miRTarBase - #MIRT586063


—
pre-miRNA Information
pre-miRNA mmu-mir-1839   
Genomic Coordinates chr7: 81529916 - 81529988
Synonyms mmu-mir-1839, Mir1839
Description Mus musculus miR-1839 stem-loop
Comment This sequence was named mmu-mir-1980 in , but is a clear ortholog of the mir-1839 sequence published in dog (MIR:MI0008087), so is renamed here.
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-1839-5p
Sequence 4| AAGGUAGAUAGAACAGGUCUUG |25
Evidence Experimental
Experiments Illumina
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B19JHB miR-1839-5p Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Urine Real-time polymerase chain reaction
Gene Information
Gene Symbol Ric8b   
Synonyms BC051080, Ric-8, Ric-8b
Description RIC8 guanine nucleotide exchange factor B
Transcript NM_001013441   
Other Transcripts NM_183172   
Expression
Putative miRNA Targets on Ric8b
3'UTR of Ric8b
(miRNA target sites are highlighted)		 
>Ric8b|NM_001013441|3'UTR
   1 AAGCATCATCACCTGCTCCACTCTCAATATGGCTTTTATCAGCATCTTTTCTCTGTAGCTCCAGGGGAATCTTTTTCTCT
  81 AAAACGTTTATGCCCTCGCTTTGGCTAGAAACACATTAACTGGTTTACTCATTGGGAATCCAGCATATTTAAGAGGTAAT
 161 CCTGTGTTTTCTGCAACATTGAGGCATTCATACAGAGCTGCAGTTAGGCAGAGTTGCGGGGCTAGAAGCAGAAGCAGACA
 241 TCCCATTGCACCAGGACAGAGTACGGGACTTCACTCGGCAAGCAGCCCTGGTCAGATCTGGCAGTCTTGTTGCCGAAGAT
 321 TCTGCGTGTCCTTCCACCCACCCATGTCAACTGCCCCTTCTGAGTCTCTCCAGCGACCTGGGGCCCCTGAGGGCCCGAGG
 401 AGCTGATAAATAAGGGCTGAGGCAAGTGACTCCTTAGATCAGCACTGACTGAACGAAAGCCAGGCAGCTGTTCTGTAAGC
 481 CTAGCCCTACCCTTCATTTCAGTTTTATACAAATGTGGAAACACACACACACGCACGCACACACACACATGGCCCCAGAC
 561 TTACAAACCTATTACACTCTAAAAGTGTGTCATTTAGCGAAAACTTGAGATTACATTTCTTCCTGGGAGGAGTTAGAAGT
 641 AATGGTTTAGTTCAGGCAGCTACACGTGCCTATTTATCCCTCGTTCCTGAACACTACTAGTACCGTAGGGCTGGACCACC
 721 ATCTGTACCGTTGCGTCCACAGTGTGCATTCTGAGGTATCACTCAGGGTGCCAAGTACACACTCATCCTCCAGGCAACAG
 801 AGAGGATGGGGCTCCCCGAGTAGTGGGAGTTCTTTTGTGGCCTGTGCTGGGGGTAGGGAGCCAACAGCACCCGTTTGTAC
 881 ATAAAGGTCATTCGTATGTCACATGTTTTAAACTGGGGTCTCTGTGTGTATTTGTGTGTGTGTTCTACCTTTCTACCATA
 961 TGTCATCAGTTTAATGGTAACTTTATTTATTTAAAAACAAAGAAACACAAATAGTTACTATTAAACTGATTAAGGCTGTT
1041 TATTTTTACTCCTAGAAATGGTCATATGAAGTAGATGTGCAATCATGTAGACAGCAGGCCAAGGTGATCAGTGGCTAAAG
1121 TTGAAAAGGGGTTGGTTTCTTTCATATATGTATGTGTGTGTACATGCGCATACATAGATATATGCACACATAGATTATGT
1201 GCTTGACCACTGCCTTTTAAAACTTTAAATTAAATAAAACATTGGGGATGATTCAATTTAGCCATCTGTGTGTGTGTTTC
1281 TTTATGGATACGTGGTCTAAGGAGACTATTGCACAGCTTATGTTTTAAAGTCTTTCTCCACCTGCTCCCTCACCTGTCAT
1361 TGTGCAGCCTCTTTCCAGGACAGAGTGTGCATAGATAGCATTGGTGAGAATTCGTTTAGCTTCAATGGTCCCTGGCCTTT
1441 GAGCTACCAGACAGATGCCAGGAAGTTCTTAAAATTTACTCTGAAGGGAACCCTTAAAGAGTAGTCACCATCACTAAGAT
1521 TTATATTCATTTCAAACATGTTTGGTCACTTGGACTTTGAGCCCTCACCCCACACAAAGGCAGAGAAGGTTAGTGTGTTT
1601 CAAGCAGGCACCCTAAAAACAGTAAAAGGCGTCAGCCGGGAGTGGGGAGCCTTCAGTGCCCAGATTCCTCCTCCAGATCC
1681 AAATGGGGGCCAGTGTGCACAGCAAGGTGAGCAGGAAGAAACACCATCCAAGGCTCAGCAGATAGTGTGTGTGACAGGTG
1761 GCCAGAGACAGCTTTCCTAATAGTGGCCCTGAGCGGCTCTAAAAGGATCAACCAAAAGACTTGTAAGAGACTCGGGAATG
1841 TCCGTACATCAAGGACTCTCATCCATAACTATTGTTTTAGCCAATGGCACCACCCAATAAGATTTTCATTTTATTCTGCC
1921 GTTCATAATTTTAGTTAAGTAGAAAAAAATTCAGAGGAGCAGGAACTTAGTTATTTTGTTACTTCATTCTACAAATTCAT
2001 TTCAAAAGTATTTTTATAATCTCTGGTCAGATAGCTTTTCCATGAGCATCAGCCTACGAAAGCATGCTGTGCCCGGTGAA
2081 ACGCCACCTTGCCGCCTCTGCGCAAGTGCTTGCACAGTGCCGTAGCTGTGCTCCGACGCTTTCAACAAGTTCCTTTCACC
2161 ATGCATCTCTTGCATCTAGGCACTTAATTTTTTTTTTTAAGGAGTAATTCTTTAAAAGATGGAGTAGCTTCACCATGCAC
2241 ACAGAGAGCACTGAGCAGCGAGCTTCATGTCTTCTTTGTAACCTCACCCCATCTCCAAGCAGAGCCTTTCCAGAGAGCTG
2321 CTTAACTTCCTAGACCCTCAGCAAGCCAGGGTCCAGCTGTGGGCTTGACACCTGCACCTTCCCTGTTGCATGTAGGACCA
2401 CTAGCCAGAGGCTTTAAGACAGCAGACAGGCTGCGGAAGGTGGTCCTTCTCAGACCATTTTAAGCAATAACTATTTGAGC
2481 AGCAGTCTCTGGTGTTCCCATCAGGGAGGTACCTGCACGAGCGGGAGAAGCTTGGTCAGTTAGCAGATTTTAGGTGAAGA
2561 CCTGGACACCCTTAGGTCAGAGAGCAACAGTGTGGGTCGGTCCTCCAGTGAGAGGGGTCAGCCAGTGACCACGGCCGTTT
2641 ACATACACTGGACTTGGGAATGCACGCCCTAAAACAAGGCATTGGAACTCCTCAGAGGAACAGTTTCCAGATGTCTGTGG
2721 CCCGTTTGCATGTCCAGTGGTTTTTAGTGGCAGTCAGGGCAAATGCTGTCCTTTCTCTATAAATGACAGGTTGAATGAAG
2801 CTTTGCAAATGGCTGGACAGCACCCTGGCACGTGAGTCTTGCTGCCCCCAGGACTAGGTATCACTCTCCTTCAGCTTTCT
2881 TTGGCCCCACCTTGTCTATCAGAGTCATACATGCTTCTTGTAGAATGTTTAGAAAGTGCGGAAACAGTAAAACTAGCTAT
2961 TGACCCAGAGCCCTCCCACCCCCGAGAGCATCACTGTTCATGTTTGGTGTATTCCTTTCCTATATTTTTTCTATGCATAT
3041 ATAATTTATTTTACTACAAGATTGGGATCATGCTGTGTTTACAGATTTGTACCCTGCTTTCCTTAACATTGTGAGCATTT
3121 TCCCATACCAATAAATAGTCTTCAAATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3201 AAAAA
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' guucUGGACA---AGAU-AGAUGGAa 5'
              |::|||   | |: ||||||| 
Target 5' gtgtATTTGTGTGTGTGTTCTACCTt 3'
 926 - 951 150.00 -11.80
2 
miRNA  3' guUCUGGA--CAAGAU-AGAUGGaa 5'
            |||::|   ||:|| |||:||  
Target 5' taAGATTTTCATTTTATTCTGCCgt 3'
 1898 - 1922 126.00 -11.70
3 
miRNA  3' guUCUGGAC---AA-G-AUAGAUGGAa 5'
            | ||:||   || | | ||| ||| 
Target 5' gaAAACTTGAGATTACATTTCTTCCTg 3'
 599 - 625 120.00 -5.50
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.

