miRTarBase - #MIRT580373


—
pre-miRNA Information
pre-miRNA mmu-mir-3065   
Genomic Coordinates chr11: 120014767 - 120014853
Description Mus musculus miR-3065 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3065-5p
Sequence 14| UCAACAAAAUCACUGAUGCUGG |35
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Tmem229a   
Synonyms 6332401O19Rik
Description transmembrane protein 229A
Transcript NM_177013   
Expression
Putative miRNA Targets on Tmem229a
3'UTR of Tmem229a
(miRNA target sites are highlighted)		 
>Tmem229a|NM_177013|3'UTR
   1 GATTAGAGGGGACAAAAAAGGAAGTATTGGAATCTGAAAAGCGATGCAATTTATTTTTACACATTTTAAACAAGGTGGTT
  81 TTGCTTTCTGTCTTTTAAGTTTTATACACTTTACCAAACTCTGCCAATATGTGCTTGACATTTTAGTTGTCTGCACTGCT
 161 TGGAATCTCTATGTAAAGTTCAGTACTTTGAAATGTTACTCAAAAATAACTCAGAATATTTAACTCATCAACAATTTAAA
 241 CTTTACGAGGCCAAACAGCAAAACCACTGGACCTTAACATCAGGAACGGGTAGTAGTCACTTGACCTCGGTGAGTGATAG
 321 CTACGTGTTTTTCTGTTCCTTCATGGAAGTTTTCAGACCAGAGAACAGTGACTTCTACAAGTTTCTGATGTAATGATCTG
 401 TTGGCTTTCCTTTCAATGCAGTTTCCTTTTACCTTCTTGCTATGTTTACCAGTGGTGGCTGAAACTCCGTGTCTTGTCCT
 481 TCAGAAACTCTAGTCCACAGCTATAAAAGTGCCTCTGTCCAGCGTGCAGATGAGAGGAAGCTGGCAAGTGGGAAAACATC
 561 CCGTGAACTCATTTTGACATGAGGAAGTCTTTCCTGTGAACCCCAACAGGTGACACTGTGTTGAGATATTTGATCACCAT
 641 CTTGGAAATGATCGCTTTCCAATGTTGGCTAGCCTTAAACACAATGCGTGTTAACATTAATCAGACCATGGTGTTATCAA
 721 AACTTTTGTAACTGTGCAATAACTTTCCTGTTTACCCTATAGATCCCAGGGCCGAATGAAATTAGACCACCTTCAATCAT
 801 GTTCTAACTCTAAGGACCCTTTTCTACACAGAGTTTCAAATATAGAAACAGTACTTTGGAATAAAATGAATCTGAATTCT
 881 CCCTCTAATTACATCAGGCCTAATTGGTTTCTCTACTTACTGATGGGGTTTTATCCATATTTCTCCCACAGTCTGCCTTC
 961 TCTCTCTCTCTCTTTTTTTTTTTTTTTCTTTCAGACCCAGAATTTGGTGTCAGGCTGATGCAGTAATGCACAGTATTAAT
1041 CCATGATAGCTTTTTGACAGCTTATGATTAATTAATGTCTAAAAGCTTCAAAGTTAAATGAGATGATGGAAGCCACTCTA
1121 AGAAATGATATCTAATTGATTAATAATGTACTCTGAGGGTGTTTGTTGTTTTATTGTATTCAGGACCGAGCAAGTAGGAC
1201 CGAGAGCAGCTCAGCCAAGGATGAATAATAACCTCTCAGCTTTCAGTACAAAGATAATCAGGAAAACTTAGAAAGTTTCT
1281 TAATGAGTTTAAATCTTCCTCTTGCCTGTGCTGTAAAAAGGGATGTTTTTGTTTCAAGAGAAAAAAAAATGTTGCTATGA
1361 AAATAGAAAAGAATGTGTATTTTACATGTGATGTGAGACACAGTTCTGACAGTGTTATATCCACCTATCCCCTGCGCTAA
1441 ATTATAAGTATTGCTATATAGTCAACTGCACCTGTGAGATGGATGATGGCCAACTAATTCTTTTCATTGGCCAAAATTTA
1521 AAAGGCTTTATGTCTGCCAAAGGTTTCTCATAAGTTGTTTGGTTTTTGTTGTTGTTGTTGTTGTTGATGTTGGTTTTTTG
1601 GGGGGTGGGGGTGGTTTTGTTTGTTTGTTTGTTTTGTTTTGTTCTTATGACAGTTTGTCACAGGTTTAAGGTTTCTGAAA
1681 ATGCTTGAGGGAAAAATATCTAGGTAGATGCCTAGACACTGGGCAAGGTATTTGTACTTCAAACATGACACGTGCATGGG
