miRTarBase - #MIRT585345


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pre-miRNA Information
pre-miRNA mmu-mir-465c-1   
Genomic Coordinates chrX: 66825955 - 66826035
Description Mus musculus miR-465c-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA mmu-mir-465c-2   
Genomic Coordinates chrX: 66832517 - 66832597
Description Mus musculus miR-465c-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-465c-5p
Sequence 11| UAUUUAGAAUGGCGCUGAUCUG |32
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Ybey   
Synonyms 1110068N23Rik, A130042E20Rik, C21orf57, ORF57, ORF66
Description ybeY metallopeptidase
Transcript NM_172550   
Expression
Putative miRNA Targets on Ybey
3'UTR of Ybey
(miRNA target sites are highlighted)		 
>Ybey|NM_172550|3'UTR
   1 TGCCACAGAGCTTTGAGACAGAGAACTTGTTGGACAGAGTCCCGTCCCTCTGCAAGACTCCAGGGAGCCTCTGCTTACCA
  81 GGGAGCCCCTGAGTGGACCACGTGGAGCCGGAATAGATGCAAAAAGCAAGAGGAATTTTTGTTCCAGTGCACTGGGGTCT
 161 TCCCAGACCCGAAGGAGAGGCGGCGACCCCCAGCACCCATTCAGGGAGTTTTTATATGGTTTCCAGGGGCAGAAGAGAGC
 241 ATCAGCAACTAGGCACAACGTGATTGGCGGAGCAGTGCACCCTTTAAACTGATTGGTCTTTAGGGAATGAAGTGACAAGG
 321 ACGTCCCTTGTCTGAAGGTGTCCTGCAGGATGTGTCCCCACCCACAGGGCAGTTCTGCCCTAAGGTCTGAGAAATGTTAA
 401 TTAGCCTCTTCCTTCTGGAGGGGCAAGTGTTTCATGACCTTCCCAAACTTCCTAAGCTGGCCTTTTTACCTCCACAGTGG
 481 ATCTCTGCTGGTCCTGTTGCCCTGGAGGGCCTCAGCCCACACTACAGCTTCACTCTGTGAGTGGACCAAGTACCAAGGAA
 561 GTGCCTGTCAGCCCTTACTCTGATTAGAAATCTATGCGGACTCTGTTGTAAGCAGAATCAGGCGTTCTAAGAGAAGAAAC
 641 ATGGACGCTCTTGTGCTTCTTTGGGTTTCTAGCTGTAGAGTCTGGGCAGATTGCCTTGTCTCCCTGAAGTGGGAGGAACG
 721 TGCCAGAACACTGAAGCCTGTTCTCCTAGGAGGAGGCGCCTGCAGACCAGCAAGCCCAAAAGGACACCTTGTGCCCTCGC
 801 CTTTCTTAAGCTGTTGGCTGCAGACACCACGGGACAGCCCACAGACCTTGTCTCCTGGGGCCAGAGAGTCAGGAGTGTCC
 881 CCCATCTGTGTTGCTGTTTGTAATTGTTTTAGATGACCTTTATTTTATTTGGAGCAGGGCAGTGGTGGCACACGCCTTTA
 961 GTCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAG
1041 CCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAGGATTTTATTTGGTGTGTGTCATGTGTGGGTAC
1121 ACATTTCCCACTGCGGGGGGTGGGGTGGTCAGCTGGGGGGAGATGTCTCTCTCGTTTATTATTTTGTCCCCAGAGATGGA
1201 ACTCTGGTTGTCAGCCTTGCCATCCCACTGACATCCTGCAGGCCACCGTAGTCCTGCCACTGGGGCTCCCCTATTGGCTG
1281 TTAGAGGCATGGTAGTTCTGCTCAAGGCCTGGAACATGGAATTCTGGTGACCTGAAGTCTAGTTCAAAGCAACATGCAAA
