PKc | RF01103 | 2 | 29 | 95 | 12 | 29 | 97 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV2_UPD-PKb | RF01104 | 3 | 29 | 93 | 13 | 28 | 91 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV2_UPD-PKl | RF01105 | 2 | 27 | 100 | 6 | 27 | 96 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV1_UPD-PKb | RF01106 | 2 | 25 | 94 | 6 | 25 | 93 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBRMV1_UPD-PKf | RF01107 | 2 | 27 | 100 | 12 | 27 | 99 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| BMV3_UPD-PK1 | RF01108 | 2 | 26 | 100 | 7 | 26 | 91 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBRMV1_UPD-PKd | RF01109 | 2 | 21 | 100 | 13 | 21 | 98 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| PSLVbeta_UPD-PK2 | RF01110 | 2 | 22 | 100 | 3 | 22 | 95 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| SBWMV2_UPD-PKk | RF01111 | 2 | 21 | 100 | 8 | 21 | 100 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| UPD-PKg | RF01112 | 2 | 21 | 62 | 12 | 21 | 89 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| BMV3_UPD-PK3 | RF01113 | 2 | 23 | 93 | 15 | 23 | 93 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| TMV_UPD-PK1 | RF01114 | 2 | 22 | 100 | 32 | 22 | 99 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| TMV_UPD-PK2 | RF01115 | 3 | 22 | 92 | 61 | 22 | 94 | Cis-reg; | Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR |
| Yfr1 | RF01116 | 37 | 58 | 71 | 191 | 56 | 79 | Gene; sRNA; | Cyanobacterial functional RNA 1 |
| ciona-mir-92 | RF01117 | 2 | 81 | 75 | 2 | 81 | 75 | Gene; miRNA; | Ciona microRNA mir-92 |
| PK-G12rRNA | RF01118 | 368 | 108 | 78 | 12499 | 108 | 79 | Gene; rRNA; | Pseudoknot of the domain G(G12) of 23S ribosomal RNA |
| sR32 | RF01119 | 3 | 57 | 92 | 5 | 51 | 83 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR32 |
| sR33 | RF01120 | 2 | 55 | 76 | 4 | 54 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR33 |
| sR38 | RF01121 | 3 | 59 | 96 | 4 | 59 | 91 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR38 |
| sR39 | RF01122 | 5 | 57 | 87 | 11 | 58 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR39 |
| sR35 | RF01123 | 2 | 57 | 95 | 5 | 51 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR35 |
| sR36 | RF01124 | 5 | 55 | 87 | 8 | 55 | 89 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR36 |
| sR4 | RF01125 | 11 | 57 | 65 | 23 | 57 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR4 |
| sR41 | RF01126 | 3 | 53 | 85 | 5 | 53 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR41 |
| sR42 | RF01127 | 3 | 63 | 84 | 3 | 63 | 84 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR42 |
| sR43 | RF01128 | 3 | 56 | 93 | 7 | 61 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR42 |
| sR44 | RF01129 | 3 | 55 | 87 | 5 | 54 | 89 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR44 |
| sR46 | RF01130 | 7 | 56 | 84 | 7 | 56 | 84 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR46 |
| sR47 | RF01131 | 7 | 55 | 76 | 12 | 55 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR47 |
| sR48 | RF01132 | 2 | 57 | 79 | 4 | 57 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR48 |
| sR3 | RF01133 | 17 | 61 | 65 | 23 | 61 | 65 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR3 |
| sR30 | RF01134 | 3 | 56 | 90 | 3 | 56 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR30 |
| sR24 | RF01135 | 3 | 55 | 97 | 4 | 53 | 97 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR24 |
| sR28 | RF01136 | 6 | 54 | 75 | 12 | 54 | 79 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR28 |
| sR21 | RF01137 | 2 | 66 | 57 | 2 | 66 | 57 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR21 |
| sR23 | RF01138 | 6 | 53 | 67 | 11 | 54 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR23 |
| sR2 | RF01139 | 10 | 55 | 58 | 23 | 54 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR2 |
| sR20 | RF01140 | 6 | 55 | 65 | 15 | 56 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR20 |
| sR18 | RF01141 | 5 | 55 | 73 | 8 | 55 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR18 |
| sR19 | RF01142 | 3 | 63 | 93 | 6 | 62 | 91 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR19 |
| sR16 | RF01143 | 2 | 55 | 56 | 3 | 54 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR16 |
| sR17 | RF01144 | 6 | 55 | 66 | 10 | 53 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR17 |
| sR14 | RF01145 | 8 | 54 | 69 | 16 | 54 | 72 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR14 |
| sR15 | RF01146 | 2 | 60 | 57 | 3 | 58 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR15 |
| sR12 | RF01147 | 5 | 54 | 71 | 10 | 54 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR12 |
| sR13 | RF01148 | 6 | 55 | 67 | 15 | 55 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR13 |
| sR10 | RF01149 | 4 | 54 | 86 | 5 | 54 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR10 |
| sR11 | RF01150 | 8 | 57 | 57 | 20 | 55 | 54 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR11 |
