miRTarBase - #MIRT584738


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pre-miRNA Information
pre-miRNA mmu-mir-3057   
Genomic Coordinates chr10: 81271597 - 81271687
Description Mus musculus miR-3057 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3057-5p
Sequence 14| AUUGGAGCUGAGAUUCUGCGGGAU |37
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Atp2b2   
Synonyms D6Abb2e, Gena300, PMCA2, Tmy, dfw, jog, wms, wri
Description ATPase, Ca++ transporting, plasma membrane 2
Transcript NM_001036684   
Other Transcripts NM_009723   
Expression
Putative miRNA Targets on Atp2b2
3'UTR of Atp2b2
(miRNA target sites are highlighted)		 
>Atp2b2|NM_001036684|3'UTR
   1 CTGAGGCCCCTGTCGCCTGGCCACGCTCATGGACCCGCCGCCACCCGCCTCCAGGCGCACACCCTTCCAGGCACCAACTC
  81 CCCGACACAGCAAGGAGCACTGGGCGGAACCCACACAGCAGAGAGGGAACCAGACCTTTCTCTGGCAGCCATGCTGTTTG
 161 AACTCTTTTTCACTCCTTAGGCCTTGGGCGGGGTTGCCCTGGGGTCATCTGGAGCAGAGAGTGGCGTGGATTTTTTTTTC
 241 TCCAAAACATAAAAAATAATAATAACGAATTAATTAAAAAAAAAAAGAGCCTTTCCAGGCTCCAGCCCAGACACGGACCA
 321 GCCATGCACCCGCCGGCCACCGTGGCCCCAGCATGAATGTACCTGGACACTATTAATCCCCTCCCTCATTTGGTTCTTGG
 401 AGGGCTAGGGAGGGGAGTTTTTTGTTTGTTTCCTTAGGCGGGAACTGCAAACAGGAACTGGAACAGAGACTACTGTTCGT
 481 TCAGTCCACTGGTCTATGAGGTTTCAAATGCTTGCCCAGCATGGTCTCAAATGTCTAGATTAATTTAATAACTTTTTGAA
 561 ATCACAGAGTAGGTTTGCACCAATGAAACCCAAGAACTCCACAGACACTCACGAGGTTATATCCGTTTCTTTGTATCTAT
 641 ATCAACGTATACTTCTTGAAGACTGTATACGTGCGTATAGATAAGTAGATATTATATATATATATATATACATATATATA
 721 CATGGATATATAAAGTTCCTTTGCCGGCATGTTGCCTTGTTTCTGCTTAAATTGCTCTATTTTAACTTATGTCCTAAAAG
 801 AAGAATGTAATTTGTTTACAAACCTGTAGATAATGTCTTTGGCTATTTGTGTGGTTTAAGGACACTGGTGGCCAAGATGC
 881 TTACAAACAGCTCGGGCCCAACAGACACATCCCCTGGATTGCATCCTTGAAGTTTTACGATAGCCATGCTCTGATTTTTG
 961 CCTGCTATTTCCGTTCAATAATGTCACTACTGTGGGAAGCTCAGGCAGAAAGCCAACGGCTCCCAAGGATCCACCCTGAG
1041 GAGCTAAGCAACGCGCTCGCTCACTCCACCGTAGACAAGGGAGAAGAGGAGAGAAGGCTTCCTGGGTTTGCAACACGGCC
1121 GTCCAGGTCTGGTGACGTCAACGTCTGTAGTGCACCCGGAGAAGGAAGACTTTTCTCTCAATGAAACTCGCTTGAGTTTA
1201 CAGAGAGCATTTCAGAACTGAGTTGTCTTTGGCACTGTCTGTGAGTCAAGGTAGTGTTCAGATATTACAAATGCTATTGT
1281 GTTGAATTTTTTTTTTTTTTTAGTTAGTAATTTAGAAGTTTCTTTTCTTATAAACGGCAGCATAGACACTGCTGACATAC
1361 TGGATGAGGGTTGGTACGGCTTGCTGCTTTTGTTTTTTTTTTTTTTCTTTTTGAAGAAGAATAGCCTTTTTTCTCTGCAC
1441 TATTTAGATCCGAATGAACCTTATAATGTGTACATTGAGATGTATTCAGTGTGATTTTTAAACCAAATTGTCTTCCTGTA
1521 GTTACAATATATACTGTAGCCTTTTAACAGCAAGTCCTGCTTTCCCAGACAGAAAGCCATTCTGATATCTTCCCATATCA
1601 CAGGTGAGAAAAGGTGGCTATCCCCTCTCCCAACAATAACAGCACTAGTTATCCCACTTAATAAGAGCTTGTCTGTCGGC
1681 CTCTTACTGCTAAGCACTTTGTGGGTCTCAGCTTTTTTTCATAAAAGAACTTTTGTATTTAATACAAAGTTTGCTTTGAG
1761 ACTTTTCAGCATACAATCTTTTTCCATAAACTTGTACAGTGCAAAAGACATTTTGAATACCATGACCGATGATGTCCCGT
