Table 2.
Zebrafish novel miRNA and their characteristics.
| Tissue type | Chromosome | Novel miRNA | Sequence | MiRNA length (nt) | Read count | Precursor position | Strand | Precursor length | % GC | MFEI (− kcal/mol) |
|---|---|---|---|---|---|---|---|---|---|---|
| Brain | Chr 1 | Dre-mir-nov49 | AGAGGCUGUCCGAGUGCUGAU | 21 | 156 | 10303253–10303335 | + | 83 | 49.4 | − 1.56 |
| Chr 20 | Dre-mir-nov8 | GACCUGUAACCAUUGACUUCCU | 22 | 102 | 962031–962117 | + | 87 | 36.78 | − 1.4 | |
| Chr 3 | Dre-mir-nov46 | AAAAGCGUACCAAACUGAACCGU | 23 | 122 | 46496327–46496412 | + | 86 | 48.84 | − 1.3 | |
| Chr 17 | Dre-mir-nov19 | AGACUAGUAGCCAUUGAGAUCUU | 23 | 264 | 20769194–20769271 | − | 78 | 33.33 | − 1.27 | |
| Chr 18 | Dre-mir-nov16 | UGUUUUUUUAGGUUUUGAUUUUU | 23 | 1142 | 45964887–45964967 | + | 81 | 33.33 | − 1.26 | |
| Chr 4 | Dre-mir-nov38 | GAAUAACUCAAACCGGAGGACU | 22 | 106 | 31535442–31535523 | + | 82 | 47.56 | − 1.26 | |
| Chr 4 | Dre-mir-nov42 | AAUAACUCAAACCAGAGGACU | 21 | 126 | 54513045–54513126 | + | 82 | 43.9 | − 1.19 | |
| Chr 18 | Dre-mir-nov15 | UUUCCAGAAAGGUCUGUAUGUGU | 23 | 130 | 26647915–26647993 | + | 79 | 46.84 | − 1.16 | |
| GRCZ10_NA262 | Dre-mir-nov2 | AGACUCUCCAGUACACUGGCCCU | 23 | 862 | 744–825 | − | 82 | 58.54 | − 1.16 | |
| Chr 10 | Dre-mir-nov25 | GAAAACCUGUAACCAUUGACUUCU | 24 | 221 | 29746032–29746122 | + | 91 | 35.16 | − 1.14 | |
| Chr 20 | Dre-mir-nov10 | AAACUUGUAAUCACUGACUUCCU | 23 | 125 | 35014623–35014703 | + | 81 | 33.33 | − 1.12 | |
| Chr 2 | Dre-mir-nov48 | AAUGACUCAAACCCAAGGACUCG | 23 | 1182 | 8746947–8747032 | + | 86 | 40.7 | − 1.1 | |
| Chr 6 | Dre-mir-nov29 | AAACUCUGCAGGACACCAGCUGU | 23 | 268 | 18113026–18113108 | + | 83 | 46.99 | − 1.05 | |
| Chr 17 | Dre-mir-nov18 | AAACUCUGCAGGACACCAGCUG | 22 | 748 | 47039884–47039964 | + | 81 | 46.91 | − 1.02 | |
| Chr 4 | Dre-mir-nov39 | UAAACUCUGCAGGACACCAGCUG | 23 | 1020 | 42571226–42571306 | + | 81 | 46.91 | − 1.02 | |
| Chr 6 | Dre-mir-nov30 | ACUGUACAGACUACUGCCUUGC | 22 | 361 | 41457248–41457346 | + | 99 | 45.45 | − 0.98 | |
| Chr 18 | Dre-mir-nov17 | ACUCUUCACUCGUCUGUGUUCA | 22 | 116 | 50849750–50849835 | − | 86 | 55.81 | − 0.96 | |
| Chr 23 | Dre-mir-nov3 | UCAAAAGGCGUACCAAACUGUAC | 23 | 155 | 18099730–18099807 | − | 78 | 43.59 | − 0.95 | |
| Chr 5 | Dre-mir-nov37 | UCCAUCAGUCACGUGACCUACCA | 23 | 7106 | 35345784–35345875 | − | 92 | 51.09 | − 0.94 | |
| Chr 5 | Dre-mir-nov33 | GGCCCGUCCGGUGCGCUCGGAUCC | 24 | 767 | 824650–824740 | − | 91 | 84.62 | − 0.93 | |
| Chr 5 | Dre-mir-nov31 | UAAACUCUGCAGGACACCAGCUGU | 24 | 158 | 10220904–10221001 | + | 98 | 46.94 | − 0.93 | |
| Chr 5 | Dre-mir-nov32 | GAUGACUCAAACCCAAGGACUCA | 23 | 115 | 15221789–15221886 | + | 98 | 39.8 | − 0.89 | |
| Chr 8 | Dre-mir-nov28 | AAUGACUCAAACCCAAGGACUCGU | 24 | 108 | 2766509–2766596 | + | 88 | 44.32 | − 0.88 | |
| Chr 4 | Dre-mir-nov44 | AGUGAGGUCCUCGGAUCGGCCC | 22 | 1835 | 76320181–76320279 | + | 99 | 68.69 | − 0.87 | |
| Chr 22 | Dre-mir-nov4 | AACGACUCAAGAACCAGAAGACU | 23 | 315 | 18571986–18572067 | + | 82 | 46.34 | − 0.86 | |
