Table 2 Porcine miRNAs with hairpin forming precursors and genomic locations.
From: Deciphering the porcine intestinal microRNA transcriptome
conserved miRBase 14.0 | internal ID | mature sequence | precursor sequence | mfe (kcal/mol) | gen. location | subject ID | start | end |
|---|---|---|---|---|---|---|---|---|
Genomic duplications | ||||||||
ssc-miR-194 | MDM9 | UGUAACAGCGACUCCAUGUGGAC | UGUAACAGCGACUCCAUGUGGACUGUGCCCCAAUUUCCAGUGGAGAUGCUGUUACCUU | -37.4 | X | emb|FP565626.1| | 43462 | 43519 |
| Â | Â | Â | Â | Â | 10 | emb|CU466937.2| | 6280 | 6223 |
ssc-miR-365-1 | MDM48 | UAAUGCCCCUAAAAAUCCUUAU | GAGGGACUUUUGGGGGCAGAUGCGUUUCCAUUCCACUAUCAUAAUGCCCCUAAAAAUCCUUAU | -33.8 | 3 | emb|CU896561.2| | 167752 | 167814 |
ssc-miR-365-2 | MDM45 | UAAUGCCCCUAAAAAUCCUUAU | GAGGGACUUUCAGGGGCAGCUGUGUUUUCUGACUCAGUCAUAAUGCCCCUAAAAAUCCUUAU | -35 | 12 | emb|FP016089.2| | 194688 | 194749 |
| Â | MDM123 | AAACGAUGAUGGAAGGUGCUGAGGA | CUCUCUGGUCCCUUCUCUCCCCUCUUCAUGGUUGACAGCAACCCCAGAAACGAUGAUGGAAGGUGCUGAGGA | -35.4 | 2 | emb|CU896534.2| | 31001 | 30933 |
| Â | MDM266 | AAACGAUGAUGGAAGGUGCUGAGGA | AAACGAUGAUGGAAGGUGCUGAGGAAGGGGUGCUAAUGUCCUAGCGUUUCCUCCUUCCAUUGUUAGGAGGC | -32.7 | ND | ND | ND | ND |
| Â | MDM208 | UCUGGCUGUGGUGUAGGCCGU | GGAUCUGCGCAUUGCCGCGAGCUGCAGUGUAGGUCACAGAUGUGGCUCAGAUCCAGCAUUGCUCUGGCUGUGGUGUAGGCCGU | -40.3 | 16 | emb|CU571054.2| | 59166 | 59247 |
| Â | MDM116 | UCUGGCUGUGGUGUAGGCCGUC | AGGUCACAAACACGGCUCAGAUCUGAUGUUGCUCUGGCUGUGGUGUAGGCCGUC | -41 | 13 | emb|CU582976.2| | 156369 | 156318 |
mmu-miR-1896 | MDM214 | AUGGGUGAGGAGUGUUGUGUAUAUA | AUGGGUGAGGAGUGUUGUGUAUAUAUAUUUGUGUGUUUGUAUAUACACAUCUCAAAGCUUAUUU | -27.2 | 6 | emb|FP236156.2| | 77046 | 76983 |
| Â | Â | Â | Â | Â | 16 | emb|FP085480.3| | 108843 | 108906 |
hsa-miR-1977 | MDM262 | GACUUGGAAUUAGUAGGGUGCUUA | GACUUGGAAUUAGUAGGGUGCUUAGAACAGUGCCUGAUACAUAGUUUCACAA | -26.2 | 4 | emb|FP236645.1| | 179755 | 179704 |
| Â | Â | Â | Â | Â | 14 | emb|CT737346.2| | 42310 | 42361 |
| Â | MDM284 | GCCGCGGCGUCCGGGCUG | GCCGCGGCGUCCGGGCUGUGUCCGCCCUGGCGGGCGCGCGGGGGCGGGAAGGCGCGGGCUGUCAAGGGCGCUGCGGCAG | -61 | X | emb|CU466457.2| | 83369 | 83334 |
| Â | Â | Â | Â | Â | 13 | emb|CU582896.2| | 20953 | 20988 |
Genomic clusterings | ||||||||
