miRTarBase - #MIRT593830


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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 Klhl31   
Synonyms 9830147P19Rik, D930047P17Rik, Kbtbd1
Description kelch-like 31
Transcript NM_172925   
Expression
Putative miRNA Targets on Klhl31
3'UTR of Klhl31
(miRNA target sites are highlighted)		 
>Klhl31|NM_172925|3'UTR
   1 ACGCATTGCTTCCCAATGTGGTCAAACTGTGAGTGGGCCACCAGGAAAATATACACCATTTACTACAGTGACGGTGGTTC
  81 AAATCGATCCAGAGGAGTGCCTGGACCGCTTTAAATTCTTAGTTTAGCACCATCTACCTCAGTCTTTCCCTCCAAAAAAA
 161 AAAAAATAATAAAGGGCTGTAGCCAACAAAAGAAGCAATTTCATTATGCAGCCACTGGGTGGCCACTAGAGTTTGTTACA
 241 GGCACTCTTGCAAGGAGGCTCGCTTCCTAAATTCATAGCAGTTACACACACGCTGAGATTTTCCCACGGTGTACACGTGA
 321 AACCTACTCGTCTATACAATTTCCTATCCAAAGGAGTATTTTCCTCTCTGTTTCTTTGAAGGAAGTTGAAAATACCCACT
 401 TCACATTTGCAAATGAAAATAGTCTACATCTATAAAGATTTAATTCTATATTTCAACAGAAAATTATTCTTTGTCCCTAC
 481 TTGACTGGAAAGAACTTTTAAAAAGATCTCATGACATAGCCACAAAGCTTTTAACAGGATGTGGCTGGAAAGCTATACAT
 561 TCTACCTAGGAAACGACAAGGTGGCAGTTTGGGGTTAACGGTGTATACCCCCTCATTCTGTCCTTGAAGCTTCTGCCATT
 641 TTCTAACATAAAATCCTACTCTCAGAAAAGGAACAGTTTCCTGTCATTTAATTTATAGTGTAAATTCAAATCATTTGGCA
 721 TTTTTCTTAGAAATATTTCCACTTGTATCTCTAATCCTTATATGGACAGAGTTGTTTTTTTTTTCTTTTTTTTTTTTTTT
 801 TTTTTTTTTCCTTTTTTCTGGATGGGCCTGGTACACACTAGTACTCTACCCGGGAGCTAACTACATATCCAGTCTTCGCT
 881 TTATTTTAATATTTGAGACATGGTTTCATTAAGTAGACCAGGCTAGCCTCAAACTCCCAGTGCCTCCTGAGTGATGGGAT
 961 TAAAGGTGTGTGCCACCACTCACAGCCCTCTTTCTTATTTTAAAGTAGGATTTTACTAGGTTGCCAGGCTGCTCCTCCTG
1041 CTTCAGCATCCCCAGTAGGCTGGAATTACAGGCGTGTACCATCGGGTACAGCTTTATCTTACTCAGGTATGGTCAAATTG
1121 CCTCTAACATTAGCCCGAATAATCACCAAATCACACTATGTTCTTGGATGAATATCATTAACTGCAGCTTAGCCTTTGGC
1201 TGTACAGCCAATAGCAGTAATTTTACTGACCCCTCGTTCACGTGGAGATGATGAAGGAAATATTTGGGGTTCTCGGACTT
1281 GGCAATTACCAGATGAATAGATGGGTTCCTCACTGAGGAGTGCTGATAGCTAACTTAAAATATTAACCCCCAAAATAATG
1361 CTCTTTATGATTTACTTTTGTTAATACCACTTTGCAAATCAAACTGTATCTATTTGGTTGGTTGGTTGGATCTTTTCTTT
1441 TCTTTTCTCTTCTTTTCTTTTCTTTCCTTTTCTTTTCTTTTCTTTTCTCTTCTTTCTTTTTCTTTTTTCCTTTTTCTTTT
1521 CTTTTCTTTTTTTTTTTAGACAGGGTCTCACTATGTAGCTCTGGCTGCCCTAGAACTCATTTAGGTAGACCAAGCTGGTC
1601 TCAGACTCAGTAAGATCTGTCTCTGCCTCCCGAGTGCTGAAATTAAAGGCTTATGTCATCCTGCCTTGCAACGTGTATTT
1681 TCCTGCTACCATTTCCTTGAGTTATCTGCCAAGTTTGGAAGAAAGGGGAAGAACTGTAGTAAATGATGGATATTTTCCTT
1761 TAATATATCAGTTTATCTTCATAGTATATTTGTTTGGGGAAGGAAATGCCTATCATCCATGCCTTCTGTACAACTAGAGA
1841 ATTTGGAGGGATGGAGAGGCATCTGGAACTGTATCTTGGTTATTACCAATCCCAGCCTTTCCTATTACATGTGTGTTGTA
1921 GCTGTCATGGTCATGTCTAAAGCCCAGTCCCCTTGTCTGTGGGTTAACACATCTGTAGGTGCAGCTAGACCCAAGATGAA
