miRTarBase - #MIRT587588


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pre-miRNA Information
pre-miRNA mmu-mir-1906-1   
Genomic Coordinates chr12: 109544541 - 109544620
Description Mus musculus miR-1906-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA mmu-mir-1906-2   
Genomic Coordinates chrX: 88759474 - 88759553
Synonyms mmu-mir-1906, Mir1906
Description Mus musculus miR-1906-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-1906
Sequence 48| UGCAGCAGCCUGAGGCAGGGCU |69
Evidence Experimental
Experiments Microarray
Putative Targets

Gene Information
Gene Symbol Cox15   
Synonyms 2900026G05Rik
Description cytochrome c oxidase assembly protein 15
Transcript NM_144874   
Expression
Putative miRNA Targets on Cox15
3'UTR of Cox15
(miRNA target sites are highlighted)		 
>Cox15|NM_144874|3'UTR
   1 TTCTCAGAGGATCATTTCCTAGGACTGGAACTGCCTTGGAAACTCATCACCAAACACAAGAACTTAGCCTTTTCTAAGAC
  81 GGTGGTATTGACATGCCACATGGTTTCCAAATTGGTCAAGTCATTCAGAACTGTTCTGAGATGGGCACTGGACCACGAAC
 161 ATTACTAAGGTGTGCTTATACCAGAGGTTTCCTTTAAAACTCTGCTACATAAACAAGGATCTGCCATTTGCTGCTTCATA
 241 AGAGGCGGGCTGACTTCTTAGATCTTGGTTTCTATGTCCTGCCCACTAGTCAGGCTTCTGGTGACAGTGACAGATTCAGG
 321 AACACGTGCCCCTGTGGAGCTACTCGACCAGTTGGCTGGTGACTGCATGTTAGTTTGTTACCAAGGTCTAAAATTGTCAT
 401 ATTTTCTGGTTTTGATAAGCAGCTAACTAGCTAGGTTTGTGAAGTGAATATTCTTTTATGCATATGTGTGTTTGTGTTAA
 481 TATATGCCATGTGTGTACGGGTGCCCATGGAGGCCAGGGAAGGTGCTGGGTCCCTGGAGCTGGACTTAAAGGTGATTTTA
 561 ATATGCCTGATACGGGTGCTAGTAACCAAACACGGGTCCTCTGGAAGAGCAGCAGGCACTTTTAACAGCTAAGCCATCTC
 641 TCCAGCCCTGGAGTGTATATTATTAAAATTAAATGTTGACAATTTCAAGTTTTAAAAAATATATGGAGGCTTAACATGTC
 721 TGACCTGAGGTTGCACATTTGCAGTTTCTGAACAAGATGATCAGGTTTTTTTTTTTAACTCTAATAATTATTCTGTGAGT
 801 CTCGGTGTATCCTAAAGGATACTGTTCTTAGCTAGTCTTAGCAAAAACAAACGCACATGTGTTTCACTCCTCAAGTCCCA
 881 GGCCCTGCTGGGCTTGTGTTATTGCACAAAAGAGGTTCCCTCAACCTCAGAACAAGACTCATCCTAGACCTAAGCGATCA
 961 CAAGGCCTCTGAACAGGACTGGGCTGGGTTGAAGTTCTGCCAGCTTGTTCCCATTCCCTCCGAATCGCTACCGCACCTAC
1041 CGTGCCTCATTTAACCTGTTGGGCCTGTGTCAGCAGGGTAGAAACTCCGCTAGACAGGAGCCTTCCAAGAAGGGGACCAG
1121 GGCAGCTTGCACACCCTCTGCTTCCCAACTCCAAATCCGCACTCTTCAGTTAGAAGCAATCAGCACAGGGCTGGAGGGTC
1201 CAGCCAGAGACCACTCGGAACCGGTTTATAGTCACCCCAAGCACATGGCAACTGGAGTCAGCTCAAGTCTCAGATATTTT
1281 GCTGCAGGTTTTTGTTTGTTTGTTTGTTTGTACTACAGTTAAGCATGTTCGGAACAGATCCAATATTTAGCTGTTTAACT
1361 GCTTTATGGTATATATATATATATATATATATATATACACATACATACACACACACACACACACACACACACACCCTAAA
1441 TACACCCTAATACAATTATTGATTTATGCCCCAAATGTCTATTTCAGAAAAATCCATTGCACACTTAAAGGATTAAATAA
1521 TTTCTTTTAATGTTTTCAACAGTCTGTCCACAATTCTGTCAATTGTTTTTAATTTATAAATAAAGGTAATTAAAACATGT
1601 ATTTTCAGTCAGCTAACCCAGGATTTTTGTTTGGGATTGATTAGGCCATTAACTCTTATGACATCATTTAATTTTTCTAA
1681 GAATTTACTTATTATTGTGTGTGCATGTACATGACAGGGGATATGCATTGTACATGCACGTGCATGCAGAGAAAAGGGGA
1761 CAACTCCTGCGAGTTGGTTCTCTCCTTCTGTCTTTGTGTGGCGATTGCTTTGTACCGCTGAGCTGTCTCACTGGCTCAGG
1841 TTTGCGTCTTTAACCTGCACTGAGATCTGGTTTCCTGCGGCAGGGTCAGTGAGACTGCCTGAAGTGAAGTTGGTTGCAAA
1921 GACCAGCTCTGATAATCAGGAGTTTAGAATAGCAGTTTACCTGCAGCCCTCCTGGTCTTGGGGTGAATGGGGGGTTCTAT
2001 GTGGGCATATGCCACACAGAGCCACATAAGACGCTGCACATTTTCTAGAGCTCCACATCTATCAGAATATTAAGAACTAT
2081 TCCATGAAATTTAAGAATTCCACAAAAATTCGTTTTTCCACCGCCTGGCTGACAAAATTCTTAACGTAAAGCATGTAAAA
2161 AGAGCCGCCTCAGCCACCGGAAGCAGGGCGGTCCCAAAGCCTTTGTCCTTAAGGTCATGGGTCACAGTGGAAGGAGCCGT
