miRTarBase - #MIRT581000


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pre-miRNA Information
pre-miRNA mmu-mir-384   
Genomic Coordinates chrX: 105344282 - 105344369
Synonyms Mirn384, mmu-mir-384, Mir384
Description Mus musculus miR-384 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-384-5p
Sequence 16| UGUAAACAAUUCCUAGGCAAUGU |38
Evidence Experimental
Experiments Cloned
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
BZV7T3 miR-384-5p Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Serum Real-time reverse transcription PCR
Gene Information
Gene Symbol Six4   
Synonyms AI047561, AREC3, TrexBF
Description sine oculis-related homeobox 4
Transcript NM_011382   
Expression
Putative miRNA Targets on Six4
3'UTR of Six4
(miRNA target sites are highlighted)		 
>Six4|NM_011382|3'UTR
   1 GCCCGATTCACTCCACATCCCTCCTTCTCTGCTTTAACAGGAGCAAATCCTTTTCTTTGCGAAGCCCCGAGGATGGAGAG
  81 CTTCTATTCATTTAGAGGAAAACACTGTACTTCTGCAAGCAAGCGCATCTGGCTTGGGCTGCATGAAGAGCGTAGTTAAA
 161 TACACAGGAGTGGACCTGCACTGCCGAAGCCCCTCTGGTCACATCGTGCTCGCTTTGAAACAGATGGGGCGAGGCAACAG
 241 TGAATGCATCCATCTAACCATCGTCTATCATTTAGTCAGCAGTATAACTCCACAGGCGAAATGGAAGGTGACAGTATTTC
 321 AGATTTAAAATGCATACACCTAATTTAGGAGATTAAATAATAGCTCCAGGCTCTTGGAAGCGATGCAGTTGGTTTTTTGT
 401 TTGTTTGTTTGTTTGTTTACTTTTACTCCATGGGCATTGAGATGGTTAAGAAACAATGGTACTCTAGACTATCATAAGGG
 481 TATATTTTTCAAATTATGTAGCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATACACACATTCATCGTTTTCA
 561 GCATTTGGGGGAAAGGCTTGGTTTTAAGTCTCTACGTGTTTCCAAATGTGATTGCTAATAGTCAAACGTGGCAGAGTAAG
 641 TTTGAGACGCCACTAAACTCTGACACAACTTGGGTACGAATGTAAATACAGGTCTCTAAGCAAGATCTGAGTAAGTACAG
 721 TGAGTTTTTATTTATACCTTGTATGTCTCCCTTCAGGCTCTGTGAACTGAAAAGAAAATGTCTTCTTACTGTTTAATTTA
 801 TATTTATTGTTTGAGCGGGAATAGGACATCTTTGTTTCCAACCAAGGTTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTG
 881 GTTTTTTTTTTTGTAATTGTTATCAAGAGTCTATTGAGGTCAATATTAATTAACACTGAAACAGGAACTGTTAACCCCCA
 961 GTACTGGAACTTTGTCACTTCTCATCACATCCTTCTTACTTTAACAACTTTGATTCATTTAAATATGTTTTCTATAGACT
1041 CCTATGTGCCTTTTTACCTTGTGGCCTTTTTATTACTAGTCAGGTACAGAAGTGTCAACAGCAGTGTTGATGGTTCTTTT
1121 GTACCGTCAAACAGGGTTAAGTTTACCACAGAACCCCTGCATAAGGCAGGACTTCCGTTTCACTAAATATCATGTGGAAG
1201 GTTTGCCATGCACATGGATAGACAGATATAGTCGATGCTTTTCATTATAATGAAAGTAGAAAAGTATAGAAAGACCATGA
1281 AACAGCAGTTCTGCAGGCTATGACTATGAAAACAACCTTTTTTTTTTTAATTCTGTTTTGGTTTTAGTTTTCTTGAGACA
1361 GGGTTTCTCTGTTAAACAGAGAAACTGTTACTGACCATCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCACA
1441 GAGATTCACCTGCCTCTGCCTTCCAAGTACCGGGATTCAAGGCATGGGCCACCACTACCCAGCTTGACAACAACCACTTA