| snoU82P | RF01151 | 13 | 55 | 88 | 57 | 53 | 86 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U82P |
| sR1 | RF01152 | 12 | 55 | 65 | 24 | 54 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR1 |
| sn3060 | RF01153 | 3 | 66 | 99 | 9 | 66 | 96 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn3060 |
| snoU43C | RF01154 | 3 | 65 | 73 | 6 | 60 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U43C |
| snoR101 | RF01155 | 5 | 64 | 84 | 26 | 65 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR101 |
| SNORD123 | RF01156 | 12 | 69 | 89 | 52 | 69 | 94 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD123 |
| sn1185 | RF01157 | 4 | 69 | 92 | 9 | 69 | 90 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn1185 |
| SNORD108 | RF01158 | 4 | 71 | 76 | 18 | 70 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD108 |
| snoU18 | RF01159 | 16 | 71 | 81 | 99 | 60 | 65 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U18 |
| sn2841 | RF01160 | 2 | 71 | 98 | 9 | 71 | 97 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2841 |
| SNORD5 | RF01161 | 21 | 71 | 79 | 110 | 65 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD5 |
| sn668 | RF01162 | 4 | 73 | 93 | 10 | 70 | 94 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn668 |
| snoR64a | RF01163 | 4 | 77 | 71 | 22 | 73 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR64a |
| SNORD107 | RF01164 | 14 | 73 | 86 | 53 | 72 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD107 |
| sn2317 | RF01165 | 4 | 71 | 83 | 9 | 71 | 86 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2317 |
| sn3071 | RF01166 | 2 | 76 | 98 | 10 | 76 | 96 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn3071 |
| sn2429 | RF01167 | 4 | 76 | 90 | 8 | 76 | 92 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2429 |
| SNORD126 | RF01168 | 6 | 77 | 86 | 42 | 76 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD126 |
| SNORD112 | RF01169 | 9 | 76 | 83 | 732 | 70 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD112 |
| snoU61 | RF01170 | 6 | 83 | 76 | 62 | 77 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U61 |
| snoR4 | RF01171 | 2 | 79 | 62 | 16 | 63 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR4 |
| sn2343 | RF01172 | 3 | 79 | 89 | 8 | 78 | 91 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2343 |
| snoU105B | RF01173 | 13 | 79 | 79 | 40 | 79 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U105B |
| snoU43 | RF01174 | 8 | 80 | 81 | 21 | 80 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U43 |
| snoU83D | RF01175 | 8 | 79 | 83 | 26 | 77 | 83 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U83 |
| snR78 | RF01176 | 8 | 82 | 75 | 34 | 78 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR78 |
| snR67 | RF01177 | 16 | 90 | 72 | 37 | 85 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR67 |
| snoR77Y | RF01178 | 6 | 85 | 75 | 68 | 84 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR77Y |
| snoU83 | RF01179 | 6 | 84 | 62 | 23 | 82 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U83 |
| snoR110 | RF01180 | 2 | 86 | 91 | 6 | 81 | 83 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR110 |
| snR77 | RF01181 | 15 | 83 | 83 | 36 | 84 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR77 |
| SNORD11 | RF01182 | 18 | 84 | 86 | 92 | 81 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD11 |
| SNORD19B | RF01183 | 16 | 82 | 76 | 54 | 81 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD19B |
| snR79 | RF01184 | 18 | 85 | 72 | 74 | 81 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR79 |
| snR75 | RF01185 | 62 | 87 | 69 | 108 | 86 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR75 |
| SNORD127 | RF01186 | 13 | 84 | 86 | 48 | 84 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD127 |
| snoU83C | RF01187 | 2 | 86 | 82 | 13 | 79 | 60 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U83C |
| snR56 | RF01188 | 16 | 84 | 69 | 159 | 79 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR56 |
| sn1502 | RF01189 | 4 | 87 | 94 | 9 | 86 | 96 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn1502 |
| snR50 | RF01190 | 3 | 88 | 94 | 28 | 77 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR50 |
| SNORD121A | RF01191 | 26 | 82 | 81 | 125 | 79 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD121A |
| SNORD11B | RF01192 | 27 | 84 | 76 | 85 | 84 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD11B |
| snoR20a | RF01193 | 5 | 85 | 71 | 33 | 88 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR20a |
| sn2903 | RF01194 | 4 | 91 | 99 | 9 | 91 | 98 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2903 |
| snR52 | RF01195 | 5 | 91 | 97 | 25 | 88 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR52 |
| snoZ30a | RF01196 | 10 | 91 | 81 | 19 | 91 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z30a |
| snR39 | RF01197 | 4 | 97 | 84 | 31 | 91 | 77 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR39 |
