miRTarBase - #MIRT602604


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pre-miRNA Information
pre-miRNA mmu-mir-3961   
Genomic Coordinates chr13: 82698275 - 82698333
Description Mus musculus miR-3961 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3961
Sequence 38| UGCCCUCAGCUCAGUUGGA |56
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Chrna1   
Synonyms AI385656, AI608266, Achr-1, Acra
Description cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)
Transcript NM_007389   
Expression
Putative miRNA Targets on Chrna1
3'UTR of Chrna1
(miRNA target sites are highlighted)		 
>Chrna1|NM_007389|3'UTR
   1 GCAGAGGCTGAGCTAAGCCTACCTCTGTCCCAGCCATAGCCATCGCTAGGAAAGATGGAAGAGAGGAAGGTCTGTCTCCT
  81 TGAATCCTTTCACACTTACCAAACATGCAGTGTTCTACATGTCCTACATGTTAATGAGAGTGATCTCTGCTCACACGGCT
 161 GTATTCTTGAAGTGTCTCCCCTTTGCTTCTGCTTTTAACACTATGGGCCTCCTTAAAGGGCGAACCCTTTGAAGTAAATA
 241 AAAGTGAGCCCTCAAAAGAAGTGTTTGCTTCTAAATGGCCCCTGGGAGAGTTTTGCTTGGATACTCAAGGTTTTCTGTTT
 321 GTATTGCCATGGCTAGTTGTTTTTGTTTTCTTTCCTTTAATAAATATAATTGTACTTATATGAGTGATCCGCCTACGTGT
 401 ATGTCTCACATACACGCCTAGTGTCCATGAAGGTCAGAAGAAGGTATCCCATCTCCTAGAACTGGAACTACAAATGGTTG
 481 TGAGCGTCCACATGGAACCTGGGAATCAGGCCCTCTGGAAGAGCACCCAGTGTTCTTAACCACTGAACCACCCACCTATC
 561 GGGCTCAGTTAATTTTTATTTTTAAAGTGCTGAGAGTCCCTTACTTAAGACACACGGTTTCATACCTACTAGAAAAGTCG
 641 TGTCTACCAGATTCCCCAGATTTGATGTGGACACAAAGGAAGTGGTAGAAAGGAAATTAGGTAACTTTAAACTTAAAAAA
 721 AAATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATACTCGCACACATTGATGAAATTGGGGGACAACTTT
 801 TAGGAGTTAGTTCTCATCTTTTATCTCATTTGAGGCAAAGTATCTTGTGATTTCTGCCGCTGTGTTACATTCTCATGTAA
 881 AGCTTCCTGGGGCATTTTCCTTTCTATACTTCTCGGCCCATGAACAGAGTGCAGGGATTCCAGATGCATGCCGCCATCTC
 961 CAGCTTTTCATAGGTCCTAGGATAGAATTTAGGTCGTTAGGTTTGTCCAGCAAAAAACTACTTTTACCTGCTTAATCCAT
1041 TTCACTGGCCCAAAGGTAATTTTAGGGCGATCACATACAAATAGTATCAAAACCTCATGGTTTAAAGTAGACTTCTGAAA
1121 CCAGGAGAGGGAGAATGCTTTCTTAAGTGATTTCTGTTTGAGAGGCCTTCTTGAAAGGGCGCTTGGGATTCCTTGGGATT
1201 GTACCTAGAGCTTTGCACACAGAGCTATAACTGAGCCTCAGCTCTCCCAACTTAACGGAGCCCCTGGATTTTGTTCTCAG
1281 GACCCGAGGAAGGGCAGATCCCATCCTCATCAAGGGTGTGCCTCTGACCCCATGAGAATCGTCTCGCCCGCATGGGTTTA
1361 TTTTATCCAAATTGTTTTACACAGTCTCCATAATGTCCCTAATTTACAAATGGAAAAAAAAATTTTTGGGGAAAGTTAAA
1441 CTCTGCTCCATCTAGAAGTAGAAGAACTGAGATCTGAACCCAGACAGAACTTAAGATTCTAAAACAGGGGCTGGAGAGAT