1361 TGTCTGTGCAAATCTGGATCACGAGAGTCTTCCCAGCAGGTAGCCAGGGACCTTGAACCTAGATAGGGTTTCCTGACCCC
1441 TCTGCTGGGTGTACCCGCATATACACCTATGCCAGCCTGTTCCCTTCTTCTCGGCCATCTAACTGGTTCCTCGCCTTTGA
1521 GCATCCTTAAGGAATGACTGCTTCTGTGCCCTTCATTTTTCTATTTCCCTTTTTCTCTGCTTGGTATTTCTGGTTTAATT
1601 TGGTGGGGTTTTTGGTTTTTTTGGTTTTTTGGGGGGTTTTTTTGTTTTTTTTTTTTGTTTTTGTTTTTGGTTTGGTTTGA
1681 CCTTGCAGCTCTGGGCATGGAATCCAGGATCTTGTCAGGCTTGGCAAGGCTCTGCCACATTCCCAGCCTGTTGCTCAGCT
1761 GCCCTAAATCTGTGGGTTGGTCAGCAGCTGTCTCTGAGTCCAGCCACATTGTTATGATGACTCCAAGCCTGAGGGGGCAC
1841 TATCTGCCCTGTTCCAGGAGGCACAGCATCCTCACTTGGGGCTTCCTCACTTTGTGTTTATTCCAGATTTCATTTCGTCC
1921 CTCACTTCCCTGAAGGGCCTGTGATGTTTTTTAATTTTTAAAAAAGATTTACTTGGGTATGGGGGACTTTTGGTATAGCA
2001 TTGGAAATGTAAATGAGCTAAATACCTAATAAAAAAAAGATTTACTTATTTTATGTATATGAGTACACTGTAGATGGTTG
2081 TGAGCCATCGTGTGATTGCTGGGAATTGAACTTAGGATTTCTGCTCGTTCCGGCCCTGCTCGCTCCAGCCCAAAGATTTA
2161 TTAATTATATGTAAGTACACTGTAGCTGTCTTCAGATAAACCAGAAGAGGGCGTCAGATCTCATTACAGATGGTTGTGAG
2241 CCACTGCGTGGTTTCTGGGATTTGAACTCGACCTTCAGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGC
2321 TGGGGCCTGTGATCTTGATGAGAGTTTCATGGACTCTGTGGATTGGCCGCTCACACACTTGAGCCATCTTTAAAATCTCT
2401 GGGGCGTACTGTGCATCTTCTCAGAGTAAAGTTGTGCACAGTGGTGCAGTCCCTGTCACCACTGTTAAGGGGCATGGCCA
2481 GGAGAAGCTTTTCCCTGAGTCACTGGGGACCCCCTAAGCCCACTACAGGGCCTGCTCAGACTCTTTAGTCTCCCACAGGT
2561 GGTCCTCAGACAGCAGGCTTGAAAGGGACGGGGAAGACTGTGTGTGAGGGTGGGTCCATGTACACTCCCATAGCTTCCAG
2641 AGGCTGATGGTGCTCCCAGAGCCAGGATGCTCCCAGGCTACTTCCTCCTTGTTAGCCCAGCATTGCCAGGCCATCTGAGA
2721 CAAAACATCTGCCAAATATCTTCCTTCTATCAGATCAATAATCATATGAGAGGAAAATCGTGTTAGAAACATCATCTAGG
2801 AAGGAAATTATGTGAGCTCTTTAACTGGTGCTTTTAACAAAACCAAGTTTCTCTGGAACCACACCCCAAGGCGCACTGAA
2881 AGACAGGTCTGTCTTTATGGATTCTTCTCTACCTGATGGGCTGGGGTGGAGATGGAGGAGAGAGAGCAACCATCCAACCC
2961 TCCCGGAGTGAACAGTGCTTTGTAAACAGCGTGTGTAAATACCCATACTTACACAGCCTGCAGTGCCCACGTGCATGCAT
3041 GTGGACCTCACATGTACCTGGGCCTTGTTATGATTATAAAATGTTATAAGTATGAGTATCTTGCCTGTGTGTATTTATGT
3121 GTGCACTCCTGATGCCCTTGGAGGTCAGAAGAGGACATTGACTATCCTGGAACTGGAGTCACAGAGAGTTGTGGATTGCC
3201 ATGTGGTGCTATTGAAAGAAAATAAAACTTGAGTCCTGTGATTCATGTAATAGCCCAAAGAGTTGTTTGTGAGCTTTGAA
3281 GCCTGGGACTGAGAACATAGCAGAACAGGCCAGGACATGCCTGGGCAGGCCCATCATTAAGACATTCCTGAGGCTGCTTG
3361 GCCATAAAGATAAAGAGAATGCAAAGACATGTCCAGACTGGCCTGGCGCCTCCCTATCTCCCACCCTTCTGACATGGGTT
3441 AAATGTTAACCAGATGCTCTGCTGTTACCTCCATCTGCACATACACTCTGCTGATGTTTAAATGAACCAATCGTGTGAAA