| snoR69Y | RF01198 | 7 | 98 | 68 | 60 | 95 | 69 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR69Y |
| snR58 | RF01199 | 3 | 97 | 80 | 32 | 92 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR58 |
| SNORD125 | RF01200 | 16 | 97 | 81 | 47 | 96 | 84 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD125 |
| snR40 | RF01201 | 17 | 88 | 77 | 37 | 89 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR40 |
| sn2991 | RF01202 | 4 | 98 | 89 | 8 | 98 | 89 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2991 |
| snR47 | RF01203 | 14 | 95 | 70 | 175 | 75 | 67 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR47 |
| snR65 | RF01204 | 5 | 99 | 93 | 65 | 94 | 58 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR65 |
| snR62 | RF01205 | 2 | 100 | 95 | 32 | 92 | 65 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR62 |
| snoR109 | RF01206 | 6 | 94 | 80 | 23 | 93 | 72 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR109 |
| snR73 | RF01207 | 5 | 104 | 82 | 89 | 95 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR73 |
| snoR99 | RF01208 | 9 | 103 | 69 | 44 | 101 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR99 |
| snR76 | RF01209 | 15 | 99 | 78 | 43 | 97 | 78 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR76 |
| snoU13 | RF01210 | 35 | 102 | 76 | 7629 | 100 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U13 |
| SNORD124 | RF01211 | 18 | 103 | 82 | 42 | 102 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD124 |
| sn2524 | RF01212 | 2 | 107 | 66 | 30 | 105 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2524 |
| snoR103 | RF01213 | 11 | 106 | 69 | 51 | 105 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR103 |
| snR51 | RF01214 | 17 | 96 | 72 | 64 | 93 | 59 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR51 |
| snoR97 | RF01215 | 7 | 107 | 72 | 45 | 105 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR97 |
| snR87 | RF01216 | 4 | 109 | 91 | 27 | 109 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR87 |
| snoR72Y | RF01217 | 10 | 87 | 64 | 99 | 87 | 59 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR72Y |
| snR41 | RF01218 | 18 | 103 | 75 | 45 | 102 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR41 |
| snoR100 | RF01219 | 9 | 114 | 72 | 40 | 112 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR100 |
| snoR104 | RF01220 | 8 | 117 | 67 | 36 | 117 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR104 |
| snoU6-47 | RF01221 | 3 | 130 | 72 | 16 | 126 | 58 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U6-47 |
| sn2417 | RF01222 | 3 | 122 | 93 | 10 | 122 | 92 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sn2417 |
| snR13 | RF01223 | 2 | 123 | 96 | 52 | 78 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR13 |
| snoR80 | RF01224 | 9 | 128 | 72 | 40 | 129 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR80 |
| ACA64 | RF01225 | 26 | 127 | 77 | 230 | 124 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA ACA64 |
| snoZ5 | RF01226 | 8 | 116 | 82 | 83 | 96 | 51 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA Z5 |
| snoR83 | RF01227 | 7 | 129 | 70 | 62 | 121 | 65 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR83 |
| snoR111 | RF01228 | 6 | 126 | 66 | 17 | 129 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR111 |
| SNORA84 | RF01229 | 28 | 133 | 77 | 104 | 128 | 75 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA84 |
| snoR77 | RF01230 | 5 | 129 | 74 | 42 | 128 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR77 |
| snoR74 | RF01231 | 9 | 132 | 67 | 89 | 126 | 61 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snoR74 |
| snoU40 | RF01232 | 9 | 110 | 83 | 47 | 101 | 62 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U40 |
| snoU109 | RF01233 | 26 | 136 | 83 | 313 | 129 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA U109 |
| SNORA47 | RF01234 | 20 | 136 | 78 | 68 | 133 | 73 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA47 |
| snR68 | RF01235 | 4 | 137 | 94 | 23 | 122 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR68 |
| snoU19 | RF01236 | 3 | 142 | 67 | 16 | 135 | 56 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA U19 |
| snR161 | RF01237 | 10 | 162 | 67 | 28 | 158 | 72 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR161 |
| snR70 | RF01238 | 8 | 163 | 79 | 31 | 150 | 56 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR70 |
| snR49 | RF01239 | 6 | 171 | 75 | 39 | 151 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR49 |
| snR85 | RF01240 | 5 | 179 | 81 | 22 | 162 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR85 |
| SNORA81 | RF01241 | 24 | 177 | 81 | 194 | 165 | 63 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA SNORA81 |
| snR36 | RF01242 | 10 | 184 | 70 | 63 | 182 | 53 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR36 |
| snR33 | RF01243 | 5 | 183 | 89 | 18 | 177 | 83 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR33 |