1521 GGCTCTATGGTTAAGATCATTCCCAGCAACCACAGGGTGCATGGTGGCTCACAACCATCTACAGTGGGATCTGATGCCCT
1601 CTGCTGGTGTGCAGGTGTGCATATACAAAGCACTCACACATAAATACATAAACAAACAAACAAATATTTTTTAAAGATTT
1681 ATTTATTTATTATATGTAAATACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCATCAGATCTTGTTACAGATGGTT
1761 GTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCAGAAGAACAGTCGGGTGCTCTTACCCACTGAGCCATC
1841 TCACCAGCCCCAAATATTTTTTTTAAAAGTCAAAAAGAAAAGGGATTCTAAACCGACTTGCAGCTGATGGGGTCACCTGC
1921 TCCCTGCTCTCCCAGCATGCCTGGCGTGATCTAAGTAGTTCTGGTCTGTGTTGGTGGGGACTCTGTGATATCCTATTTCC
2001 TGCCTTCTCAATTAAAACCCCTGGCTTTTCCTTCAGTCCTTGGACGCAATCATGTTTGGAGTTCAGGCCCTATGAATGGA
2081 ACCAGAAACGTATGCACACACCATCACCATTTCTGAAATCTGAAAAATAAATTCTCTGTGCCAAACTCTAGGCTCTAGTA
2161 CAATTTACCCAGACCAAGAAGCCGTGTGGCTCTGGACGCAGAAAAGGCCTTTGAATCACAAACACATCTGATCCGTCATC
2241 TCCAGGGAGAGCTATAAACTGCATAACCAGGAGGCCAGTGCGAGCCCAGGTGGCTTCAATCTCCTGAGGGACTTCCCATC
2321 ACCCCTGCACCAGTGCTGGGCTCTTTCATCTCAAATAGTTTGCACTTTAAAGTGGAAACAATTGGCAGTTTCTCAGAAAG
2401 TCACACTCGGGTCACCAAGTCACTCAGCAGTCCCATTCCCAGGTAGAGAGCCAAAGAAATCGAAAGAAAGACTTACACAA
2481 TTTGTATGAGAACGCGCACAGAAGGCAAGAGCCAGAGAAAGCGGTCTAGGCTCCAACCCACAGACGACAAGCAAAAGGGA
2561 TGTGGAGAATGGGTTTTGGGGTGTATGTGTGTAGGCCTGGGGGGCCATCGCCTTTTTGTTTTGTTGTTGTTTTTGAGATA
2641 GAGTTTCTCACTGGCCTGGAACTTGCCAAGTAGTTTAGGCTGGCTAGGCAGGCCATTCCGAGATCTGCCTGTCTCCTCTT
2721 TCTGCAAACAATTTAGTTGGCATGGGTTCTGGGGCTCTTACTCAGATCTAAAAACAAGCATTTTGTCAGTTGATCTAATT
2801 CTTTAGCTTTTTCTACTCACGACCACTTTTTGCTTGAGAAATGTTATGTAGAAATATAAAATATGTATAAAAATAAATAA
2881 CAAAGAAATTTAATT
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' agGUU-GACUCGACUCCCgu 5'
            ||| ||   |||||||  
Target 5' ttCAATCT--CCTGAGGGac 3'
 2295 - 2312 129.00 -14.20
2 
miRNA  3' agguugacucgaCUCCCGu 5'
                      |||||| 
Target 5' gacactccagaaGAGGGCa 3'
 1720 - 1738 120.00 -14.50
3 
miRNA  3' aggUUGACUCGACUCCCGu 5'
             |: | | :| ||||| 
Target 5' caaAGGTAATTTTAGGGCg 3'
 1051 - 1069 116.00 -8.90
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 GSM622571. RNA binding protein: AGO2. Condition:WT1B HITS-CLIP data was present in GSM622572. RNA binding protein: AGO2. Condition:WT2 HITS-CLIP data was present in GSM622573. RNA binding protein: AGO2. Condition:KO1 ...