1841 GCTTCGAGGAAATCAAACACTTTCCGCCTCACTTGTGAACTCCATCCTTCACTCTCTCCCTCCTCACAATCGCTCCTCCT
1921 CGCTCTTCAGCCTGGCCCCCCAGCCCTCCTCCAGGCCCAGAGACCTCTTCACTAAACAAGATGACAGCCACTTGGGAAAA
2001 GAGCCATAGTCAGCTGGGAGGGCCCACGTCTGGATGGCTGTGAAAAACTTGAGTTCTTGGTTTGGGCTTCAAAGTCTGCC
2081 CATCCCACCTGGCCATAATCTTTCTATAAGGAAGAATATCTCTGAAGGATTCTGATTGTATCCAGGAGAGAGAGAGAGCT
2161 ACCTCTCCAGCAGGTGGACCAGCCCTAGATGTACTCACTGGATTCCAGTACAGACACCACCAGAGCCAGTCCATAGTACC
2241 CCTCCAAGGGAGGGAAGGAAACCCGGGGCTGCCTTGGAACAGGATAGGTTTTTGGTTTGGTTTTGTTGTTGTTGTTGTTG
2321 TTGTTGCTGCTGCTGCTGTTGTTGTTTGATTGGTTTGGGACTTTTGGTGGGGAGTCCTTTGTCACATTTTTCATCCTGCC
2401 CTCCTTCATTCAACCATGCATCTATGACCTCATTCCATGCCACCAGGGTTCTTGCTCTTAACAAACCGGGGTCCTCGGGC
2481 TTTGGAACCAGGCCTCCAGGGCAAAGAGGAAGGGGTTCTCTGAGCAGAGCCAGGTTCTCAGACAGGAGCAGAGGAAACTA
2561 GCAAGGAGGCCTGACATTAGTGCTGGCTTCCCGGTGTCAGGAATGAGAGATAGCCTATGCCCCAGCCCCTCACTCTCACA
2641 CTCTTCCATACACACACACACCTACACAGGAGATGGTTGGTTTGTCAGAACTCACTGTAATACACAAGCTTGCACTTCTG
2721 CGTCCTATATCTAGCAGCATGGGATACGTTTGGCAGTTCACCCCATTAGGGGGTCAATAATTTATGACCATTCATCTGTT
2801 TTTATGAATTTTTTTATCTAGACAATAATTGTAAATAAAGAATTCACCGTCTCTGCTCATTTAATACTATGCAATGGTTA
2881 TGTTTTCCATGGCTGGCTCTTCTGGCTCACATAGGTGTTTCTGATGTGTCTATGGTATTTAAAAAAAAATCAAGCAGAAA
2961 TAGGAAATCTCTACTCTTTTCTAGCGTGGCCCCCACCCCCTTCTTTCCTGTCCTCTGCATTCTGTAAGTGCATCAATCCC
3041 CTAGCCTGTCAGATAACTGAGAAAACACAGGTGAGCATCCAGCAGGGGACCTGAACTTTGGCTCTGGCTACTTCAGAGTC
3121 ACCCATCTGTGGAGGGATAGGGAGAGGCTCAACTTGCTGCTCCCAGCTATCCAGGATTGAGGAGCAGCCTCCATGTCTCC
3201 ACCCACCCATGCTCTCCTATCCTCAACCCAACCACAGCAGAGCTGACTGGAGGGAGGTGCCCTATTTCTGAGAGTGGATG
3281 TGGCACTGGCTGCTCCCAAGCCAGAGCCCATCCTATCCTGGGTCCTCTGGTTAATAAAGAACCACTGTGTCCCCATGCCT
3361 GTTGAAAAGCCACCTTTGCCTTCTCCTAATTTTTTACACAGACTTCAGTCCAACTCTAGAATTTCTCTTTCACTCCCTTA
3441 TCTGGCACCAACCACATGTTCTAATTACTGTCCCTCTCAAACATGTTAGTGTACGGCAGGGGAGTAAGTCCCCCTCCCTG
3521 TTCACAAGATTTCCCCACCCCACCCCCATCTGTTCTTCTGAAGAAATACTAAGTTTTGCCAGATCCTCCAACCTTCTCTT
3601 ACTCCAGACTCTGGGCCCTGTTGCTGTGTGTGCCACCCCCACCCCCATTGTAATCACTGTCCACTGAGATCCTCTATGTG
3681 CAGAATGTCCTATGAGAACAGACAAAGCAACACCTGAATTCTGAGAAGCTATCAACTTACTTGTCCCCTAAGCCCCGGAA
3761 TTGTCGAGAGAGACCACCAAGCCCCACCTAACAAGTCATCGCCTGTGGTTGTCCCAGAGCAAGCCCCCATATGCTCCTTG
3841 TCTGGATGGGAAAGGAAGACCTCTCCCAGGCCCAGTACTTGGACAGAACATTCCGACTCATCAGACCCACACAACAGAGG
3921 GACAGAGGGACAGTGGGACAGAGGGACGTTTTCTGTCTGCCTTTTCTAAACTGGCTTTTGGTCATTTTATTTGGGTTACT
4001 GGGAGTCATCTCTTATTCAGAGTTTTAACACCTTTGGGATACAAGAATGTCTTGCCTGGATGTCGTTGCACCCTTGATGT
4081 AGCTATAGGAGGTTGCCAACTGAACCACACACTGACAAGCTTTCCACCCAACACACTGACAGTTTTCCACCTGAGGCCCC
4161 ACCCTTGGAGAACCCTAGGAGTGAGGATTCTTCTAGAAGCACCAAGGCCACACTCAGACCCTAAAAGTTCCCATGTGTTT
