miRTarBase - #MIRT588450


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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 Ybx1   
Synonyms 1700102N10Rik, C79409, EF1A, MSY1, Nsep1, YB-1, dbpB, mYB-1a
Description Y box protein 1
Transcript NM_011732   
Expression
Putative miRNA Targets on Ybx1
3'UTR of Ybx1
(miRNA target sites are highlighted)		 
>Ybx1|NM_011732|3'UTR
   1 ATGCCGGCTTACCATCTCTACCATCATCCGGTTTGGTCATCCAACAAGAAGAAATGAATATGAAATTCCAGCAATAAGAA
  81 ATGAACAAAGATTGGAGCTGAAGACCTTAAGTGCTTGCTTTTTGCCCTCTGACCAGATAACATTAGAACTATCTGCATTA
 161 TCTATGCAGCATGGGGTTTTTATTATTTTTACCTAAAGATGTCTCTTTTTGGTAATGACAAACGTGTTTTTTAAGAAAAA
 241 AAAAAAAAAGGCCTGGTTTTTCTCAATACACCTTTAACGGTTTTTAAATTGTTTCATATCTGGTCAAGTTGAGATTTTTA
 321 AGAACTTCATTTTTAATTTGTAATAAAGTTTACAACTTGATTTTTTCAAAAAAGTCAACAAACTGCAAGCACCTGTTAAT
 401 AAAGGTCTTAAATAATAATGTCTAGTTTTGTCATAATTGAGTACTCTCTCCCACTTTTAGAATAACAGGTAACACCAGCA
 481 GTAAGCAGTCTGTCAGGAGTGCTGTGAGGCATCAGCTGTAGCCACGTGAGTGGGGTAGAGAAGCTTTGTGGGGCCGGGCT
 561 AGTCTGGGGTGTTTCCCTCTAGAGAAGCTCCAGGGCGAGCGCACTGGCATCGCACTAAAGAACTGCTGCTGAGTGGGGAC
 641 TAATGGCTGCTAGTTGTCCGCCAAGTCCATCAACTTTTTAGGCCAATTCTTTGTAGTAGAAACTAATAGGAATTGATGAA
 721 AGACTTCAGCAGCCCTATTAACATAAACACACAGAGACATGTTAGTGTTAGCTCATACCAGTCATGGTGACTGCTGTAAA
 801 TACTCTGCTGTCAAGAGCATAGTGAAAGAATTCCTGGGTAAGATTCACAGGTGTGAGTTTACCGATAACAGACAGTGTTG
 881 GTTAAAACCTAATGTTGGGGGCCGGGTGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGTAGAGGCAGGCGGATT
 961 TCTAAATTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGAGCTACACAGAGAAACCCTGTCTCAAAAAA
1041 TAAATAAATAAATAAATAAATAAATAAAACCT
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' gucuaGU-CGCGGUAAGAUUUAu 5'
               || |||   |||||||| 
Target 5' agaggCAGGCGGATTTCTAAATt 3'
 946 - 968 153.00 -13.10
2 
miRNA  3' gucuAGUCGCGGUAAGAUUUAu 5'
              |:| || : ||:||||| 
Target 5' acctTTAACGGT-TTTTAAATt 3'
 270 - 290 137.00 -5.60
3 
miRNA  3' gucUAGU--CGC-GGUAAGAUUUAu 5'
             :|||  |:| |:: | ||||| 
Target 5' ccaGTCATGGTGACTGCTGTAAATa 3'
 778 - 802 121.00 -9.30
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions mESCs
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 GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011, Nature structural & molecular biology.

Article - Leung AK; Young AG; Bhutkar A; Zheng GX; et al.
- Nature structural & molecular biology, 2011
MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer(-)/(-) mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
LinkOut: [PMID: 21258322]
Experimental Support 2 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 GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_011732 | 3UTR | AAUUCGAGGCCAGCCUGGUCUACAGAGUGAGUUCCAGGACAGCCAGAGCUACACAGAGAAACCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1385342
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_GM_Ago2_CLIP-Seq_myoblast
Location of target site NM_011732 | 3UTR | AAAUUCGAGGCCAGCCUGGUCUACAGAGUGAGUUCCAGGACAGCCAGAGCUACACAGAGAAACCCUGUCUCAAA
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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