miRTarBase - #MIRT579217


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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 Ccdc157   
Synonyms 4930562D19Rik, mKIAA1656
Description coiled-coil domain containing 157
Transcript NM_001164620   
Other Transcripts NM_177616   
Expression
Putative miRNA Targets on Ccdc157
3'UTR of Ccdc157
(miRNA target sites are highlighted)		 
>Ccdc157|NM_001164620|3'UTR
   1 CCCGCAGCAGGGGTAGGGCTGGAGGGCAGGTGGCTAGCAGTCCCCCATGGAATAAAAGCCCCAGCCATCTGCCCACTGCG
  81 ATCTTGGCCTCAGTGTGGCTGAGCTGGAGGAACAGACCTCCCCTTCTTGTTGGGTAAGGTCCTCCGTGATCCCACCATGT
 161 TGGTTGCTGGCCAATGGTAGCCTCGCGTGAGTTGGGAGCTTCCTGTCTGTGTCTGGCAGGCGCTGTGGGAGGACCACATT
 241 GAGAGGCAGCATCTGAGCCAAGTGAAGCCCAGCCTTTGTGTCCCATAGAAACGGCTGAGGGGTAACTCCACATCCATTGG
 321 CCAGCACTCGGGGTAGGGCTTGGGGTATGAGGACACATCTGAAACAACGAGCTAGGCTAGGAGCTGGACCTCTGGTTCAG
 401 CAAGGCAGGCAGAGAGCAGTGTTGCCTTTGCCTTCCACCTGGGCTCTACATCTGATACAGGACCAAAGGGCACCAGGCAG
 481 CTCACCGGGAGCTTGTTCCTCTAGGAACAACTGGGAAGTCCCTCTTAAGTCCTAGAAGTCAGAGCCCCACCAAATCATTG
 561 GAGGACAGTCCAGGCCTTTGGATACCTTAGCCAGCCGTGGGGCTCACCCAGTTACAGGATGACACAAGATGGAGCAAGGA
 641 TGCTACCAGCCACACCATGCACACAGTGGTCATTCTTCTAAGCAAGCCACTAGCCTACCTTGAGTTGTGTTGTTTGTGAT
 721 GGACAGGCTCTAAATTTTTACTGAGGATTTCTCAGGGCACACTCACCTAGTGTGGGTGGCATTATTTATTGTGTAGGTTT
 801 GAGTGCCTAAGTCAATAGTGAAGGTTTCCCAACCTGCTTCTTTTTTGGAGAGGGGTGTATTTCAAGACAGCACTTCTCTG
 881 TGCAGCCCTGGCTGTCCTAGAGCTCTGTAGACCAGGCTGGCCTTGAACTCACAGAGATCTACCTGCCTCTGCCTCCCAAG
 961 TGCTGGGATTAAAGGTGTGCGCCACTACTGCTGGCCCAACTCTGCTTCTTAACAGCCCAAGGGTTCTGGGGGAGACTGGA
1041 GGCTCTGAGCCACTCTACCTGGGGAGAGCCAGCTTTGGGCACAGCTCCCCGAGAGAGGCCCTGTGACTGCTGAAGATCCC
1121 ATGCCTCTGCTGAGTCAGCATCTACTTACTCACTCTCGCTTGTGCCAGGCAGTAGGCCAGATCCTTCTCATTTAGGTGAC
1201 ACATACCCTAGGGAGGCTGAAACAGGAAGACTGAGAGCTTGAGGCTAGCCTATGCCATATAGCAAGGACCTAACTCAGAC
1281 AACACATGGACAGGCATAAAACGATAGGAAACAATCAAAAAAGTCCAGAAGTCCATCTATTTGATCAGGCCCTTTGCTCA
1361 GGGTGCTCAGAGGGGGAAACTAAGGTATCACTCAGGATGGCTCCTTTAGATGGCTCTGGGCAAGAGTCCTCTTACAAGCT
1441 CCTGGCTGTGACAGAGCTTTAGGCTTAGGCTTAGGCTGTGGGGTTGGAGCCTTGCTGCTTCAAGGAGCCTTCCTTGCCTG
1521 GCTTCTTATTGGTACCACCCATCTTCAAGAAGGCAGCAGAGGTGGGCATGGTAGCACTTTAATCCTGGCACTCAGGAGGC
1601 AGAAGCAGGAGTCTCTCTTTGAGTTTGAGGCTAGGCTGGTATACAGAGAAAGCTCCAGGACAGCCAGAGCCACTTACAAA
1681 CCCTGTCTCAAAAAGAAAAAGAGAAAGAAATGGAGGGTGTGCAGCAGACAATGTGTGTCCTGTATGGGATGCCCCAAGGT