4241 TCCAAGGTCCAAATGAAGCCCTCTGATTTAATATAGAGATCCGACCCACCCAAGGCATGGGACCCCAGGCCCTGGGTAGC
4321 TGCCATCATCCCCTGCTCCCAAAAACAAAAGGTTTGAGGCTGCTTGGGCCCTTCCAGGCCCTTGGTCTGTTTTGTAACGT
4401 CTGTGGTGCTCTCCCTCCAGGGCCCCTCCTCTCGGGGGGTCACCACACTCTGCTATCTCTCGTGTGCACATCTTTTATAA
4481 CGGAGTAGCGAGGGAATGGTGCCGCCTCCAGCTTCCATAAGCTGCCTGGGCTCTGGGGGGCTCTGGGACAATCGGGGCTG
4561 GGAAGTGACTGTGCTCTTATTGTACACTCTTTATTTCTCTGTATCTCTGGCTTGTGCTCTTTGTAACTAACAGGATTTGT
4641 CTGCCTTTTCAACACTATACTAAGCAATAACAATAAATGCACACATGGAAACGCAGGCATGGTAAAAAAAAAAAAAAAAA
4721 A
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1 
miRNA  3' uagggcgUCUU--AGAG--UCGAGGUUa 5'
                 |||:  |:||  :||||||: 
Target 5' aaaaaaaAGAGCCTTTCCAGGCTCCAGc 3'
 279 - 306 137.00 -13.40
2 
miRNA  3' uagggcgucUUAGAGUCGAGGUUa 5'
                   ::|:| :|||:||| 
Target 5' tgagttcttGGTTTGGGCTTCAAa 3'
 2050 - 2073 135.00 -11.80
3 
miRNA  3' uaGGG--CGUCUUAGAGU---CGAGGUUa 5'
            |:|  ||||||   ||   ||||| | 
Target 5' agCTCAGGCAGAAAGCCAACGGCTCCCAa 3'
 998 - 1026 128.00 -16.80
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions C2C12
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1385343. RNA binding protein: 聽AGO2. Condition:C2C12_DM_Ago2_CLIP-Seq_myotubes ...

- Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uagggcgucuuagagucGAGGUUa 5'
                           |||||| 
Target 5' -----ggauuuuuuuuuCUCCAAa 3'
 		1 - 19
Article - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al.
- Cell, 2014
MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.
LinkOut: [PMID: 25083871]
CLIP-seq Support 1 for dataset GSM1385343
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_DM_Ago2_CLIP-Seq_myotubes
Location of target site NM_009723 | 3UTR | GGAUUUUUUUUUCUCCAAAACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
14 mmu-miR-3057-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT580946 Slc25a46 solute carrier family 25, member 46 2 2
MIRT581084 Serpinb5 serine (or cysteine) peptidase inhibitor, clade B, member 5 2 2
MIRT584738 Atp2b2 ATPase, Ca++ transporting, plasma membrane 2 2 2
MIRT591856 Iffo2 intermediate filament family orphan 2 2 2
MIRT593687 Sco1 SCO1 cytochrome c oxidase assembly protein 2 2
MIRT593742 Pld5 phospholipase D family, member 5 2 2
MIRT593830 Klhl31 kelch-like 31 2 2
MIRT593961 Col4a1 collagen, type IV, alpha 1 2 2
MIRT594311 Nr3c1 nuclear receptor subfamily 3, group C, member 1 2 2
MIRT595177 Zfp953 zinc finger protein 953 2 2
MIRT598903 Gla galactosidase, alpha 2 2
MIRT603414 Samd7 sterile alpha motif domain containing 7 2 2
MIRT603667 Opa3 optic atrophy 3 2 2
MIRT606751 Tns4 tensin 4 2 2

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