1521 AAATAAAAAATATATATGTAAATTGTACTAAAAATCTGTTCAACTGAAGCTCATTTCCAGTGTTTTGAATTGGTCGGTAT
1601 ACATGACTGTTGCCTGTCGTATTTAATGAAGTAAATCCTTCCGGTTTCTGTGGGAAATTTTGTTTAAAAGTTTTAGTAGG
1681 ACTCTGCATCTATGATATAACAATGCAATGCCTTTATGCTGTTAGTCCAGGGCATCTCTGATTTCAGAAAGAAGGCGACT
1761 TTTTCTAAGGTGACTTCTCAGTTGCTAAGCACAAAGATAGTACCACTCCTTGGTTTTGTTAAGGTGGTGGAAGGGTTTCT
1841 AACTAACACACTCATCAGCTGAGCCTGCAGAGTAACGGTCACTGGGGACTTAACATTTGTTGTTACACAAGGGAACTTTC
1921 AGTCAAGATTAAGAGCCCTATGAAGAATTCTGTGCCCATCATTTTGATCAAGAACCTAAATCCCATTTTTGTGAAATTGG
2001 TGAATGTCCCTCAATTGCTGAAATATGCAATTTGGGCCAGAGGTTGTTGTTTGTTTGTTTTGGATGTTCTTGTTTTATTT
2081 TCATGAAGCCAGTTGCTTCAGTGTGGTTTTCCACTCTGACACTACTTACACAGCTTGGCTGCCCCCGTCTCCCAGTTATT
2161 TACTGATCATATTAATGTGATTAGCATCCTGGTCTTGTAGTATAGTTTACATTTTTAAAAAATGTTATTTTTTACTAGAT
2241 TGCTGCAGATATCAAGAGGACATTATTTTAAAATACCTGTCTGGTAAGGGAAGTGGGAAAGTCAAAACGTTCTATAAGGC
2321 GGGTGTGTGTGGGTGTCTGCGTGCGTGTGATGGAAAACTCCCATATATCTGACAAAAGTATCTTTTTTATTCCGAGTTCT
2401 TCCTCCTTTTCTCCTTATGAGAAAGAAAAGATAGCACAAAACTAAGTACTTACCTAGGAAATGTCTTCATATTCCAACAT
2481 GATGAGCTTCTAGCCCTACAAACACCCCAGGTATCTATACAATCCACCCGGTAAGACTCAGTGCTCATTATGAGAACTTA
2561 CTGTTCTAGTCTATTCTTTCAGTAAAATAAGGGCCAGTTGATATGCAGCCCATGTATGTGTGAATGGAATATGGTAAACC
2641 CCGTGATCTCCTTGCACAGAATTGCAAATGACTTTTTTCCCCAACACCAAGGGCCCAGCCTCGGAGCCCTTGGAGTTCAC
2721 GTGGCAGAATATCCTTCTTACATAAACCAATGCTTGAAGATGCTGCAAAGGATCCTCTAGTGATTCCTGATGAGGAATCA
2801 GAATAGAGGTAAATAACCCCCTTTAAATCCCACCCCTGCTGCTGGCTGTGGGGTTTTCTGGTGCCAGCCTATCTATGCAC
2881 TCTATAGCCAGAATTGGCACTCAGCTCTTAGTTACGTCTAGTAGAGAGAATGGTCTCTAGCATTCAAAGGAGGTTCATTC
2961 CCTCCCCCCCCAAAACAAACAAAGGCCCCTGTGTTGTACTGTATAAATATCTCATGTAGATTTATAGTGAAGACTTAATA
3041 CATGTCTGGTGCCTTTCTTGTGTTGTGAAAGGCAAGTAGATGTTGTAGCCATAGGTCTGTTTTTTAAATCCATAGTTGAA
3121 TTGCACACTGACCTTAACTCTCTGTATGTACCCTTGTTATTCTGCATGTTAAAGCTGGAATTC
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' uguAACGGAUCCUUAACAAAUGu 5'
             |||::|   : |||||||| 
Target 5' tgtTTGTTT---GTTTGTTTACt 3'
 402 - 421 153.00 -8.80
2 
miRNA  3' ugUAACGG-AUCCUU---AACAAAUgu 5'
            :|| |: |:||||   |||||||  
Target 5' cgGTTTCTGTGGGAAATTTTGTTTAaa 3'
 1642 - 1668 145.00 -8.50
3 
miRNA  3' ugUAACGGAUCCUUAACAAAUgu 5'
            | ||:||    | ||||||  
Target 5' aaAATGTCTTCTTACTGTTTAat 3'
 775 - 797 133.00 -7.20
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 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' uguaacggAUCCUUAACAAAUGu 5'
                  || | || |||||| 
Target 5' --------UA-GUAUAGUUUACa 3'