ssc-miR-215 | MDM1 | UGACCUAUGAAUUGACAGACA | UGACCUAUGAAUUGACAGACAAUGUGGCUAAAUCUGUCUGUCAUUUCUGUAGGCCAAU | -29.8 | X & 10 | emb|FP565626.1| | 43758 | 43815 |
ssc-miR-194 | MDM9 | UGUAACAGCGACUCCAUGUGGAC | UGUAACAGCGACUCCAUGUGGACUGUGCCCCAAUUUCCAGUGGAGAUGCUGUUACCUU | -37.4 | X & 10 | emb|FP565626.1| | 43462 | 43519 |
ssc-miR-421 | MDM86 | AUCAACAGACAUUAAUUGGGCGC | CCUCAUUAAAUGUUUGUUGAAUGAAAAAAUGAAUCAUCAACAGACAUUAAUUGGGCGC | -35.8 | Â | Â | Â | Â |
ssc-miR-374a | MDM23 | UUAUAAUACAACCUGAUAAGUG | UUAUAAUACAACCUGAUAAGUGUUACAGCACUUAUCAGGUUGUAUUGUAAUU | -41.2 | Â | Â | Â | Â |
bta-miR-2316 | MDM279 | CGGCCGGAGCCUGGACUGCUGC | GGCGCUAGGGAGCCAGGCCGGGGAGGACAGCUGCAGCCAGCCUGUCCUCCCGUCCGGCCGGAGCCUGGACUGCUGC | -63.5 | 15 | emb|CU914511.2| | 63040 | 62965 |
| Â | MDM371 | CGCGGGUGGGAAUGGGAAGG | CCCCCACCCCCGCCCCGGCUGACGCAAGAACCUGGCGGGCCGCGGGUGGGAAUGGGAAGG | -49.5 | 15 | emb|CU914511.2| | 63388 | 63431 |
Alternatively predicted precursors | ||||||||
| Â | MDM62 | UGUGUCUGUGGCCUAGGCUGGCAG | UGUGUCUGUGGCCUAGGCUGGCAGGCAGCUGCAGCUCCAGUUCAACCCCUAGCCUGGGAACUUCCAUAUGCUCAGG | -36.4 | 9 | emb|CU915614.1| | 87273 | 87348 |
| Â | MDM109 | UGUGUCUGUGGCCUAGGCUGGCAG | GAGACAUGGUGUAGGUUGCAGACGUGGCUCAGAUCUGGCAUUGCUGUGUCUGUGGCCUAGGCUGGCAG | -46.9 | 9 | emb|CU915614.1| | 87229 | 87296 |
| Â | MDM128 | GCCGGAGCUGGAGGUGGG | GCCGGAGCUGGAGGUGGGCGAGGCCGCGGCACCCCCUCCGCUGCCGCCGCCGAGGGCCGCCUCCCUGGCCUCGGUGC | -52.7 | 17 | emb|FP325255.2| | 141939 | 141863 |
| Â | MDM129 | GCCGGAGCUGGAGGUGGG | CCUCUUCAGCGAGCGCGGCCGCUCCGUGCCCCUCGAGGAGCUGCCGGAGCUGGAGGUGGG | -50.4 | 17 | emb|FP325255.2| | 141981 | 141922 |
| Â | MDM196 | AGAGGUUCGGCUGUGCGGGCA | CUCCGCGGCGCUCGGAUAUCUGGCAGACCCGGGCGCGGGGAGGCUAGAGGUUCGGCUGUGCGGGCA | -50.6 | 3 | emb|FP475960.2| | 151377 | 151312 |
| Â | MDM382 | AGAGGUUCGGCUGUGCGGGCA | AGAGGUUCGGCUGUGCGGGCACUGCGCUCCGGGGACGGCCGCUGCACCUGC | -29.2 | 3 | emb|FP475960.2| | 151332 | 151282 |
mmu-miR-2145 | MDM238 | AUCAGGGUCGGGCCUGG | AGUGCCACCCUGAAUGCACCCGAUCUCAUCUGAUCUUGGAGGCUAAUCAGGGUCGGGCCUGG | -34.8 | 2 | emb|CU929491.4| | 132342 | 132283 |
mmu-miR-2145 | MDM392 | AUCAGGGUCGGGCCUGG | AUCAGGGUCGGGCCUGGUACUUGGUAGGGAGACAUGAGAUUUGGACCCAGAUCUGAUUA | -28.8 | 2 | emb|CU929491.4| | 132299 | 132241 |