miRTarBase - #MIRT595177


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pre-miRNA Information
pre-miRNA mmu-mir-3057   
Genomic Coordinates chr10: 81271597 - 81271687
Description Mus musculus miR-3057 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3057-5p
Sequence 14| AUUGGAGCUGAGAUUCUGCGGGAU |37
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Zfp953   
Synonyms E130120F12Rik
Description zinc finger protein 953
Transcript NM_001038651   
Expression
Putative miRNA Targets on Zfp953
3'UTR of Zfp953
(miRNA target sites are highlighted)		 
>Zfp953|NM_001038651|3'UTR
   1 AAGTGTGAAGTAGGTGGCAATGCCATCCATTATCCATCAATACTTTCTTTTTTTTTTAAATTTATTTTTTTATTAGGTAT
  81 TTTCCTCATTTACATTTTCAATGCTATCCCAAAAGTCCCCCATACCCACCCCCCATCAACACTTTCAAACTGTACGAAAA
 161 TTCATACAAGAAAGAAACCATACAGTTGTGAAATGTGTGGCAAAGCCTTTGATTATCCATCAGGACCTTAGAAACATAAG
 241 AAAGTTCAAACAGAAGAGAATCCCTACAAGTGTGAAGTATGTGGCAAGGTCTTCAATTATCAGTGGCGACTTTACAAACA
 321 TAACAATCCATGCAAGAGAGAAGTCCTACAAATATGAAGTACGTGGCCTGACCTTCTATTGTCCATAAGTACTTTCTGAA
 401 AAGAGAATCCACACAGGTGAGAAACCCTAAACTTGGGATGTATCAGGTAAATCCTTTAGAACTTTCCAGATTCTTTTTCC
 481 TTATTTGATAACTCATTCTGGAAAGAAAATATGCAAAAGTGAGGATCGTGGAAAAGCCTCCTTTACAAAGTTATACCTGT
 561 ATCTAGACCAATTAACTCACAATGTAGAGAATATTTACAAATGAAAAGAACACGTCAAAATGCTCAACAAATTTAGGGAT
 641 CATCAAAGAATTCATTCTGGAAAGAAACCATACAAATGTAAAAAAATGTGGCAAATATTTTTGAATTCCATTGCATGGTC
 721 TGAACACAGAATAATTCCTATTGGAGATAAACACTATGCATGTGAAAAATGTGGCAAACACTGTATTACCAGTCTTTGGG
 801 TCTTAAGCAACATCAAAGAATTCTTCTATGAGAGAAACCACACAGTGTGAAGAATGTTTTACAGAAACCTTGGGGAAAAC
 881 CTCATAATTCATACTAGACTGAAATGTCACAAGTGTGAAAAATATTGCAAACCCTTTAATAAGCATTCTTATATTTCTGA
 961 ACACAAGGTAGATTAAACTGGAATGAAATAATACAAATGTTAAAATGCTCATAACATCTTAATACTTCTCCAGACCCTCA
1041 AAATTTATCAACAGCTTCATGCTGAATCGAAGTCCTATAAGTTTAGGGGATGTGGTAAAGGCTTTGGAATCATCCATACT
1121 ACCATGCCAAAAGGAGAGCGATCGGGCTGTGTGGTTGTCATTCTCAATTTGGGGCTGATCCTTTCTTACTGTCTTTTGTT
1201 TCTTCTGTTTTAGAATTGAAACTCTTGTTCTATACCAGTATGTGGAAAAGTAGTCACTTGTTCTTATGTTTAGGAGCTCA
1281 CAGTCAAAAGATTGCCTTGAATCTCATGTGACACATGGACTGTGGTCTTTTATAGTGTTGTAATTGTTAAATCCTTTGGG
1361 GACCTTTCAAGTTGTAGCCTATTTTACTTATGAGGTGAAAGTTAGGTTGGAGAAAGGGAAGGGATGTTACGACTTAAAGC
1441 TTTATGGGTAGAGCTAGCATGTTGACTTTGGGAACATACTGAATGCCAAGAAGACCCACACCCATGTTAGCATTCCCAGT
1521 ATCCTCACATAGAAAGAGGTAATTACCTCTAAAGCTTGTCCTCTGACCTTCTTGCATGGACCCCCACACAAACATAAATT
