Table 2 |
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Porcine miRNAs with hairpin forming precursors and genomic locations. |
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|
conserved miRBase 14.0 |
internal ID |
mature sequence |
precursor sequence |
mfe (kcal/mol) |
gen. location |
subject ID |
start |
end |
|
|
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|
Genomic duplications |
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|
ssc-miR-194 |
MDM9 |
UGUAACAGCGACUCCAUGUGGAC |
UGUAACAGCGACUCCAUGUGGACUGUGCCCCAAUUUCCAGUGGAGAUGCUGUUACCUU |
-37.4 |
X |
emb|FP565626.1| |
43462 |
43519 |
|
10 |
emb|CU466937.2| |
6280 |
6223 |
|||||
|
|
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|
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 |
|
|
||||||||
|
MDM123 |
AAACGAUGAUGGAAGGUGCUGAGGA |
CUCUCUGGUCCCUUCUCUCCCCUCUUCAUGGUUGACAGCAACCCCAGAAACGAUGAUGGAAGGUGCUGAGGA |
-35.4 |
2 |
emb|CU896534.2| |
31001 |
30933 |
|
|
MDM266 |
AAACGAUGAUGGAAGGUGCUGAGGA |
AAACGAUGAUGGAAGGUGCUGAGGAAGGGGUGCUAAUGUCCUAGCGUUUCCUCCUUCCAUUGUUAGGAGGC |
-32.7 |
ND |
ND |
ND |
ND |
|
|
|
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|
MDM208 |
UCUGGCUGUGGUGUAGGCCGU |
GGAUCUGCGCAUUGCCGCGAGCUGCAGUGUAGGUCACAGAUGUGGCUCAGAUCCAGCAUUGCUCUGGCUGUGGUGUAGGCCGU |
-40.3 |
16 |
emb|CU571054.2| |
59166 |
59247 |
|
|
MDM116 |
UCUGGCUGUGGUGUAGGCCGUC |
AGGUCACAAACACGGCUCAGAUCUGAUGUUGCUCUGGCUGUGGUGUAGGCCGUC |
-41 |
13 |
emb|CU582976.2| |
156369 |
156318 |
|
|
|
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|
mmu-miR-1896 |
MDM214 |
AUGGGUGAGGAGUGUUGUGUAUAUA |
AUGGGUGAGGAGUGUUGUGUAUAUAUAUUUGUGUGUUUGUAUAUACACAUCUCAAAGCUUAUUU |
-27.2 |
6 |
emb|FP236156.2| |
77046 |
76983 |
|
|
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|
16 |
emb|FP085480.3| |
108843 |
108906 |
|||||
|
|
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|
hsa-miR-1977 |
MDM262 |
GACUUGGAAUUAGUAGGGUGCUUA |
GACUUGGAAUUAGUAGGGUGCUUAGAACAGUGCCUGAUACAUAGUUUCACAA |
-26.2 |
4 |
emb|FP236645.1| |
179755 |
179704 |
|
14 |
emb|CT737346.2| |
42310 |
42361 |
|||||
|
|
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|
MDM284 |
GCCGCGGCGUCCGGGCUG |
GCCGCGGCGUCCGGGCUGUGUCCGCCCUGGCGGGCGCGCGGGGGCGGGAAGGCGCGGGCUGUCAAGGGCGCUGCGGCAG |
-61 |
X |
emb|CU466457.2| |
83369 |
83334 |
|
|
13 |
emb|CU582896.2| |
20953 |
20988 |
|||||
|
|
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|
Genomic clusterings |
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|
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 |
|
|
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|
ssc-miR-421 |
MDM86 |
AUCAACAGACAUUAAUUGGGCGC |
CCUCAUUAAAUGUUUGUUGAAUGAAAAAAUGAAUCAUCAACAGACAUUAAUUGGGCGC |
-35.8 |
||||
|
ssc-miR-374a |
MDM23 |
UUAUAAUACAACCUGAUAAGUG |
UUAUAAUACAACCUGAUAAGUGUUACAGCACUUAUCAGGUUGUAUUGUAAUU |
-41.2 |
||||
|
|
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|
bta-miR-2316 |
MDM279 |
CGGCCGGAGCCUGGACUGCUGC |
GGCGCUAGGGAGCCAGGCCGGGGAGGACAGCUGCAGCCAGCCUGUCCUCCCGUCCGGCCGGAGCCUGGACUGCUGC |
-63.5 |
15 |
emb|CU914511.2| |
63040 |
62965 |
|
MDM371 |
CGCGGGUGGGAAUGGGAAGG |
CCCCCACCCCCGCCCCGGCUGACGCAAGAACCUGGCGGGCCGCGGGUGGGAAUGGGAAGG |
-49.5 |
15 |
emb|CU914511.2| |
63388 |
63431 |
|
|
|
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|
Alternatively predicted precursors |
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|
MDM62 |
UGUGUCUGUGGCCUAGGCUGGCAG |
UGUGUCUGUGGCCUAGGCUGGCAGGCAGCUGCAGCUCCAGUUCAACCCCUAGCCUGGGAACUUCCAUAUGCUCAGG |
-36.4 |
9 |
emb|CU915614.1| |
87273 |
87348 |
|
|
MDM109 |
UGUGUCUGUGGCCUAGGCUGGCAG |
GAGACAUGGUGUAGGUUGCAGACGUGGCUCAGAUCUGGCAUUGCUGUGUCUGUGGCCUAGGCUGGCAG |
-46.9 |
9 |
emb|CU915614.1| |
87229 |
87296 |
|
|
|
||||||||
|
MDM128 |
GCCGGAGCUGGAGGUGGG |
GCCGGAGCUGGAGGUGGGCGAGGCCGCGGCACCCCCUCCGCUGCCGCCGCCGAGGGCCGCCUCCCUGGCCUCGGUGC |
-52.7 |
17 |
emb|FP325255.2| |
141939 |
141863 |
|
|
MDM129 |
GCCGGAGCUGGAGGUGGG |
CCUCUUCAGCGAGCGCGGCCGCUCCGUGCCCCUCGAGGAGCUGCCGGAGCUGGAGGUGGG |
-50.4 |
17 |
emb|FP325255.2| |
141981 |
141922 |
|
|
|
||||||||
|
MDM196 |
AGAGGUUCGGCUGUGCGGGCA |
CUCCGCGGCGCUCGGAUAUCUGGCAGACCCGGGCGCGGGGAGGCUAGAGGUUCGGCUGUGCGGGCA |
-50.6 |
3 |
emb|FP475960.2| |
151377 |
151312 |
|
|
MDM382 |
AGAGGUUCGGCUGUGCGGGCA |
AGAGGUUCGGCUGUGCGGGCACUGCGCUCCGGGGACGGCCGCUGCACCUGC |
-29.2 |
3 |
emb|FP475960.2| |
151332 |
151282 |
|
|
|
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|
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 |
|
|
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|
The chromosomal organization of selected miRNAs that were identified by miRDeep either showing valid expression in microarray experiments or being conserved was determined by blasting against the porcine HTGS database at NCBI. Identified genomic duplications, clustering and alternatively predicted precursors are shown. Abbreviation: ND, not determined |
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|
Sharbati et al. BMC Genomics 2010 11:275 doi:10.1186/1471-2164-11-275 |
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