| snR4 | RF01244 | 5 | 185 | 81 | 28 | 158 | 59 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR4 |
| snR9 | RF01245 | 5 | 186 | 90 | 24 | 174 | 73 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR9 |
| snR81 | RF01246 | 3 | 188 | 90 | 15 | 170 | 95 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR81 |
| snR32 | RF01247 | 11 | 194 | 65 | 43 | 180 | 55 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR32 |
| snR8 | RF01248 | 11 | 181 | 70 | 36 | 180 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR8 |
| snR190 | RF01249 | 5 | 197 | 90 | 28 | 169 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR190 |
| snR189 | RF01250 | 4 | 192 | 90 | 22 | 176 | 78 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR189 |
| snR3 | RF01251 | 4 | 191 | 86 | 28 | 175 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR3 |
| snR5 | RF01252 | 11 | 191 | 76 | 36 | 184 | 67 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR5 |
| snR46 | RF01253 | 6 | 199 | 80 | 36 | 171 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR46 |
| snR34 | RF01254 | 4 | 205 | 90 | 24 | 203 | 80 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR34 |
| snR35 | RF01255 | 10 | 198 | 75 | 29 | 195 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR35 |
| snR43 | RF01256 | 17 | 206 | 60 | 42 | 199 | 58 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR43 |
| snR31 | RF01257 | 8 | 221 | 73 | 27 | 216 | 77 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR31 |
| snR10 | RF01258 | 14 | 247 | 74 | 38 | 250 | 77 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR10 |
| snR63 | RF01259 | 5 | 255 | 91 | 22 | 237 | 83 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR63 |
| snR11 | RF01260 | 6 | 255 | 73 | 22 | 238 | 74 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR11 |
| snR82 | RF01261 | 5 | 273 | 77 | 35 | 222 | 55 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR82 |
| snR44 | RF01262 | 7 | 206 | 86 | 36 | 178 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR44 |
| snR191 | RF01263 | 11 | 270 | 68 | 29 | 271 | 64 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR191 |
| snR83 | RF01264 | 5 | 307 | 87 | 20 | 291 | 80 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR83 |
| snR42 | RF01265 | 5 | 348 | 84 | 37 | 252 | 69 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR42 |
| snR45 | RF01266 | 8 | 183 | 76 | 23 | 170 | 89 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR45 |
| snR37 | RF01267 | 9 | 381 | 69 | 24 | 381 | 76 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR37 |
| snoU2-25 | RF01268 | 17 | 414 | 79 | 51 | 400 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U2-25 |
| snR80 | RF01269 | 6 | 175 | 87 | 40 | 166 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR80 |
| snR84 | RF01270 | 6 | 557 | 75 | 16 | 549 | 81 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR84 |
| snR30 | RF01271 | 5 | 611 | 91 | 21 | 589 | 79 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR30 |
| snR86 | RF01272 | 5 | 998 | 69 | 14 | 999 | 78 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA snR86 |
| sR34 | RF01273 | 4 | 54 | 95 | 9 | 53 | 91 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR34 |
| sR45 | RF01274 | 4 | 55 | 90 | 7 | 57 | 82 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR45 |
| sR22 | RF01275 | 4 | 58 | 94 | 7 | 58 | 93 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR22 |
| sR53 | RF01276 | 3 | 59 | 92 | 4 | 59 | 92 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR53 |
| snoU54 | RF01277 | 26 | 67 | 77 | 89 | 67 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U54 |
| SNORD109A | RF01278 | 7 | 67 | 89 | 65 | 67 | 92 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA SNORD109A |
| snoR53Y | RF01279 | 7 | 82 | 71 | 23 | 78 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR53Y |
| snoR14 | RF01280 | 7 | 87 | 80 | 28 | 84 | 71 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR14 |
| snoR35 | RF01281 | 12 | 80 | 75 | 38 | 80 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR35 |
| snoU30 | RF01283 | 5 | 85 | 75 | 14 | 83 | 70 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U30 |
| snoR8a | RF01284 | 7 | 88 | 73 | 34 | 86 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR8a |
| snoU31b | RF01285 | 7 | 84 | 68 | 54 | 85 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U31b |
| snoR26 | RF01286 | 8 | 93 | 74 | 46 | 94 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR26 |
| snoR27 | RF01287 | 6 | 93 | 70 | 40 | 92 | 56 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR27 |
| snoR31 | RF01288 | 6 | 94 | 74 | 58 | 94 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR31 |
| snoR17 | RF01289 | 2 | 104 | 63 | 23 | 64 | 54 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR17 |
| snoU6-77 | RF01290 | 22 | 140 | 65 | 64 | 140 | 64 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U6-77 |
| snoU97 | RF01291 | 22 | 147 | 86 | 59 | 151 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U97 |