1761 AGTCTGAGTTTAGTGTATCACGGCTACACATCCCACATTCCTGGGAAGGTTGGTCGAGTCAGCCCCATGGCTACTGAAAT
1841 GCTTATTAAATTATCCGCACTCACTTCCTCCCTCTGCTGCATTCAGAGCTACAGAGGAGCCCACTAGCCTTCTCTGACTG
1921 AAAAACCCCGTGTAGGGACACACGCCATTTCAGTCTCCTTTTAATATTACTCCTATCAGAAGGACAGAGCAAAGTTTTCA
2001 CTCATTAAACTTATTTAAGTTTAATGATTGGTCTTGGTGTTGTTCAAGACTGTTGGTGTTGGTGACCGGTAGTTGGAGTT
2081 GTAACTCTCATCAGTCCTGTCCCAGGAATACTATGATCTATAATTCTTAAAAATTAACCCAATTACCAGCCCCTCTGCCA
2161 GTTCTGCAGATTGCTAGTTGTGTATTCAGGAAACGATTAACCTGCCTGGTAACTCAGTGTGCTGTTTTAGGGCTTCTCAT
2241 TTCGTGTTTGCTCCACTTCTTAAAGGAGACTTTTTGCTATGATCTTTGAACCTTCAGGAAAAGAAAAACATCAGATCATT
2321 TAACTTTGTTATTATTAATAGTTTAGAGATGGAAATGATAAGACAGTATGATAGTTAATATTTAAAAAGCATTTGCTATC
2401 TGACAAAACTTCCCTAAAGTGTTTATGTATATGTATTATATAGATATCAAATTGAGAACACATTCTTATATACTATGCCT
2481 TAAGTGAATATACATACAGTATATATTTTAAGTACATATTCATATATGTGTATATATTCACTTAAACTTACAATAACCCT
2561 GATTTTATAGATGAAGGCAATAAAACTAAAGCCCAAATAGATTCAATAACTACCCAAGATACATAGCTTTTGAGCATATA
2641 TTTGAATTAATGGATGCTGGACTCCTCAGTTTGTTTTTAACAGCAGCTTGATTGTGCCTCGGTCTAATGGCCTCAGTGAT
2721 TTAGATCTTGTCTGGACTGCACTTCCCTTGACTGTTAGAGATGCACAGACAACTGTATAGACAGCAGATGTTGTTGTTGC
2801 AAAAGATTCATGTTGCTCCTTTAGTATAAGGTACATAACAAATTAATTAATATCAGGATAAATAACTGACAATCAGCCTT
2881 CTTTTACATTTAAATATAATGCCTTTATATTTAATCAGTGCTCTGAAAGGAAGCTCATCCTATAAGCTAAAATTATCCAC
2961 AACATATAAATGTAAAACTAATATGCTAAGAAGCAAAGTAGGTCATATCACAAGGTATGAATACACATAAAATTAATCAC
3041 TGTTATACATTAAATATTATACTTAAAGCAGATATCATTGTAAGAACTAAACACACTCAAACTGAGAACAGTGTTAGCCA
3121 ACTGTGGTAGCACACCACCCTAATCCTCGTACTGAAGCTACTGCGGCAGGAGGATTGCAGGTTTGAGGTCACTGTAGGGC
3201 ACATAAGGATATCCTGCCTTTTAAAAGGACCCATTTTTAAAAAGACATTTATTCAGAGTTCTGCTGAGAAAATACACTCT
3281 TAATGGGAAAACATAAAAGGAACAAGTGTGCTTAATATATACAATGTTGAGCTTTCTTTTTAGAAGTACTTGACATTTTA
3361 AATCAATTCTATTAATTTCTGTGAATCTAAAGAGGAATATAAGCTCTTGAATTTTGATGTTAACAATAGATACAGAAGTC
3441 CGGATATCAAAGAGAAACCCCAATAAAGTTGCTAAACACATTGCATTACTTCAAGCA
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' ggucGUAGUCA------CUAAAACAACu 5'
              ||| |||      | |||||||| 
Target 5' ttctCATAAGTTGTTTGGTTTTTGTTGt 3'
 1545 - 1572 156.00 -8.40
2 
miRNA  3' gguCGU-AG--UCACUAAAACAACu 5'
             |:| ||  || |  ||||||| 
Target 5' aatGTACTCTGAGGGTGTTTGTTGt 3'
 1145 - 1169 149.00 -8.40
3 
miRNA  3' ggUCGUAGUCACUAAAACAAcu 5'
            :|::  :|||:|||||||  
Target 5' ggGGTGGGGGTGGTTTTGTTtg 3'
 1602 - 1623 144.00 -12.50
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 GSM622572. RNA binding protein: AGO2. Condition:WT2 ...

