miRTarBase - #MIRT593445


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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 Slc25a27   
Synonyms 3632410G24Rik, 9430092A03Rik, D530043E16Rik, Ucp4
Description solute carrier family 25, member 27
Transcript NM_028711   
Expression
Putative miRNA Targets on Slc25a27
3'UTR of Slc25a27
(miRNA target sites are highlighted)		 
>Slc25a27|NM_028711|3'UTR
   1 GCCCTTAAAGCTAGAGTGCTCATTGTCACTGAACAAGAGCATCTGCGACACACGCCCCTGTTATTTCTACCTCTTTAGGA
  81 AGATACTTTACTCCACAGAGACTGCGATTTGCAGGGGGCAGCACTTTATCTCTTTATGGAATCCCCATGGAGCTCCCTCT
 161 GACTCCTCCTTTTACCTAAGAGCAATCTGTCTGGTCCAATCTCTCAAGACCAACCACTGAGACACAGCAAGGCGTTTGCT
 241 AACGGATGGAACCCAGACCACTTTGACCTTGGGCCAGGAGGTTTGGACGTTGAGCTGCTGATCTGTGCAGAAGCAGCATC
 321 TGCCTTAGAGGAGCAGCAGAGACAGCCAGCATCCCAGGCCTGGATAGACGTCATCCATGTGGAAGACTAGTGCTTAGGAA
 401 ACACATTTAACCTTTGAGCCAGTTATTTATTGTTGCCGTTTGACAACTCTCGCTTTTCTGTTCGTAGAGTGCACATATCG
 481 TAATCTACACAGAGGCAAATGAGAAGTCATGAATAAACATCTTGAGTTTTCTTAGTGCTGAAAGAAGTCGCTTAACCTTT
 561 TCCTGCAAGGAGGATGGAAAGATAAAAGAGGCAACTTGAAGTGATGTTGGATTGCAAGGAAAGAGGCCTCTTGATCCTGG
 641 GTCTGCTGCCTTTGCAGGTGTCCTTTACTGGTTGCCACTGCTTTATGCATGCTAGAGGCTAGAGATATCCCCTGACAGCC
 721 ACAGTCTGTCCGTAAGAACAGAACGCTTGCTCTGGAACACATTCCATTACAACCACATTGGCCCATAGCTCTGAGAAGCA
 801 TAACCAAGAGAACCACAATATACTTGTCTGAGACTGAGCTCTCGGGGCGTTCTTAGGAAGCGCCTCATACGGTCATCAGC
 881 TTTTCAGGAATGTTTTGGGAGCAAGCTTACTCTCTCTTGTGTCACCCTCTGCATCTCTCTTCTCTGTTACAGAGAGGAGA
 961 GGGCAGAGAGAGAGAGAGAGACAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAACTCAGATGTCGTGAAACTTTCA
1041 GAAACCTGAGTGTTAATCATTGAGTCTTACTCATCCTCGCCTGTGGTGTGGCAAGTGCTCGCCGTCCGTGGTCCCTGGTA
1121 GCCTCTCCAGTCTTTGCATCCAGTCCTTTTCTCTCTTTCTAGAAAGGTTTCTGCAGATTCACACTCCCCCCCCCCCCCCA
1201 GCCTCAGACACAGGGTGTTTTAGGATGGATGGCTACAGCTCAGGGGTAACAGCTTGGGGATATGACTAGAAAAACTCCGA
1281 CCACTCAGGCCCAAGGTAGATCTCAGAGCCAACCGAATAGCTGCTCTGATGGGCAGATGCTCCGACACGGCAGCGGCCCC
1361 GTCAGCGCTGTACGAATGAGCGGATGAAGAATCACTGCCACTTCAAAGGAGGAAGCACACTTTTAAGGCCCTTTCAATGT
1441 GTGTAACAATCTCACTTTTCTACCGACAGAAGGTGGCGTTTGATCCCTGTACATCTTCAGGTTACCCACCTTTCTGTTGC
1521 ATCTGTCAGCCTGCAATTGAGTTGCTAAGTAATATCTGTTAGCCTATAGTATGTGCTTAAGTCCCCAAGCATTCTGCTCC
1601 ACAAACAAAATCACTTTGGGGGAGATTTTGGTTTTTCTATGTTTTCTAATGTTTATGACTAAGTAAAAAATGGAATCAAA
1681 TAATTACATGCAAACACAACTATTG
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' agGUUGACUCGACU-CCCGu 5'
            :|:|||  |||| |||| 
Target 5' aaTAGCTGCTCTGATGGGCa 3'
 1316 - 1335 129.00 -19.20
2 
miRNA  3' agguugacucgaCUCCCGu 5'
                      |||||| 
Target 5' ttacagagaggaGAGGGCa 3'
 947 - 965 120.00 -17.30
3 
miRNA  3' aggUUGACUC--GACUCCCGu 5'
             :||||||  || :|||| 
Target 5' tgaGACTGAGCTCTCGGGGCg 3'
 829 - 849 118.00 -20.40
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 GSM622572. RNA binding protein: AGO2. Condition:WT2 HITS-CLIP data was present in GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

- 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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Liver
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 ERR266281. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 48h ...

- Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.

Article - Schug J; McKenna LB; Walton G; Hand N; et al.
- BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
CLIP-seq Support 1 for dataset GSM4751759
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 4
Location of target site NM_028711 | 3UTR | AGAGAGAGAGAGAGAGACAGAGAGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_028711 | 3UTR | AGAGAGAGAGAGAGAGACAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAACUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_028711 | 3UTR | AGGGCAGAGAGAGAGAGAGAGACAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAACUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset ERR266281
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / A_Liver partial hapatectomy 48h
Location of target site NM_028711 | 3UTR | AGAGAGAGAGAGAGAGACAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
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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