1601 TCTGTGCCCAGAAATAATATAAACCTAGATCACACTTTTGAAATGACTTTGTGTTTTACATGGAAAAGTGTAAACTAATG
1681 ATACAAACTCAGTTGTTAGCAGCATGAGTTCTAGAATCATTTGAATTGCAAGCCTCTTGTTGGTTTGTTGAATTTCTCTT
1761 GATTAATTAAATTGATTTCAGGAGGTCTGTTGATTGCAGTTTTAATCATCTGTTTGACTGAGATGCTGCAGTATCAGATA
1841 ATACCCTGAGACCAACTATTTATCCATCTCCTGCTTCCTGACTGTGGAAGAAACATGACCAGCTGCTTATGTTCCTGATG
1921 TTTTAACTTTCTCACCATGTGTTGTGGTTGGAATAAGAATTGCCCCAAGGGCTCATAGAATAGATTTGAATGCTTAGTCA
2001 TCAGGTAATAACACTGCTGGAAAAGGATTAAGAAGTGTGGCATCATTGGTGTAAGAGTGTCACTGGGGGACATATATTTG
2081 AGGTTTCAAAGGTTCAGACCCAGTGTCCCCCTCTTTTCCTGACTATGGGTCAGTATGGATAATTCTCAGCTACTTCTCAA
2161 GCTCCATGTCTACCTACATGCCAATGAGCTCCCTAGCTTGTTCACCACAATAATAATGGACAAACCTCAGAAACTGTTTA
2241 CAAGCTCCAATTAAGAAATATAAGAGAAAACAGTCTCATTCCCAAAAGGCAGGGTGGATTTTTCCATGTATGATGAAAGT
2321 TTGTAATTGTTTAAGGGGATTTTGGTCAATAGTTGTTAATGGTGTTTGAGAGGAAACAAAGCAAAAATGGCAAGATTCAA
2401 GAATCTCTTCTTTTTCCTTTCTTTGTCTTTCTTTCATCCTTCTTTCTTTTCTTGCTTGTCCTAGGGGAAAAGTAGTGGAG
2481 AGGGGATGAAAAGAAAAAGGGTATATATAAATAATAAGATGAAAGGGTAGATTTTTGAGTCTGTTTAAACTAAAGACCAT
2561 CAAGAGGTCAAATAACTTACATTGGTATAGAATTGATTGATTTATTGATACAAATTTAAGGTTCTTTACATTTCAAAATT
2641 CTATATTATGTTTTAACCATGTTTTAGGTATCCTACACAAACAATTACAGTCTTTAAAGGCTACTATGTCAAACTGTTTT
2721 GGATAATTATAATAATACAAGTTGGTAGTCATTTAATCAAAGTCTTGTTAGCTACTTCTTTAGTTATTTATGAAAATAAG
2801 CTTTGTTTGCCCTCCTGTAGCTGTTTTCAAAGTTAAACAGATAAATGGCTAGAAAAAACCTACACACTCAGATCTCTTTG
2881 ACATATAGGTAGTTTTTAAACACTTCAGAGATCTACAGGCTATGGCATTTAAGATGCTTTAATAATAAACGTCTTTTCGT
2961 GACAGCAAGACACATCAGCTTCTGACAGCACCCCCAATCTACTTCCAAGAAGATGATGGGCACCAAAGAACCTCCCACTG
3041 TAGTCTACTTCAAATATGGCAAAGGTAGCTACTGGTTAAAAACCTACCTTTGCCTAGACTGCACAAAGTATGTCATCCAA
3121 AGTGTGGACAAATAGGACACCGGGAAGTTGACTGACTAATTTTGCAGGGACAAAGTATGACTATCCTTCTATATCCCTGC
3201 TTAACAAGAATCCTGTCAGGTATTCTAGACTTCTAGGCTAAATATGGATGCCCAAGTGTTGCAGAGGAATGTGGGTAACT
3281 GTCCAGGCAGCTAGTGGTCTCTGTTGTTTCTATAATTTTGGAAGTTTCTTGCTCTGCATTTCCTGTTTTCTCAGGTAATT
3361 TTATCCTTGTCAGGTCTCTGATGAGGATGAAGAGAGATCATGAAATTTTTCATCTAAAATGTATTGATTTTAGAGAAAAA
3441 AAGACATTCATTAGACTAAAAAGGAAGTGATACTGGGATAGAATTTTGTACAGTGTATAAAGGTTTTCTTTGTATTATTC
3521 AGACATTGATTTGTCTACCAGGAGAATGTCGACTGATGCCTGGACTTTGGTGTTGTTATTTTTATGGCTCATTCCTTGCA
3601 TCAGTGTTTTGTAAACATATACCTCTCTTACTTTCGGATTGTCTCAATAAAGAACTGATGGCC
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' uagGGCGUCUUAGA-----G-UCGAGGUUa 5'
             || ||||| ||     | |||||||| 