| snoR2 | RF01292 | 11 | 150 | 74 | 85 | 148 | 73 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR2/U65 |
| ACA59 | RF01293 | 3 | 154 | 73 | 42 | 147 | 62 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA ACA59 |
| snoU89 | RF01294 | 16 | 263 | 76 | 58 | 248 | 68 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA U89 |
| snoU90 | RF01295 | 18 | 329 | 80 | 46 | 321 | 80 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U90 |
| snoU85 | RF01296 | 21 | 323 | 62 | 104 | 293 | 52 | Gene; snRNA; snoRNA; HACA-box; | Small nucleolar RNA U85 |
| sR40 | RF01297 | 2 | 61 | 100 | 7 | 57 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR40 |
| snoU35 | RF01298 | 3 | 69 | 99 | 6 | 66 | 74 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U25 |
| snR39B | RF01299 | 18 | 71 | 76 | 133 | 66 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snR39B |
| snoU49 | RF01300 | 2 | 73 | 95 | 61 | 77 | 75 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA U49 |
| snoR4a | RF01301 | 2 | 77 | 100 | 4 | 66 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR4a |
| snoU36a | RF01302 | 16 | 88 | 73 | 71 | 88 | 70 | Gene; snRNA; snoRNA; CD-box; | SnoRNA U36a |
| sR49 | RF01303 | 3 | 56 | 90 | 4 | 52 | 81 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR49 |
| sR5 | RF01304 | 10 | 53 | 60 | 21 | 53 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR5 |
| sR51 | RF01305 | 3 | 54 | 85 | 7 | 50 | 85 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR51 |
| sR52 | RF01306 | 2 | 58 | 88 | 2 | 58 | 88 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR52 |
| sR55 | RF01307 | 4 | 63 | 90 | 7 | 62 | 83 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR55 |
| sR58 | RF01308 | 5 | 55 | 88 | 9 | 55 | 87 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR58 |
| sR60 | RF01309 | 4 | 55 | 91 | 7 | 55 | 92 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR60 |
| sR7 | RF01310 | 6 | 57 | 57 | 13 | 56 | 63 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR7 |
| sR8 | RF01311 | 7 | 52 | 64 | 11 | 50 | 66 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR8 |
| sR9 | RF01312 | 3 | 59 | 48 | 15 | 55 | 68 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA sR9 |
| HHBV_epsilon | RF01313 | 6 | 57 | 92 | 54 | 56 | 93 | Cis-reg; | Heron HBV RNA encapsidation signal epsilon |
| mir-1227 | RF01314 | 3 | 88 | 98 | 15 | 84 | 89 | Gene; miRNA; | microRNA mir-1227 |
| CRISPR-DR2 | RF01315 | 28 | 30 | 76 | 5220 | 30 | 82 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR3 | RF01316 | 20 | 30 | 87 | 771 | 30 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR4 | RF01317 | 42 | 28 | 86 | 4052 | 28 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR5 | RF01318 | 12 | 37 | 81 | 1953 | 36 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR6 | RF01319 | 7 | 30 | 92 | 635 | 30 | 89 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR7 | RF01320 | 10 | 37 | 79 | 728 | 36 | 82 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR8 | RF01321 | 5 | 36 | 71 | 78 | 36 | 74 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR9 | RF01322 | 7 | 37 | 83 | 291 | 37 | 84 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR10 | RF01323 | 5 | 37 | 75 | 452 | 37 | 81 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR11 | RF01324 | 5 | 36 | 89 | 38 | 36 | 94 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR12 | RF01325 | 5 | 30 | 91 | 213 | 30 | 95 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR13 | RF01326 | 4 | 30 | 95 | 139 | 30 | 96 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR14 | RF01327 | 6 | 29 | 91 | 1080 | 28 | 92 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR17 | RF01328 | 3 | 25 | 97 | 62 | 25 | 97 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR15 | RF01329 | 3 | 37 | 82 | 15 | 37 | 91 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR16 | RF01330 | 6 | 37 | 86 | 71 | 36 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR18 | RF01331 | 6 | 37 | 86 | 120 | 36 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR19 | RF01332 | 4 | 36 | 80 | 1288 | 36 | 86 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR20 | RF01333 | 3 | 36 | 78 | 73 | 36 | 84 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR21 | RF01334 | 2 | 37 | 100 | 548 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR22 | RF01335 | 9 | 36 | 84 | 526 | 36 | 90 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR23 | RF01336 | 3 | 36 | 95 | 210 | 36 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR24 | RF01337 | 4 | 30 | 93 | 303 | 30 | 94 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR25 | RF01338 | 5 | 25 | 94 | 529 | 25 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR27 | RF01339 | 3 | 25 | 94 | 136 | 25 | 96 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR29 | RF01340 | 2 | 37 | 100 | 24 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR30 | RF01341 | 3 | 38 | 85 | 