- 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 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' ggucguagucACU-AAAACAACu 5'
                    ||: |||||||| 
Target 5' ----------UGGUUUUUGUUGu 3'
 		1 - 13
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]
133 mmu-miR-3065-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT430695 Atp2b2 ATPase, Ca++ transporting, plasma membrane 2 1 1
MIRT577276 Zfp619 zinc finger protein 619 1 1
MIRT577437 Ttyh1 tweety family member 1 1 1
MIRT577647 Sod2 superoxide dismutase 2, mitochondrial 1 1
MIRT577852 Rassf9 Ras association (RalGDS/AF-6) domain family (N-terminal) member 9 1 1
MIRT577896 Prrg4 proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane) 1 4
MIRT577952 Pole4 polymerase (DNA-directed), epsilon 4 (p12 subunit) 1 1
MIRT578007 Pgpep1 pyroglutamyl-peptidase I 1 1
MIRT578136 Noc3l NOC3 like DNA replication regulator 1 1
MIRT578205 Naaa N-acylethanolamine acid amidase 1 3
MIRT578451 Ints7 integrator complex subunit 7 1 2
MIRT578772 Gatsl2 GATS protein-like 2 1 2
MIRT578776 Gata1 GATA binding protein 1 1 1
MIRT578863 Fam163a family with sequence similarity 163, member A 1 1
MIRT578864 Fam159b family with sequence similarity 159, member B 1 1
MIRT579037 Cts8 cathepsin 8 1 1
MIRT579539 Coa5 cytochrome C oxidase assembly factor 5 1 1
MIRT579653 2010106E10Rik RIKEN cDNA 2010106E10 gene 1 1
MIRT579710 Zic1 zinc finger protein of the cerebellum 1 1 1
MIRT579721 Zfp92 zinc finger protein 92 1 2
MIRT579828 Zfp106 zinc finger protein 106 1 1
MIRT579873 Zbtb8b zinc finger and BTB domain containing 8b 1 1
MIRT579938 Zbtb34 zinc finger and BTB domain containing 34 1 1
MIRT580092 Usp54 ubiquitin specific peptidase 54 1 1
MIRT580347 Tmem33 transmembrane protein 33 1 1
MIRT580373 Tmem229a transmembrane protein 229A 1 2
MIRT580541 Tcp11l2 t-complex 11 (mouse) like 2 1 1
MIRT580657 Stxbp5l syntaxin binding protein 5-like 1 2
MIRT580728 Srrm4 serine/arginine repetitive matrix 4 1 1
MIRT580766 Spp1 secreted phosphoprotein 1 1 1
MIRT580853 Slc8a1 solute carrier family 8 (sodium/calcium exchanger), member 1 1 1
MIRT581257 Rras2 related RAS viral (r-ras) oncogene 2 1 1
MIRT581367 Rcor3 REST corepressor 3 1 1
MIRT581452 Ranbp3l RAN binding protein 3-like 1 1
MIRT581626 Prkar2a protein kinase, cAMP dependent regulatory, type II alpha 1 1
MIRT581835 Pkia protein kinase inhibitor, alpha 1 1
MIRT581897 Phc3 polyhomeotic-like 3 (Drosophila) 1 2
MIRT582138 Npr3 natriuretic peptide receptor 3 1 1
MIRT582434 Mllt3 myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3 1 1
MIRT582435 Kmt2a lysine (K)-specific methyltransferase 2A 1 1
MIRT582473 Med28 mediator complex subunit 28 1 1
MIRT582523 March1 membrane-associated ring finger (C3HC4) 1 1 2
MIRT582739 Kpna1 karyopherin (importin) alpha 1 1 1