Target 5' aaaCCTCAGAAACTGTTTACAAGCTCCAAt 3'
 2222 - 2251 165.00 -19.60
2 
miRNA  3' uaGGGCGUC--U-UAGAG-UCGAGGUua 5'
            ::| |||  |  |||| |||||||  
Target 5' aaTTCTCAGCTACTTCTCAAGCTCCAtg 3'
 2141 - 2168 140.00 -19.90
3 
miRNA  3' uaGGGCGUCUUAGA-----GUCGAGGUua 5'
            ||| || |||:|     |||||:||  
Target 5' gaCCCTCAAAATTTATCAACAGCTTCAtg 3'
 1033 - 1061 138.00 -17.10
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions CD4+ T cells (C57BL/6)
Disease MIMAT0014822
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 GSM1013593. RNA binding protein: AGO2. Condition:CD4+ T cells ...

- Loeb GB; Khan AA; Canner D; Hiatt JB; et al., 2012, Molecular cell.

Article - Loeb GB; Khan AA; Canner D; Hiatt JB; et al.
- Molecular cell, 2012
MicroRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3' untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA-miR-155-in a genetically controlled manner. We found that approximately 40% of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these noncanonical sites feature extensive complementarity to the miRNA seed with one mismatch. These noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. Thus, noncanonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
LinkOut: [PMID: 23142080]
CLIP-seq Support 1 for dataset GSM1013593
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep7
Location of target site NM_001038651 | 3UTR | AUUAAGAAAUAUAAGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
14 mmu-miR-3057-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT580946 Slc25a46 solute carrier family 25, member 46 2 2
MIRT581084 Serpinb5 serine (or cysteine) peptidase inhibitor, clade B, member 5 2 2
MIRT584738 Atp2b2 ATPase, Ca++ transporting, plasma membrane 2 2 2
MIRT591856 Iffo2 intermediate filament family orphan 2 2 2
MIRT593687 Sco1 SCO1 cytochrome c oxidase assembly protein 2 2
MIRT593742 Pld5 phospholipase D family, member 5 2 2
MIRT593830 Klhl31 kelch-like 31 2 2
MIRT593961 Col4a1 collagen, type IV, alpha 1 2 2
MIRT594311 Nr3c1 nuclear receptor subfamily 3, group C, member 1 2 2
MIRT595177 Zfp953 zinc finger protein 953 2 2
MIRT598903 Gla galactosidase, alpha 2 2
MIRT603414 Samd7 sterile alpha motif domain containing 7 2 2
MIRT603667 Opa3 optic atrophy 3 2 2
MIRT606751 Tns4 tensin 4 2 2

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