 		1 - 14
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 GSM1385343
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_DM_Ago2_CLIP-Seq_myotubes
Location of target site NM_011382 | 3UTR | UAGUAUAGUUUACAUUUUUAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
37 mmu-miR-384-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577998 Pgr progesterone receptor 2 2
MIRT578191 Narg2 interactor of little elongation complex ELL subunit 2 2 2
MIRT578276 Mesdc2 mesoderm development LRP chaperone 2 2
MIRT578464 Ints12 integrator complex subunit 12 2 2
MIRT578486 Il18r1 interleukin 18 receptor 1 2 4
MIRT580032 Wdr89 WD repeat domain 89 2 6
MIRT580041 Wdr44 WD repeat domain 44 2 2
MIRT580302 Tomm70a translocase of outer mitochondrial membrane 70 homolog A (yeast) 2 2
MIRT581000 Six4 sine oculis-related homeobox 4 2 2
MIRT581273 Rrad Ras-related associated with diabetes 2 2
MIRT582217 Nfatc3 nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3 2 2
MIRT582447 Mgea5 meningioma expressed antigen 5 (hyaluronidase) 2 2
MIRT583055 Hoxb3 homeobox B3 2 2
MIRT583626 Strip1 striatin interacting protein 1 1 1
MIRT583683 Amer1 APC membrane recruitment 1 1 1
MIRT583923 Dpy19l1 dpy-19-like 1 (C. elegans) 2 2
MIRT584696 Cep170b centrosomal protein 170B 1 3
MIRT585027 Gskip GSK3B interacting protein 1 1
MIRT585242 Zfp446 zinc finger protein 446 2 2
MIRT586100 Reep4 receptor accessory protein 4 2 4
MIRT587716 Cd300a CD300A molecule 2 4
MIRT588342 Zfp711 zinc finger protein 711 2 2
MIRT588629 Tnrc6b trinucleotide repeat containing 6b 2 6
MIRT589300 Pigh phosphatidylinositol glycan anchor biosynthesis, class H 2 2
MIRT590164 Eno2 enolase 2, gamma neuronal 2 2
MIRT592642 Lpar3 lysophosphatidic acid receptor 3 2 4
MIRT593646 Tbc1d5 TBC1 domain family, member 5 2 2
MIRT595037 Camk4 calcium/calmodulin-dependent protein kinase IV 2 2
MIRT595222 Slc16a1 solute carrier family 16 (monocarboxylic acid transporters), member 1 2 2
MIRT595455 Ptrhd1 peptidyl-tRNA hydrolase domain containing 1 1 1
MIRT595822 Fam227a family with sequence similarity 227, member A 1 1
MIRT596023 Cdk13 cyclin-dependent kinase 13 2 2
MIRT596361 Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 2 2
MIRT596421 Ing1 inhibitor of growth family, member 1 2 2
MIRT596514 Zfp9 zinc finger protein 9 2 2
MIRT599311 Csf1 colony stimulating factor 1 (macrophage) 2 2
MIRT603174 Trp53rk transformation related protein 53 regulating kinase B 2 2

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