Table 1. Characterization of a subset of novel medaka miRNAs predominantly expressed in the ovary.
| miRNA | QPCR heterologous | Locus | Sequence | Location | Folding | QPCR homologous | miRNA origins |
|---|---|---|---|---|---|---|---|
| miR-6352-5p | + | 1 | CAGGGAACAGGACCCCAGCT | 9:31095668–31095687 | + | + | miRtron/ENSORLG00000017404 |
| 2 | AACTGGGAAAAGGACCCCAG | 3:26171679–26171698 | − | + | miRtron/myo5aa | ||
| 3 | TTTGGGAAAAAGATCCCAGCT | 1:31427215–31427235 | − | − | NC | ||
| 4 | AAATGGGAAAAGCACCCCAG | 20:10904125–10904144 | − | − | NC | ||
| miR-4785–3p | + | 1 | GAGTCTGCGTCGCCGCCAGC | 16:16874299–16874318 | + | + | miR/rasip |
| 2 | TGATCTCGGAGACGCCGCCAGC | scaffold983:45388–45409 | + | + | miR | ||
| 3 | CGAGTCGGCGATGCCGCCGCC | 9:761851–761871 | − | − | NC | ||
| miR-878–3p | + | 1 | GCATGACAACATACTGGGTA | 12:12844102–12844121 | − | + | miR |
| 2 | GCATGAAACCATACTGGGTC | 13:25685522–25685541 | − | − | NC | ||
| miR-1288-3p | + | 1 | TGGACTGTCCTGATGTGGAGA | 6:5567815–5567835 | − | − | NC |
| 2 | TGGACAGCCCTGATGTGGAG | 1:27438143–27438162 | + | + | miR | ||
| miR-4653-3p | + | 1 | GAGTTAAGGGTAGTTTGGAGA | 18:4398355–4398375 | − | + | miR |
| 2 | CTCTGTTAAGGGTTGCCTGGA | ultracontig49:380302–380322 | − | − | NC | ||
| 3 | AGAAAGTTGAGGGTTGCTTGG | 21:27820909–27820929 | − | − | NC | ||
| miR-729–3p | + | 1 | CATGGGTATGAAACGACCCGGGT | 20:6728838–6728860 | − | − | NC |
| 2 | CATGGGTATGATACGACCTCA | scaffold1021:47363–47383 | + | + | miR | ||
| 3 | GGTATGATTCGGCCTGGGTT | 15:3091445–3091464 | − | − | NC | ||
| miR-487b-3p | + | 1 | CGGCGTACAGGGTCATCCAC | 22:3962447–3962466 | − | − | NC |
| 2 | GTCCCCTACAAGGTCATCCACTT | 10:7430304–7430326 | − | + | miRtron/mrpl11 | ||
| miR-202-3p | + | AGAGGCATAAGGCATGGGAA | 15:1382691–1382710 | + | + | miR | |
| miR-743a-3p | − | 1 | GAAAGACGCCAAAGTGGGT | 2:28436804–28436822 | − | + | miR |
| 2 | GAAAGTCGCCAAACTGGGT | 18:15585090–15585108 | − | + | miR | ||
| miR-1305-3p | − | 1 | TTTTCAACTCTATTGGGAAA | 12:19213569–19213588 | − | − | NC |
| 2 | ATGTTCAACTCTAATGTGAGA | 24:18349479–18349499 | − | − | NC | ||
| 3 | TTTTCACCTCTAATGGGATAG | 16:14807294–14807314 | + | − | miRtron/fam171a1 | ||
| miR-4716-3p | − | CTGGGGGAAGCAAACATGGAGA | 7:23549695–23549716 | + | − | miR | |
| miR-6131-3p | − | 1 | CGCTGATCAGATGGGAGTCG | 15:2799945–2799964 | − | − | NC |
| 2 | ACTGGTGAGATGGGAGTGGC | 12:21774089–21774108 | + | − | miR | ||
| miR-10d-3p | − | TACCCTGTAGAACCGAATGTGT | 15:4353766–4353787 | + | − | miR | |
| miR-6717-5p | − | 1 | GGCGATGGGGGGATGCAGAGA | 19:8376541–8376561 | + | − | miRtron/shank1 |
| 2 | AAAGATGTGGGGATGTGGAGA | scaffold1101:27027–27047 | − | − | NC | ||
| miR-345-3p | − | 1 | CCCTGAACTCGGGGTATGGA | 16:8875414–8875433 | − | − | NC |
| 2 | CTGAACTAGGGTTCAGGAGA | 16:14238722–14238741 | − | − | NC | ||
| miR-697-3p | − | 1 | AGCATCCTGTTCCTGTGGAG | scaffold5397:869–888 | − | − | NC |
| 2 | ACATCCTGGACCTGTGGA | scaffold692:99305–99322 | − | − | NC | ||
| miR-3198-3p | − | 1 | GTGGAGTCCTGAGGACTGGAG | 5:11964002–11964022 | − | − | NC |
| 2 | GTGGAGTCCTGCAGAATGGAG | 19:5590938–5590958 | − | − | NC | ||
| miR-4713-3p | − | 1 | TGGGATCCAGACAGAGGGAGAA | 15:20189222–20189243 | − | − | NC |
| 2 | TGGGATGCAGAAAGTGGGAGAA | 17:30648359–30648380 | − | − | NC | ||
| 3 | AAAGATCCAGACAGTTGGAGA | scaffold693:106481–106501 | − | − | NC | ||
| miR-5581-5p | − | 1 | AGCCTTCCAGGAAAAATGGAG | scaffold4519:2360–2380 | − | − | NC |
| 2 | AGCCTTCCAGGAAAAATGGACA | scaffold5870:432–453 | − | − | NC | ||
| miR-892b-3p | − | 1 | ACTGGGTCCTTTCTGTGTAGA | 3:12292877–12292897 | − | − | NC |
| 2 | CACTGGCTCTTTTCTGGGAA | 23:15587446–15587465 | − | − | NC |
Eight miRNAs displayed an ovarian-predominant expression profile when using heterologous and homologous QPCR primers. In addition, in silico folding predictions allowed characterizing 13 loci that encode 11 different miRNAs. +, successful QPCR or hairpin structure prediction. NC, not confirmed.