1761 CCTCTACTTCCTCCTGCTTTCCGTGGGCTTGTGTGTTGGTCAGATGCTTTCCTCATTTTTATTGTTAGTGTTTAGTGTTG
1841 GGAACTGAATTCAGGCCCTTGTGCATTCTAGGCAAGTGCTCTACCAGCTCCCCATGCCCCAGTCCTTGCCTCTCTCATCT
1921 GAAGGTCACTTTACATAACCTGTTCACAGGGGCTAAAATGTCTTAGAGTCAATATTTTAAAGATTATGCAAGGTATGTTT
2001 GTGCAGCCCAGGAGTGCAAGGCCTTGAGGAATTTAAGAATTCTACCTGTTCCCAGCAAGAGAAACCAAGGTGACTGGTAT
2081 TTTGTTTGTTTTTCTTTTTGAGAGTAGCCCAGGCTGACTTCAAACTCCCTGTGCAGCCAAGGATGATCAGGAGTTCATGA
2161 TCCTCTGGTTTCCCTTCCCAGAGGACAAAGAACAAGGGGATTGCAGGGACTGCCCAGCAGCCTTGAACTTTTTGTTTTGT
2241 GATGTTATATTGAGACAGGGTCTCTCTGTATAGTGCTGGCTGTCCCGGAACTCGCTATGTAGACCAGGTTGGCCTTGAAC
2321 TCACAGAGGTCTGCCTGCTTCTGCCTTACCAGTGCTAGGATTAAAGGGGTGCACTGCTATGCCCAGCTGGTCTTAAACTA
2401 TGAATCCTCCTGTCTCCACCTCCATGTTTCTGGGATTATTGGCATATGTCACCACATACCCATCTTTTCCTTAATATCTT
2481 AAAGCATCACACAGATTTATGTCTTAACAGATTTATGTTAAAATAGATTCCATGTTTATTTTACTATTAAAACTTCCCTA
2561 CCCAAA
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' guUCUG-GACAAGAU-AGAUGGAa 5'
            ||:| |||  | | ||||||| 
Target 5' ggAGGCTCTGAGCCACTCTACCTg 3'
 1038 - 1061 156.00 -15.10
2 
miRNA  3' guUCUGGACAAGA-------UAGAUGGAa 5'
            :| |:||  ||       |||||||| 
Target 5' ctGGCCTTGAACTCACAGAGATCTACCTg 3'
 917 - 945 148.00 -14.50
3 
miRNA  3' guUCUGGA----C--AAGAU----AGAUGGAa 5'
            ||:|||    |  ||: |    ||||||| 
Target 5' caAGGCCTTGAGGAATTTAAGAATTCTACCTg 3'
 2017 - 2048 146.00 -14.95
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 GSM622570. RNA binding protein: AGO2. Condition:WT1A ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' guucuggacaagaUAGAUGGAa 5'
                       |||||||| 
Target 5' -------acagagAUCUACCUg 3'
 		1 - 15
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' guucuggacaagaUAGAUGGAa 5'
                       |||||||| 
Target 5' -------------AUCUACCUg 3'
 		1 - 9
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 GSM622570
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1A
Location of target site NM_177616 | 3UTR | ACAGAGAUCUACCUGCCUCUGCCUCC
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 GSM1385343
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_DM_Ago2_CLIP-Seq_myotubes
Location of target site NM_177616 | 3UTR | AUCUACCUGCCUCUGCCUCCCAAGUGCUGGGAUUA
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

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