2241 AGCCACTGCAGAGACCGTGCTAAAGGTAGAAATCCTGGAGGAGATGTAGTGTATACTCCAGCTTCAACTAAACGGACAGT
2321 GTGGGACAGCGTGGAAGGAGAACTTGAACAGAAACCTGACCGGTTGGAGGGCCCGGGATCCCTGCTGGCAGAGGCGGGCT
2401 TGAGTAAAGGGGCAGAGCCGAAATCAGGCTGGACTCACCAGGACCCCCTTCAAACTGTGCGGTAGCTCAGATTGAGAATG
2481 TCCTCCAAGGGCCATCTGTTAAAGGCTTGGTCCTCATGGTGGCATCGTTGGGAATGGTGGGACCCTCGTGGCCAAGCTTC
2561 CTAGAAGGTCTTCACATCATTGGAGGATGAGTGAGACTCCCAACTCCATCCTTTCTTGCATCCTGGTCATGAGCTAAGCA
2641 TCCACTCTGCGTCACATGCCTGCTGCAACGTACACTTCACTGCGGGCTCAGAGCAGAGGGACACTTGACTACTGAGTTGA
2721 CCATCTACAGCTGTGAGCCAGAACAACCCGTTCTCTGTATAAACGATCTCAAGTGTTTGGTTACAGTAAACGGACTAGCA
2801 GCCTGGGGGTGGGGGTGGGAGTCAGGGGTCTGGTAGTAATTGTCCTGCTTTAAGGAGAGGCTCAGGAATAGACACATCTT
2881 CAAGCTTGTCTGACATGCAGGCATGGTTAAACAGCCTATGACTCAGAACATTTTCAACTCAAGTTTTCATGCCATGGAAG
2961 CAATGGCCTGGTTCATATTTGAAAAACTGGAAGCCCTTATAGCATGAGCAATAATTCCATTTTACAATATAAAAAAAGTC
3041 TTTTTATTGCTCCGATTTCCAGAAATGAAAATGGTCTGCTGGTGTGTGGTTCTCCTCTGTCCTTCTAATGATAGTATTAA
3121 CAAACAAAAATAATGAACTACTAGGCCAAGGGGAAATATGAAACCCTTCAAAGACAGCCGATGGGGATATAAAACAAGAC
3201 AAAGCTGGCTTAAAATAGAACCTTAACAAGCCTCCCACCAAAACAGAAAGCCTGGAATGGACAGGAACCCACGCAGGGTA
3281 CAACAGCTTTTCCAGTTCGATCACATCCAAGTTAGGAGGAGGGTGAAGGTCAAGGACAGAGCCACCCACCATACAGACCA
3361 TTACCTAAAAGTATTTGATTTCAATCATTGTTTTGCAATCATGGTTTACAAAAATATTTGTTATTCTGTATTGTTAGTCA
3441 AAGGTGCCAAAACTTGGTTCTTAGTCC
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' ucGGGACGGAGU---CCGACGACGu 5'
            |:|||| |||   | ||||||| 
Target 5' caCTCTGCGTCACATGCCTGCTGCa 3'
 2643 - 2667 168.00 -24.80
2 
miRNA  3' ucGGGA---CGGAGUCC--GACGACgu 5'
            :|||   |:| ||||  ||||||  
Target 5' acTCCTCAAGTCCCAGGCCCTGCTGgg 3'
 866 - 892 142.00 -19.30
3 
miRNA  3' ucgggaCGGAGUC----CGACGACGu 5'
                |:|||||     :|||||| 
Target 5' gctcaaGTCTCAGATATTTTGCTGCa 3'
 1261 - 1286 138.00 -21.50
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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ucgggacggaguccGACGACGu 5'
                        :|||||| 
Target 5' ---------auauuUUGCUGCa 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]
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_144874 | 3UTR | AUAUUUUGCUGCAGGUUUUUGUUUGUUUGUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
27 mmu-miR-1906 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT578439 Irgq immunity-related GTPase family, Q 2 10
MIRT578971 Dhdh dihydrodiol dehydrogenase (dimeric) 2 4
MIRT580446 Tln2 talin 2 2 2
MIRT582494 Mbtps2 membrane-bound transcription factor peptidase, site 2 2 2
MIRT587588 Cox15 cytochrome c oxidase assembly protein 15 2 2
MIRT589524 Mtf1 metal response element binding transcription factor 1 2 2
MIRT591281 Klc1 kinesin light chain 1 2 4
MIRT591935 Ddx19b DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b 2 2
MIRT592084 Sorcs2 sortilin-related VPS10 domain containing receptor 2 2 2
MIRT592206 Mapkap1 mitogen-activated protein kinase associated protein 1 2 4
MIRT592349 Armcx6 armadillo repeat containing, X-linked 6 2 4
MIRT592351 Angel1 angel homolog 1 2 2
MIRT592365 4930444A02Rik protein-O-mannose kinase 2 2
MIRT592427 Spsb4 splA/ryanodine receptor domain and SOCS box containing 4 2 2
MIRT592671 Itgav integrin alpha V 2 2
MIRT592712 Fbxo21 F-box protein 21 2 4