19 | 38 | 96 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR32 | RF01342 | 2 | 37 | 84 | 30 | 37 | 92 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR33 | RF01343 | 3 | 37 | 72 | 79 | 36 | 83 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR34 | RF01344 | 5 | 36 | 90 | 75 | 35 | 92 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR35 | RF01345 | 2 | 36 | 96 | 44 | 35 | 89 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR36 | RF01346 | 3 | 36 | 95 | 158 | 36 | 94 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR37 | RF01347 | 3 | 35 | 82 | 34 | 34 | 91 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR38 | RF01348 | 5 | 35 | 86 | 121 | 34 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR40 | RF01349 | 3 | 30 | 90 | 89 | 30 | 86 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR41 | RF01350 | 2 | 29 | 100 | 131 | 29 | 98 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR42 | RF01351 | 3 | 29 | 96 | 23 | 28 | 79 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR43 | RF01352 | 3 | 29 | 86 | 220 | 27 | 97 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR44 | RF01353 | 3 | 28 | 84 | 75 | 28 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR45 | RF01354 | 3 | 24 | 100 | 327 | 24 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR26 | RF01355 | 4 | 25 | 96 | 203 | 25 | 99 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR28 | RF01356 | 3 | 24 | 94 | 508 | 24 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR31 | RF01357 | 3 | 37 | 90 | 37 | 37 | 94 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR39 | RF01358 | 3 | 31 | 81 | 104 | 31 | 89 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR46 | RF01359 | 2 | 38 | 83 | 6 | 38 | 88 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR47 | RF01360 | 2 | 37 | 97 | 45 | 36 | 99 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR48 | RF01361 | 2 | 37 | 96 | 11 | 37 | 99 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR49 | RF01362 | 3 | 47 | 88 | 325 | 46 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR50 | RF01363 | 2 | 46 | 84 | 116 | 45 | 87 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR51 | RF01364 | 2 | 37 | 81 | 24 | 37 | 97 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR52 | RF01365 | 2 | 37 | 100 | 51 | 36 | 99 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR53 | RF01366 | 2 | 37 | 96 | 14 | 37 | 98 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR54 | RF01367 | 2 | 37 | 100 | 17 | 37 | 95 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR55 | RF01368 | 2 | 37 | 96 | 52 | 36 | 90 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR56 | RF01369 | 2 | 37 | 97 | 93 | 37 | 96 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR57 | RF01370 | 3 | 37 | 88 | 127 | 36 | 92 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR58 | RF01371 | 2 | 37 | 96 | 139 | 37 | 98 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR59 | RF01372 | 2 | 37 | 83 | 18 | 36 | 93 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR60 | RF01373 | 2 | 37 | 90 | 171 | 37 | 95 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR61 | RF01374 | 2 | 37 | 96 | 83 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR62 | RF01375 | 2 | 37 | 93 | 29 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR63 | RF01376 | 2 | 37 | 96 | 23 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR64 | RF01377 | 2 | 37 | 97 | 4 | 37 | 98 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR65 | RF01378 | 2 | 37 | 79 | 101 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| CRISPR-DR66 | RF01379 | 4 | 36 | 94 | 161 | 37 | 100 | Gene; CRISPR; | CRISPR RNA direct repeat element |
| HIV-1_SD | RF01380 | 21 | 19 | 95 | 1916 | 19 | 99 | Cis-reg; | Human immunodeficiency virus type 1 major splice donor |
| HIV-1_SL3 | RF01381 | 21 | 23 | 88 | 2689 | 22 | 99 | Cis-reg; | HIV-1 stem-loop 3 Psi packaging signal |
| HIV-1_SL4 | RF01382 | 22 | 20 | 91 | 9939 | 20 | 97 | Cis-reg; | HIV-1 stem-loop 4 packaging signal |
| GRIK4_3p_UTR | RF01383 | 10 | 80 | 74 | 151 | 66 | 76 | Gene; | GRIK4 3 prime UTR element |
| InvR | RF01384 | 4 | 91 | 96 | 41 | 91 | 99 | Gene; | Invasion gene-associated RNA |
| isrA | RF01385 | 10 | 126 | 87 | 62 | 122 | 65 | Gene; sRNA; | isrA Hfq binding RNA |
| isrB | RF01386 | 4 | 88 | 64 | 28 | 86 | 78 | Gene; sRNA; | isrB Hfq binding RNA |
| isrC | RF01387 | 16 | 122 | 92 | 114 | 120 | 87 | Gene; sRNA; | isrC Hfq binding RNA |
| isrD | RF01388 | 2 | 51 | 100 | 37 | 51 | 99 | Gene; sRNA; | isrD Hfq binding RNA |
| isrF | RF01389 | 3 | 284 | 85 | 12 | 288 | 92 | Gene; sRNA; | isrF Hfq binding RNA |
| isrG | RF01390 | 5 | 279 | 87 | 55 | 275 | 83 | Gene; sRNA; | isrG Hfq binding RNA |
| isrH | RF01391 | 6 | 280 | 98 | 40 | 272 | 97 | Gene; sRNA; | isrH Hfq binding RNA |
| isrI | RF01392 | 30 | 98 | 82 | 60 | 97 | 83 | Gene; sRNA; | isrI Hfq binding RNA |
| isrJ | RF01393 | 5 | 75 | 79 | 39 | 72 | 78 | Gene; sRNA; | isrJ Hfq binding RNA |