| Pineal gland (dark treatment) | Chr 1 | Dre-mir-nov83 | AUCAGCACUCGGACAGCCUCUU | 22 | 173 | 10303251–10303335 | + | 85 | 50.59 | − 1.53 |
| Chr 17 | Dre-mir-nov59 | AGACUAGUAGCCAUUGAGAUCUU | 23 | 101 | 20769194–20769271 | − | 78 | 33.33 | − 1.27 | |
| Chr 18 | Dre-mir-nov58 | UGUUUUUUUAGGUUUUGAUUUUU | 23 | 381 | 45964887–45964967 | + | 81 | 33.33 | − 1.26 | |
| Chr 9 | Dre-mir-nov66 | UACGGGCUGAAUUUAGACAAAUU | 23 | 177 | 5548615–5548705 | + | 91 | 27.47 | − 1.25 | |
| Chr 24 | Dre-mir-nov52 | UAACGUUUCGAGCCCACUGACUG | 23 | 118 | 1825424–1825498 | − | 75 | 46.67 | − 1.19 | |
| GRCZ10_NA262 | Dre-mir-nov51 | AGACUCUCCAGUACACUGGCCCUC | 24 | 997 | 743–826 | − | 84 | 58.33 | − 1.14 | |
| Chr 12 | Dre-mir-nov62 | UUUCCGGAAAGGUCUGUAUGUGC | 23 | 1654 | 44383412–44383489 | + | 78 | 47.44 | − 1.14 | |
| Chr 4 | Dre-mir-nov77 | GAAUAACUCAAACCGGAGGACU | 22 | 103 | 49472235–49472316 | + | 82 | 46.34 | − 1.11 | |
| Chr 6 | Dre-mir-nov72 | UACGGAUAGAAUCAGCGGAGCGA | 23 | 221 | 56909252–56909333 | + | 82 | 60.98 | − 1.11 | |
| Chr 8 | Dre-mir-nov70 | AACCUGUAACCAUUGACUUCCU | 22 | 140 | 10454696–10454780 | + | 85 | 38.82 | − 1.04 | |
| Chr 1 | Dre-mir-nov84 | UAAAGCGUACCAAACUGAACCGU | 23 | 150 | 41154258–41154343 | + | 86 | 46.51 | − 1.00 | |
| Chr 11 | Dre-mir-nov63 | GCUGAAGUCAUUAUUAUUAGGGC | 23 | 116 | 5486604–5486685 | + | 82 | 35.37 | − 0.98 | |
| Chr 6 | Dre-mir-nov71 | ACUGUACAGACUACUGCCUUGC | 22 | 220 | 41457248–41457346 | + | 99 | 45.45 | − 0.98 | |
| Chr 4 | Dre-mir-nov76 | GCAGAGAGAAAUGUCUAUGGCUU | 23 | 1712 | 5403781–5403855 | + | 75 | 48.00 | − 0.97 | |
| Chr 5 | Dre-mir-nov74 | UCCAUCAGUCACGUGACCUACCA | 23 | 15,880 | 35345784–35345875 | − | 92 | 51.09 | − 0.94 | |
| Chr 20 | Dre-mir-nov54 | CUCAUCCCUCUGCUCUAUCCCCU | 23 | 115 | 37928243–37928325 | + | 83 | 50.60 | − 0.93 | |
| Chr 8 | Dre-mir-nov69 | AAUGACUCAAACCCAAGGACUCG | 23 | 224 | 2766510–2766595 | + | 86 | 44.19 | − 0.90 | |
| Chr 12 | Dre-mir-nov61 | AACGACUCAAGAGCCAGAAGACU | 23 | 323 | 3216161–3216240 | + | 80 | 45.00 | − 0.88 | |
| Chr 20 | Dre-mir-nov55 | CAGGGGGUCGGGAAGCACUGCCU | 23 | 4876 | 48676465–48676553 | − | 89 | 58.43 | − 0.85 | |
| Pineal gland (light treatment) | Chr 1 | Dre-mir-nov100 | AUCAGCACUCGGACAGCCUCUU | 22 | 100 | 10303251–10303335 | + | 85 | 50.59 | − 1.53 |
| Chr 9 | Dre-mir-nov91 | UACGGGCUGAAUUUAGACAAAUU | 23 | 101 | 5548615–5548705 | + | 91 | 27.47 | − 1.25 | |
| GRCZ10_NA262 | Dre-mir-nov85 | AGACUCUCCAGUACACUGGCCCUC | 24 | 491 | 743–826 | − | 84 | 58.33 | − 1.14 | |
| Chr 12 | Dre-mir-nov89 | UUUCCGGAAAGGUCUGUAUGUGC | 23 | 1075 | 44383412–44383489 | + | 78 | 47.44 | − 1.14 | |
| Chr 6 | Dre-mir-nov94 | UACGGAUAGAAUCAGCGGAGCGA | 23 | 130 | 56909252–56909333 | + | 82 | 60.98 | − 1.11 | |
| Chr 4 | Dre-mir-nov97 | GCAGAGAGAAAUGUCUAUGGCUU | 23 | 903 | 5403781–5403855 | + | 75 | 48.00 | − 0.97 | |
| Chr 5 | Dre-mir-nov95 | UCCAUCAGUCACGUGACCUACCA | 23 | 8256 | 35345784–35345875 | − | 92 | 51.09 | − 0.94 | |
| Chr 4 | Dre-mir-nov99 | AGUGAGGUCCUCGGAUCGGCCCC | 23 | 144 | 76320181–76320279 | + | 99 | 68.69 | − 0.87 | |
| Chr 20 | Dre-mir-nov88 | CAGGGGGUCGGGAAGCACUGCCU | 23 | 2104 | 48676465–48676553 | − | 89 | 58.43 | − 0.85 |