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_001013441 | 3UTR | UGUAUUUGUGUGUGUGUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
17 mmu-miR-1839-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577441 Ttll1 tubulin tyrosine ligase-like 1 2 4
MIRT577494 Tnfrsf26 tumor necrosis factor receptor superfamily, member 26 2 4
MIRT579217 Ccdc157 coiled-coil domain containing 157 2 4
MIRT580960 Slc25a42 solute carrier family 25, member 42 2 4
MIRT586063 Ric8b RIC8 guanine nucleotide exchange factor B 2 2
MIRT586499 Neu4 sialidase 4 2 2
MIRT587074 Glt28d2 glycosyltransferase 28 domain containing 2 2 2
MIRT587351 Ecm2 extracellular matrix protein 2, female organ and adipocyte specific 2 2
MIRT588006 Akap8 A kinase (PRKA) anchor protein 8 2 4
MIRT588053 Fam211b leucine rich repeat containing 75B 1 1
MIRT594341 Mfsd4 major facilitator superfamily domain containing 4A 2 2
MIRT594432 Fli1 Friend leukemia integration 1 2 2
MIRT598593 Il7 interleukin 7 2 2
MIRT600042 2410012M07Rik proline rich 23A, member 3 2 2
MIRT602743 Azi2 5-azacytidine induced gene 2 2 2
MIRT603358 Slc11a2 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 2 2
MIRT605032 Eif2s1 eukaryotic translation initiation factor 2, subunit 1 alpha 2 2

Error report submission