| isrK | RF01394 | 55 | 77 | 61 | 458 | 75 | 59 | Gene; sRNA; | isrK Hfq binding RNA |
| isrL | RF01395 | 4 | 347 | 86 | 44 | 345 | 92 | Gene; sRNA; | isrL Hfq binding RNA |
| isrN | RF01396 | 17 | 141 | 62 | 163 | 138 | 62 | Gene; sRNA; | isrN Hfq binding RNA |
| isrO | RF01397 | 6 | 198 | 84 | 46 | 192 | 89 | Gene; sRNA; | isrO Hfq binding RNA |
| isrP | RF01398 | 7 | 148 | 97 | 38 | 146 | 97 | Gene; sRNA; | isrP Hfq binding RNA |
| isrQ | RF01399 | 6 | 161 | 97 | 39 | 161 | 97 | Gene; sRNA; | isrQ Hfq binding RNA |
| istR | RF01400 | 7 | 130 | 84 | 101 | 129 | 86 | Gene; sRNA; | istR Hfq binding RNA |
| rseX | RF01401 | 4 | 95 | 99 | 42 | 93 | 97 | Gene; sRNA; | rseX Hfq binding RNA |
| STnc150 | RF01402 | 10 | 265 | 87 | 52 | 212 | 79 | Gene; sRNA; | STnc150 Hfq binding RNA |
| STnc290 | RF01403 | 6 | 65 | 99 | 36 | 65 | 99 | Gene; sRNA; | STnc290 Hfq binding RNA |
| STnc440 | RF01404 | 4 | 76 | 99 | 39 | 75 | 100 | Gene; sRNA; | STnc440 Hfq binding RNA |
| STnc490k | RF01405 | 76 | 123 | 95 | 1699 | 122 | 96 | Gene; sRNA; | STnc490k Hfq binding RNA |
| STnc500 | RF01406 | 8 | 284 | 99 | 36 | 273 | 99 | Gene; sRNA; | STnc500 Hfq binding RNA |
| STnc560 | RF01407 | 13 | 217 | 93 | 104 | 218 | 87 | Gene; sRNA; | STnc560 Hfq binding RNA |
| sraL | RF01408 | 7 | 141 | 83 | 122 | 138 | 92 | Gene; sRNA; | sraL Hfq binding RNA |
| STnc250 | RF01409 | 4 | 94 | 91 | 43 | 92 | 97 | Gene; sRNA; | STnc250 Hfq binding RNA |
| BsrC | RF01410 | 29 | 85 | 78 | 268 | 84 | 78 | Gene; sRNA; | BsrC |
| BsrF | RF01411 | 11 | 110 | 76 | 100 | 110 | 92 | Gene; sRNA; | BsrF |
| BsrG | RF01412 | 6 | 257 | 52 | 64 | 255 | 50 | Gene; sRNA; | BsrG |
| miR-430 | RF01413 | 46 | 89 | 59 | 1096 | 87 | 54 | Gene; miRNA; | microRNA miR-430 |
| class_I_RNA | RF01414 | 21 | 56 | 78 | 57 | 54 | 78 | Gene; | Class I RNA |
| Flavivirus_SLIV | RF01415 | 20 | 73 | 83 | 325 | 73 | 88 | Cis-reg; | Flavivirus 3'UTR stem loop IV |
| NrrF | RF01416 | 3 | 158 | 96 | 27 | 159 | 89 | Gene; antisense; | NrrF RNA |
| RSV_RNA | RF01417 | 8 | 289 | 89 | 17593 | 284 | 44 | Cis-reg; | Retroviral 3'UTR stability element |
| HIV_POL-1_SL | RF01418 | 29 | 113 | 77 | 51426 | 112 | 92 | Cis-reg; | HIV pol-1 stem loop |
| lsrR | RF01419 | 309 | 185 | 68 | 1398 | 182 | 74 | Gene; antisense; | Antisense RNA which regulates isiA expression |
| snoR113 | RF01420 | 5 | 103 | 76 | 29 | 107 | 76 | Gene; snRNA; snoRNA; CD-box; | Small nucleolar RNA snoR113 |
| snoR114 | RF01421 | 24 | 88 | 67 | 74 | 87 | 66 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR114 |
| snoR116 | RF01422 | 5 | 86 | 74 | 14 | 88 | 73 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR116 |
| snoR117 | RF01423 | 6 | 79 | 68 | 20 | 81 | 64 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR117 |
| snoR118 | RF01424 | 8 | 86 | 76 | 52 | 84 | 78 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR118 |
| snoR121 | RF01425 | 2 | 86 | 90 | 3 | 85 | 82 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR121 |
| snoR126 | RF01426 | 4 | 99 | 66 | 23 | 98 | 68 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR126 |
| snoR127 | RF01427 | 3 | 133 | 81 | 13 | 147 | 68 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR127 |
| snoR128 | RF01428 | 5 | 87 | 75 | 14 | 88 | 70 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR128 |
| snoR130 | RF01429 | 2 | 119 | 86 | 8 | 121 | 48 | Gene; snRNA; snoRNA; CD-box; | small nucleolar RNA snoR130 |
| snoR134 | RF01430 | 5 | 146 | 70 | 52 | 145 | 74 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snoR134 |
| snoR135 | RF01431 | 6 | 146 | 76 | 58 | 144 | 66 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snoR135 |
| snoR143 | RF01432 | 3 | 170 | 62 | 31 | 157 | 61 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snoR143 |
| snoR137 | RF01433 | 4 | 145 | 77 | 45 | 140 | 58 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snoR137 |
| S_pombe_snR3 | RF01434 | 3 | 166 | 78 | 4 | 166 | 78 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR3 |
| S_pombe_snR5 | RF01435 | 3 | 142 | 84 | 4 | 142 | 80 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR5 |
| S_pombe_snR33 | RF01436 | 3 | 146 | 70 | 4 | 146 | 64 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR33 |
| S_pombe_snR10 | RF01437 | 2 | 167 | 100 | 3 | 165 | 69 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR10 |
| S_pombe_snR35 | RF01438 | 4 | 172 | 85 | 5 | 171 | 82 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR35 |
| S_pombe_snR36 | RF01439 | 2 | 164 | 100 | 2 | 164 | 100 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR36 |
| S_pombe_snR42 | RF01440 | 3 | 209 | 73 | 4 | 210 | 70 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR42 |
| S_pombe_snR46 | RF01441 | 2 | 168 | 100 | 3 | 139 | 81 | Gene; snRNA; snoRNA; HACA-box; | small nulceolar RNA snR46 |
| S_pombe_snR90 | RF01442 | 3 | 155 | 79 | 4 | 154 | 74 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR90 |