- 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]
CLIP-seq Support 1 for dataset GSM4656408
Method / RBP HITS-CLIP / AGO
Cell line / Condition mouse liver / P7
Location of target site NM_007389 | 3UTR | ACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE153876
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4656409
Method / RBP HITS-CLIP / AGO
Cell line / Condition mouse liver / Adult
Location of target site NM_007389 | 3UTR | AGCUGUCUUCAGACACUCCAGAAGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE153876
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4656410
Method / RBP HITS-CLIP / AGO
Cell line / Condition mouse liver / e185 rep2
Location of target site NM_007389 | 3UTR | AAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE153876
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4751756
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 1
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4751757
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 2
Location of target site NM_007389 | 3UTR | AUAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4751758
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 3
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM4751759
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 4
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM4751760
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 1
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM4751761
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 2
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM4751762
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 3
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM4751763
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 4
Location of target site NM_007389 | 3UTR | UAUUUUUUAAAGAUUUAUUUAUUUAUUAUAUGUAAAUACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAACAGUCGGGUGCUCUUACCCACUGAGCCAUCUCACCAGCCCCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset GSM622571
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1B
Location of target site NM_007389 | 3UTR | AGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_007389 | 3UTR | AGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGCCACCAUGUGGUUGCUGGGAUUUGAACUCUGGACCUUCAGAAGAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM622573
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO1
Location of target site NM_007389 | 3UTR | ACACUGUAGCUGUCUUCAGACACUCCAGAAGAGGGCAUCAGAUCUUGUUACAGAUGGUUGUGAGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
33 mmu-miR-3961 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT580374 Tmem206 transmembrane protein 206 2 4
MIRT588925 Sh3pxd2a SH3 and PX domains 2A 2 6
MIRT589433 Nid1 nidogen 1 2 2
MIRT592155 Paxip1 PAX interacting (with transcription-activation domain) protein 1 2 2
MIRT593445 Slc25a27 solute carrier family 25, member 27 2 4
MIRT596576 Zfp790 zinc finger protein 790 2 2
MIRT597139 Sumf2 sulfatase modifying factor 2 2 2
MIRT597636 Prrc1 proline-rich coiled-coil 1 2 2
MIRT598943 Ggps1 geranylgeranyl diphosphate synthase 1 2 2
MIRT600143 Zfp1 zinc finger protein 1 2 2
MIRT601504 Tmem88b transmembrane protein 88B 2 2
MIRT601517 Tmem151a transmembrane protein 151A 2 2
MIRT601642 Slc12a8 solute carrier family 12 (potassium/chloride transporters), member 8 2 2
MIRT601708 Rtkn2 rhotekin 2 2 2
MIRT601810 Prrxl1 paired related homeobox protein-like 1 2 2
MIRT601824 Prpf31 pre-mRNA processing factor 31 2 2
MIRT601873 Pigv phosphatidylinositol glycan anchor biosynthesis, class V 2 2
MIRT602604 Chrna1 cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) 2 2
MIRT602810 Akr1d1 aldo-keto reductase family 1, member D1 2 2
MIRT602829 AK010878 GON7, KEOPS complex subunit homolog 2 2
MIRT602860 Rmi2 RecQ mediated genome instability 2 1 1
MIRT602870 Mcmdc2 minichromosome maintenance domain containing 2 1 1
MIRT602959 Xpo7 exportin 7 2 2
MIRT603096 Zfp287 zinc finger protein 287 2 2
MIRT603386 Sgol2 shugoshin 2A 2 2
MIRT603717 N4bp2l2 NEDD4 binding protein 2-like 2 2 2
MIRT604022 Fam81a family with sequence similarity 81, member A 2 2
MIRT604137 Dclre1b DNA cross-link repair 1B 2 2
MIRT604673 Shisa6 shisa family member 6 2 2
MIRT604960 Gm5113 predicted gene 5113 2 2
MIRT606285 Nufip1 nuclear fragile X mental retardation protein interacting protein 1 2 2
MIRT606419 Fsd1l fibronectin type III and SPRY domain containing 1-like 2 2
MIRT606580 Zfp941 zinc finger protein 941 2 2

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