miRTarBase - #MIRT580946


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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 Slc25a46   
Synonyms 1200007B05Rik, AI325987
Description solute carrier family 25, member 46
Transcript NM_026165   
Expression
Putative miRNA Targets on Slc25a46
3'UTR of Slc25a46
(miRNA target sites are highlighted)		 
>Slc25a46|NM_026165|3'UTR
   1 GATTTAGGTTCTATGATTGGCTGAACCAAAAGATGTTGGATAATTTGCTATGACATTTCAAGTAATAAAAGTAAAAATAC
  81 TGCGCGGAAAGAAATAGGCTGGGAATTACCACTGGTGGAAAACCTCATGCTAATTATTCTGACTTTTTATTTTTCTTAAG
 161 GCATAGATATATAGATATATAGATATATAATACTGGGTCAAACCTTTCCAAAATTGAAAACTCAATAAAGGTAATACTTT
 241 AAATTTAAAATGTAAAGTTACATTTTAGTATAACACTCATGCTGAAGTAAAATTGATCCTGGGGAGAAACAAAAAATGTA
 321 TCAAGTATAAAATGAAATTGCAATGACTTGAATCTGTTTTACTGACCTTACTATTTGTTATGTTTGTTTAACTTGGATTC
 401 AGGTCACTGTGTTAATTATTAAAGCAGTGGATAGTGCTGGGATTTTACCTTTAAGCAAATAGAGTATGTCACCGTTGAAA
 481 AGAACTGGTGATTAGCTTTGGCACTGTGTAAGCAGTGGCTGAAGGGTTTAAATTGTATTTAACCATTTTAATTGCTGTAT
 561 ATATTTATTATATGGAGCCATTTGTGTCTGTGTGTACATGTAACTTGGAATTTCCTTCTTCCCTGCCAGTTTTCATAGAC
 641 CAGCTTATTGCATCAAATGAAGGTAGACACTTTCTGCTGGAACATCAAGTATAAGACATCAAAATGCCAGAAAATAGCTT
 721 TTTTACCTGCATCCTGTCCAGCATTGCAGTGTCAGAAACTTGAAATTTGTCCTTTGCTTGTGATGTTTGGATCATCAGAT
 801 GATTTTAGCTACTTTTAAAGAGCCTAACAATCATGGCAGCCATGACCGTTTCCACACTTACGTTAAGGAGCCCCACCTGT
 881 CTTTCATTTCTCAAAGAACTTATCTGAGAGGGAACAAAATGAAAGTTCTGGGGATTTGTGCCTCTTGCTCACCATAAATA
 961 ATCACTGCAATCTTTCTTTTTTCTTTCCTTTTTTTGTATGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
1041 TGTATGTAAAGTTTTATTCTCCAAATAAGCTACCCTGAAGATAAAAATGAGACATTCTTGGTACTCTTTATTTAAACTTG
1121 CTTGGATAAGTACTGAATTAAAGTACAAACCTCATAGGAAATTTGCCCTTATGTGTTACGAAGGAGGAGGAGGAGACACT
1201 ATATTTCAACAAATGAAACTTGTTAATCAGCTTAATAAAATGAAGTTGATGTGTTCCCATGGTGGATTAGACTCTGTAAT
1281 AAAGTGATGTATAGTTCACTGGTCACTCATGCAGCAGTTAGCATTTTATTTCTTCATGGCTATGCTCAAGTTTACAAACA
1361 CTGAAGTGCAGTGCCTGCAGGTGTTGCCCAACCTAGAATGCATGCAAACTAACACTGATGTTACATGTTAAATGTTGCAG
1441 AGGGTGTTTGGACTGTGACTGATCAGAGTGGAAGCTTAATATGGTCGTGGAAAAGCATGAAGTAAGGTGTCAGTAGCAGC
1521 TGTCCCTACCAGTCTGTGTCTTTGGAGTAATGCTGTCAACTCTTCAGTTCCTCAAAAGGGAAAATAAATGCTGTTGATCA
1601 CATTCTGTATTTTATGGTTAATCTCTTAACGTGTTTTTCTCTGTGTAAAAATGGGGTTAACATTTTTTACTGACTTTTAG
1681 CTGCTAAATTTTTAGGTGTTTATAGTCACCTTCCTCAGAATTTCATTTTGTAAGTCAAGGTAGTTTCAGAGAAGAAACCA
1761 GAAAATTTTGGTTTCAGAAAATGTTTAGAACAGTCTAAATGGAATCAAATATTTACTGGGTAAATTTTGTGGAATTTTCC
1841 ATGTGCCTGAAGATTAGATATTCAAGGATTATTTATTGACAGATACCATGAATTTAGTAATATAAATTTATTGCATCTGA