MIRT593155 Itsn1 intersectin 1 (SH3 domain protein 1A) 2 2
MIRT593662 Spen SPEN homolog, transcriptional regulator (Drosophila) 2 2
MIRT593976 Cdc14b CDC14 cell division cycle 14B 2 2
MIRT597931 Pacsin2 protein kinase C and casein kinase substrate in neurons 2 2 2
MIRT597949 Opa1 OPA1, mitochondrial dynamin like GTPase 2 2
MIRT598550 Isoc1 isochorismatase domain containing 1 2 2
MIRT599017 Fgd4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT600307 Tacc1 transforming, acidic coiled-coil containing protein 1 2 2
MIRT603647 Otop1 otopetrin 1 2 2
MIRT605000 Fam168b family with sequence similarity 168, member B 2 2
MIRT606275 Oxsm 3-oxoacyl-ACP synthase, mitochondrial 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-1 Anthocyanin NULL 145858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Caffeic acid NULL 689043 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Catechin approved 9064 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Curcumin NULL 969516 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Ferulic acid NULL 445858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Quercetin NULL 5280343 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Galactose NULL 6036 Quantitative real-time PCR lens 22736950 2012 up-regulated
miR-1 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Quantitative real-time PCR myocardial differentiation of mouse ES cells 19521018 2009 down-regulated
miR-1 Sulfonyl-hydrazone-1 (SHZ) NULL NULL Quantitative real-time PCR Murine broblast-derived Induced pluripotent stem cells 21445862 2011 up-regulated
miR-1 Cocaine NULL 446220 Next-generation sequencing ventral striatum 21708909 2011 up-regulated
miR-1 Atorvastatin approved 60823 Quantitative real-time PCR Cardiomyocyte 23860036 2013 down-regualted
miR-1 Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-1 Docosahexaenoic acid NULL 445580 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 Palmitic acid approved 985 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miR-1 Essential amino acids (EAA) NULL NULL Quantitative real-time PCR skeletal muscle of young adults 19828686 2009 up-regulated
miR-1 Hydrogen peroxide (H2O2) NULL 784 Quantitative real-time PCR Human umbilical vein endothelial cells 21527937 2011 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Microarray apoptosis-resistant breast cancer cells 21971930 2011 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR acute promyelocytic leukemia 22072212 2012 up-regulated
miR-1 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-1 Bicalutamide approved 2375 Microarray prostate 22674191 2012 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR cardia 22889704 2012 up-regulated
miR-1 Perfluorooctane sulfonate NULL 74483 Microarray zebrafish embryos 20878907 2011 up-regulated
miR-1 Quinidine approved 441074 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 up-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 down-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR post-infarction rat cardiomyocytes 21220930 2011 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 down-regulated
miR-1 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 up-regulated

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