MIRT582765 Klf12 Kruppel-like factor 12 1 1
MIRT583052 Hoxc4 homeobox C4 1 1
MIRT583070 Hnrnpul2 heterogeneous nuclear ribonucleoprotein U-like 2 1 1
MIRT583389 Fzd6 frizzled class receptor 6 1 1
MIRT583418 Fubp3 far upstream element (FUSE) binding protein 3 1 2
MIRT583486 Foxc2 forkhead box C2 1 1
MIRT583748 Ephb2 Eph receptor B2 1 1
MIRT583894 Dtna dystrobrevin alpha 1 1
MIRT583996 Dck deoxycytidine kinase 1 1
MIRT584018 Dcaf17 DDB1 and CUL4 associated factor 17 1 1
MIRT584023 Tmem245 transmembrane protein 245 1 2
MIRT584102 Csnk1e casein kinase 1, epsilon 1 1
MIRT584246 Cnnm3 cyclin M3 1 2
MIRT584385 Cdh12 cadherin 12 1 1
MIRT584396 Cdc37l1 cell division cycle 37-like 1 1 1
MIRT584462 Cbfa2t3 core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human) 1 1
MIRT584494 Camkk2 calcium/calmodulin-dependent protein kinase kinase 2, beta 1 1
MIRT584630 Bbx bobby sox HMG box containing 1 1
MIRT584793 Arl5a ADP-ribosylation factor-like 5A 1 1
MIRT584821 Arid3b AT rich interactive domain 3B (BRIGHT-like) 1 1
MIRT584838 Arhgef18 rho/rac guanine nucleotide exchange factor (GEF) 18 1 1
MIRT584952 Adamts5 a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2) 1 1
MIRT585099 Zfp945 zinc finger protein 945 1 1
MIRT585623 Tnfaip6 tumor necrosis factor alpha induced protein 6 1 1
MIRT585661 Tmco1 transmembrane and coiled-coil domains 1 1 2
MIRT585936 Slc14a2 solute carrier family 14 (urea transporter), member 2 1 2
MIRT586062 Rnd1 Rho family GTPase 1 1 1
MIRT586696 Lrrtm4 leucine rich repeat transmembrane neuronal 4 1 1
MIRT586756 Kdm5d lysine (K)-specific demethylase 5D 1 1
MIRT586958 Grhl1 grainyhead-like 1 (Drosophila) 1 1
MIRT586989 Gpr107 G protein-coupled receptor 107 1 1
MIRT586997 Gpkow G patch domain and KOW motifs 1 1
MIRT587056 Gm5464 predicted gene 5464 1 1
MIRT587297 Extl1 exostoses (multiple)-like 1 1 1
MIRT587428 Dmd dystrophin, muscular dystrophy 1 1
MIRT587531 Cxxc5 CXXC finger 5 1 1
MIRT587941 Atp1b3 ATPase, Na+/K+ transporting, beta 3 polypeptide 1 1
MIRT588042 Aim2 absent in melanoma 2 1 1
MIRT588860 Smad7 SMAD family member 7 1 1
MIRT588862 Slit3 slit homolog 3 (Drosophila) 1 1
MIRT588901 Slc16a6 solute carrier family 16 (monocarboxylic acid transporters), member 6 1 1
MIRT588916 Skor1 SKI family transcriptional corepressor 1 1 1
MIRT588918 Six6 sine oculis-related homeobox 6 1 1
MIRT588969 Sall1 sal-like 1 (Drosophila) 1 1
MIRT588972 S1pr3 sphingosine-1-phosphate receptor 3 1 2
MIRT589007 Robo1 roundabout guidance receptor 1 1 1
MIRT589016 Rnf150 ring finger protein 150 1 2
MIRT589317 Pbx1 pre B cell leukemia homeobox 1 1 2
MIRT589465 Ncam1 neural cell adhesion molecule 1 1 2
MIRT589658 Lhfpl4 lipoma HMGIC fusion partner-like protein 4 1 1
MIRT589751 Jph1 junctophilin 1 1 1
MIRT589804 Id1 inhibitor of DNA binding 1 1 1
MIRT590017 Foxa1 forkhead box A1