1921 AGTCAAAATGCTGCTGCTGAACTAAATACATGATTAGTCTCATTTCCTGTTTCCTTGCAGAAATCCACGCAAATTACCTT
2001 AAAATAAAGATGGAGAGAGTTTTTTTTTCTAACTGCTTTTTTTTTTAAATTTGTTAAAATGTAACCTTTGAAAGTCAAAC
2081 ACATTTTAGTTGGCCAGTGTTTCTCAGTGAATTGATACCTTTTACACTCAGTATGACAAATAGCCCCGTAGATGTGATTC
2161 TGTTAAGTAGAATGCAACAAAGCACTCACTCGCTGATTGTGCAAAAAAACGCTACAGTGCTTTTATTCGAGAATCTCATA
2241 ATCTGAGAAGCAGAAGACGCTGCCTTGACAGCTGTACTGTTGTTGGTCGAGGTCATGGAGGATGTGTGCTGTCTATGTGG
2321 GTGTGGATGCTGTAGAACAGAAAAGACATTTCCAGCTCCTGCAAAAACTACCTATGTGGAGAGCCGTGAACAATCGCCAT
2401 TACAAGATGGCGCTGGCTTCTGCAGTGCCTAACTAGTAAACAAGCAATGTGCACGGGTGCTGGAGTAAATTCGTGCCAAG
2481 TCACTGCCCATCTCGGGGTGTAGCAGTGGGGTGATGAGTGAGCAGCTAATCAGGAGCTGACGCGTCACACGGAGGGGTAT
2561 TTAAGCAGCTCCATTTTCCGGGTTCAGGGTCTTCCTGAGAAGTAAGCAATAAAAAGCTTTGCCGTAGAAGGACCCGGTTG
2641 TCCGAGTGTGTTTTGCTGGCGAGATGTTACAAGGACACACCTAGGTTAAGTGACTTAGAAAACTTATTTAAGGGTTCACA
2721 TCACACTGAAGTTAGAGTACTACTTACTGCTGGCATTTCTGCGTTCTCTTCAAGTATTTGGCATAATACATATCACTTCC
2801 CTGCCCCTGAATAGGTACCATCTTATTTTTATTAATAGAGTACTAGTTTGTATAGCAGAGTAACAATAATCTGTGGTTTG
2881 ACTCTTGTGTCTTGTTATTTTATTTATTTCTAAAATTTATTAAAGGTTTATTTTCTTTATTTTTTAAAATTTTGTCACAG
2961 TACCATTTTAAATGTCTTAGGTAATAAGTTGTAATGTAAAAGGTTTGATAAAATGTTGAATTC
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' uaGGGCGUCU---UAGA---GUCGAGGUua 5'
            | || ||:   ||:|   ||||||||  
Target 5' caCACGGAGGGGTATTTAAGCAGCTCCAtt 3'
 2546 - 2575 142.00 -18.10
2 
miRNA  3' uaggGCGUCUUAGAGU-CGAGGUUa 5'
              :|:| |:|:|:|  |||||| 
Target 5' tgtaTGTAAAGTTTTATTCTCCAAa 3'
 1041 - 1065 132.00 -12.40
3 
miRNA  3' uagggcgUCU-UAGA-GUCGAGGuua 5'
                 ||| ||:| |||||||   
Target 5' acagaaaAGACATTTCCAGCTCCtgc 3'
 2337 - 2362 125.00 -15.02
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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast 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.

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 GSM1385342
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_GM_Ago2_CLIP-Seq_myoblast
Location of target site NM_026165 | 3UTR | UUGUAUGUGUGCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUAUGUAAAGUUUUAUUCUCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1385343
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_DM_Ago2_CLIP-Seq_myotubes
Location of target site NM_026165 | 3UTR | UUUUUGUAUGUGUGCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUAUGUAAAGUUUUAUUCUCCAA
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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