3521 CCGCGCCAATTCCTCCCCCAGCCCCAGACCCTTTTCTATAAAAACCCCTAGCTTTCAAGCCTAGTGGTCGACAACCGCAA
3601 TCTCCTGTGTGAGATACATGTCGGCCCGGAGCTCCGTCATTAAACTACCTCATGTGTTTGCATCAAAAAAAAAAAAAAAA
3681 AA
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' guCUAGUCG-CGGUA-AGAUUUAu 5'
            |:||||| ||::| |||:|:| 
Target 5' ttGGTCAGCAGCTGTCTCTGAGTc 3'
 1777 - 1800 140.00 -16.90
2 
miRNA  3' guCUAGUCG-CGGUAAGAUUUAu 5'
            | ||||| |||   |||||| 
Target 5' ttGCTCAGCTGCC---CTAAATc 3'
 1751 - 1770 136.00 -11.50
3 
miRNA  3' gucuAGUCGCGGUA-AGAUUUAu 5'
              || || : || |:||||| 
Target 5' acacTCTGC-TGATGTTTAAATg 3'
 3483 - 3504 133.00 -5.80
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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast ...

- 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_172550 | 3UTR | UUGGGUAUGGGGGACUUUUGGUAUAGCAUUGGAAAUGUAAAUGAGCUAAAUACCUAAUAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
20 mmu-miR-465c-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577524 Tirap toll-interleukin 1 receptor (TIR) domain-containing adaptor protein 2 2
MIRT578756 Gm11559 predicted gene 11559 2 2
MIRT579164 Cdc37 cell division cycle 37 2 2
MIRT579596 4930563E22Rik RIKEN cDNA 4930563E22 gene 2 2
MIRT579614 4930430F08Rik RIKEN cDNA 4930430F08 gene 2 2
MIRT581042 Sim1 single-minded homolog 1 (Drosophila) 2 2
MIRT581082 Setd7 SET domain containing (lysine methyltransferase) 7 2 2
MIRT582172 Nkain3 Na+/K+ transporting ATPase interacting 3 2 4
MIRT582549 Map3k1 mitogen-activated protein kinase kinase kinase 1 2 2
MIRT585014 Gid4 GID complex subunit 4, VID24 homolog 1 2
MIRT585345 Ybey ybeY metallopeptidase 2 2
MIRT585446 Veph1 ventricular zone expressed PH domain-containing 1 2 2
MIRT585687 Tbc1d24 TBC1 domain family, member 24 2 2
MIRT588450 Ybx1 Y box protein 1 2 4
MIRT592140 Ppp1r1c protein phosphatase 1, regulatory (inhibitor) subunit 1C 2 2
MIRT593134 Thrb thyroid hormone receptor beta 2 4
MIRT594593 Tfap2b transcription factor AP-2 beta 1 1
MIRT595796 Dapk1 death associated protein kinase 1 2 2
MIRT595818 Arl4a ADP-ribosylation factor-like 4A 2 2
MIRT598674 Hltf helicase-like transcription factor 2 2

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