| S_pombe_snR91 | RF01443 | 2 | 144 | 99 | 3 | 143 | 79 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR91 |
| S_pombe_snR92 | RF01444 | 3 | 144 | 76 | 3 | 144 | 76 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR92 |
| S_pombe_snR94 | RF01445 | 3 | 210 | 73 | 4 | 203 | 75 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR94 |
| S_pombe_snR95 | RF01446 | 2 | 222 | 100 | 5 | 220 | 88 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR95 |
| S_pombe_snR98 | RF01447 | 2 | 212 | 100 | 2 | 212 | 100 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR98 |
| S_pombe_snR93 | RF01448 | 2 | 143 | 100 | 3 | 142 | 66 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR93 |
| S_pombe_snR100 | RF01449 | 3 | 185 | 66 | 5 | 185 | 71 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR100 |
| S_pombe_snR96 | RF01450 | 2 | 211 | 100 | 2 | 211 | 100 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR96 |
| S_pombe_snR97 | RF01451 | 3 | 147 | 100 | 3 | 147 | 100 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR97 |
| S_pombe_snR99 | RF01452 | 5 | 186 | 85 | 8 | 187 | 85 | Gene; snRNA; snoRNA; HACA-box; | small nucleolar RNA snR99 |
| RCNMV_TE_DR1 | RF01453 | 3 | 138 | 91 | 3 | 138 | 91 | Cis-reg; | 3'TE-DR1 translation enhancer element |
| RCNMV_5UTR | RF01454 | 3 | 121 | 83 | 3 | 121 | 83 | Cis-reg; | 5'UTR enhancer element |
| DPB | RF01455 | 18 | 85 | 81 | 87 | 81 | 77 | Cis-reg; | Stem loopII regulatory element in POLB |
| VrrA | RF01456 | 12 | 137 | 85 | 46 | 134 | 75 | Gene; antisense; | Vibrio regulatory RNA of OmpA |
| rli22 | RF01457 | 6 | 110 | 98 | 28 | 110 | 99 | Gene; snRNA; | Listeria snRNA rli22 |
| rli23 | RF01458 | 7 | 98 | 78 | 72 | 97 | 68 | Gene; antisense; | Listeria snRNA rli23 |
| rliE | RF01459 | 4 | 222 | 83 | 22 | 223 | 92 | Gene; snRNA; | Listeria snRNA rliE |
| rliH | RF01460 | 3 | 429 | 92 | 25 | 429 | 98 | Gene; snRNA; | Listeria snRNA rliH |
| rli24 | RF01461 | 6 | 158 | 94 | 23 | 158 | 96 | Gene; snRNA; | Listeria snRNA rli22 |
| rli26 | RF01462 | 5 | 186 | 93 | 22 | 185 | 94 | Gene; snRNA; | Listeria snRNA rli26 |
| rli27 | RF01463 | 3 | 99 | 96 | 25 | 99 | 96 | Gene; snRNA; | Listeria snRNA rli27 |
| rliA | RF01464 | 4 | 224 | 94 | 21 | 223 | 95 | Gene; snRNA; | Listeria snRNA rliA |
| rli31 | RF01465 | 3 | 115 | 90 | 25 | 115 | 98 | Gene; snRNA; | rli31 |
| rli34 | RF01466 | 5 | 84 | 85 | 30 | 82 | 82 | Gene; snRNA; | Listeria snRNA rli34 |
| rli36 | RF01467 | 6 | 84 | 96 | 25 | 80 | 98 | Gene; snRNA; | Listeria snRNA rli36 |
| rli32 | RF01468 | 5 | 147 | 93 | 25 | 146 | 98 | Gene; snRNA; | Listeria snRNA rli32 |
| rli33 | RF01469 | 3 | 533 | 94 | 27 | 513 | 78 | Gene; snRNA; | Listeria snRNA rli33 |
| rli38 | RF01470 | 6 | 149 | 88 | 31 | 145 | 73 | Gene; snRNA; | Listeria snRNA rli38 |
| rliB | RF01471 | 4 | 358 | 66 | 33 | 314 | 62 | Gene; snRNA; | Listeria snRNA rliB |
| rli40 | RF01472 | 4 | 262 | 85 | 26 | 263 | 95 | Gene; snRNA; | Listeria snRNA rli40 |
| rli41 | RF01473 | 6 | 494 | 94 | 25 | 494 | 97 | Gene; snRNA; | Listeria snRNA rli41 |
| rli42 | RF01474 | 4 | 170 | 95 | 26 | 169 | 93 | Gene; snRNA; | Listeia snRNA rli42 |
| rli45 | RF01475 | 6 | 77 | 86 | 25 | 78 | 92 | Gene; antisense; | Listeria snRNA rli45 |
| rliF | RF01476 | 5 | 212 | 76 | 31 | 210 | 78 | Gene; snRNA; | Listeria snRNA rliF |
| rli43 | RF01477 | 4 | 254 | 93 | 24 | 244 | 96 | Gene; snRNA; | Listeria snRNA rli43 |
| rli47 | RF01478 | 9 | 508 | 98 | 26 | 503 | 98 | Gene; snRNA; | Listeria snRNA rli47 |
| rli48 | RF01479 | 3 | 149 | 85 | 9 | 149 | 89 | Gene; snRNA; | Listeria snRNA rli48 |
| rli52 | RF01480 | 6 | 95 | 95 | 23 | 95 | 98 | Cis-reg; riboswitch; | Listeria snRNA rli52 |
| rli53 | RF01481 | 5 | 173 | 97 | 24 | 169 | 97 | Cis-reg; riboswitch; | Listeria snRNA rli53 |
| rli55 | RF01482 | 3 | 283 | 99 | 24 | 283 | 100 | Cis-reg; riboswitch; | Listeria snRNA rli55 |
| rli56 | RF01483 | 6 | 100 | 99 | 26 | 99 | 100 | Cis-reg; riboswitch; | Listeria snRNA rli56 |
| rli59 | RF01484 | 5 | 181 | 96 | 25 | 180 | 98 | Gene; snRNA; | Listeria snRNA rli59 |
| rli61 | RF01485 | 4 | 106 | 99 | 26 | 103 | 98 | Cis-reg; riboswitch; | Listeria snRNA rli61 |
| rli62 | RF01486 | 2 | 172 | 98 | 5 | 172 | 99 | Cis-reg; riboswitch; | Listeria snRNA rli62 |
| rliI | RF01487 | 5 | 239 | 98 | 30 | 230 | 84 | Gene; snRNA; | Listeria snRNA rliI |
| rli49 | RF01488 | 5 | 163 | 94 | 38 | 157 | 78 | Gene; snRNA; | Listeria snRNA rli49 |
| sbrA | RF01489 | 6 | 70 | 92 | 31 | 70 | 93 | Gene; snRNA; | Listeria snRNA sbrA |
| rli51 | RF01490 | 9 | 120 | 92 | 323 | 120 | 98 | Cis-reg; | Listeria snRNA rli51 |
| rli54 | RF01491 | 5 | 528 | 95 | 26 | 522 | 97 | Cis-reg; riboswitch; | Listeria snRNA rli54 |
| rli28 | RF01492 | 22 | 183 | 54 | 332 | 182 | 50 | Gene; snRNA; | Listeria snRNA rli28 |
| rli37 | RF01493 | 4 | 246 | 96 | 26 | 251 | 92 | Gene; snRNA; | Listeria snRNA rli37 |
| rliD | RF01494 | 9 | 327 | 97 | 45 | 273 | 73 | Gene; sRNA; | Listeria sRNA rliD |