2001 GATATTTGAAAAAAAAATTGCATAGCAAACATGTACCAAATATTTTCTCCCCCCCCCCAGCAATACAGCACAACAGTTTG
2081 CATAGCAATTGCATTGTATTAGATATTATAATACCCTAGAAACAATATAACTTATAGAAGAAGATGTGAGCAGGGTGTAT
2161 GTAAATAGTACATGCCACTTTGTAGATGGGACGTGAGTGTCACAGACACTGTATCCCAGCAGGGGATGGGGCATGTCCTG
2241 GTTCCAGTCTCCCAAGGACACTGAGGGATGGCTACATCTTATTCCAACTGTGAAAAGTGGTTCAAATAAAACATTCTTGA
2321 GATAACCTTCCTCATCACCCCTTACAAAAAGTTCTGTTTGGGGTATTCAACAGTGATGCTCAGGAACAGAGGAACAGACT
2401 ATAAACACTGTAAATAAGTAAGACACCATTAGCACAAAGATACAGAGAGAAAGAGGAGTTCCATCAATTGCAGGGAAAAC
2481 CTAAAGACACCTGCTCTTTTGCCTCCATGACTGTGCAGGCTGGAAAACAAAACTCTGAGCAAATATTTTGGGGATCATTT
2561 GGCCACGACTTGCTAGGGCAGCCATCACATCTTATCAGGGCAGTATAGACACACCTCTGCAATTTATGCCTACAGTATAT
2641 GGGTAATTTTGAGAGAGAAAAGGGTGCTTCATTGGGGGCTACAAATAATTGAATAGACTGATGTAATTCATTTATGTGCA
2721 CTAATAGCTGTGCCTCAATAGAGAATGTAGAGGTGTGTGAAAAGAAGGACCTAGGGCTGTGAATGAAATAAAAGTCAACT
2801 CGTTGTAACATTTTAGGATTTAAAACATGCGGAGAGAGACAGAAAATAGAGGGACCTCAGTTGGAGCTGGTAAGGTAGGA
2881 TGTAAAGCCCACGAGGTTGCTTTCCAGAGGCAAAGCACAGCCCGATTACAGCCCCTGGGTAAATTGCAATCACTTATGTT
2961 CTGTGTTGTTAATCTGAAGACTCAGAAAATATACACAGCTGGGCTTACCACGTCTTGGTGCACTGAGGTTGATAGGATAT
3041 GGTCCATGAAAGCTAGTGAATTTTTGAGCCCCAGAATAGCCTGCACTGCCATTAAGGACAAAAATGCAAGAAGATGCAAT
3121 ACGTTCTGTACCCTTCAAAGTCTTTAATCCATTTCCAAGTTGCTGCTCCTGGGAAGCAGAGTCCGCTTTGCAACTGCAAA
3201 CTTTACATGCTTGTACTGTGGTTCCTGCTTACCCCTATTCAGTTACAGCCACAAGGTAGGACCCAAACATGTACTTGTGT
3281 TTATTTTTCTCAAAGAAAATGTCTTGTGATTTTTGTTAATGCCTGAGTTCCGTGATTAAATAAATGTACCAGCTCAGCTT
3361 ATCAGAAAATACCATGTTACCCAGCAGCCAAAACAATAAAACTCAAGCTGCCTTTTTCTGAATGGACCAGAGACCCGATA
3441 AGAGCGTCTCCAGGAAGCCAGATCTTAATAGAGTATGTCCATCTTCTCTGGGCTCCCAGGCCAACCTGTGAACTCTTAAC
3521 TTACCAGTTAATTTCAGTAGGCTGAGTTCATTTCATTTTCACTTCCTGTTGTAAGGATGGGTCACAAATAGAAGGTAGGT
3601 GGCTGGTGCTTCAACATAGTTCTCTAGACTGATGGTGGGAATGTGAGGAAGCGTTATAGCTGAGGTGATAAGGAAGTGAG
3681 TCCTGAAAGGTTCTATGCTTTAAGACAGGGTGATAATGATACTGTGTGTGTTTTACAACAGTGTGTAAATAGAAGTTATG
3761 TGGCAACAGGAGGTAGGTTTCCCACCCCCACTCCCACTATCTTGCCCAAATGTCTTCGGAATTCCACTAAATTATCAAGT
3841 TAAATGGACTTAAGACAATTGGTTGCATTTGTTTTCCCTTAGTTACAACAGACTCCACCTCTGTAGTTGCTGAGAGCTGG
3921 GCCCCTACCCCAGCGTAGGCACAAGGCAGCAAGAAAAGGCATTCTTTTCATAGCAATACAAATTATACTCAATACTTTCC
4001 ATTCTAAATTACTAGAACTAAAGGATTAAAATATTAACAATTTACCCCCATAATGTGCCATTTAGCATTCCCTCGAACAG
4081 AGTTTGACACAAAATGTTTATCTTGGACACTCCTAAAATATGTTTGTTGTGGTTGTTTATCCAGCAAATTTTGGCAGAAA
4161 TCTCTTTGGCTTAAAACATTCTGGTTTCCTGTAAAGAACAACAAAGAAACCCATACGTTGTGTTATTTTGTAACTTCACC
4241 ACTGTTAATAAAGCTGCATATAAAAA
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' uagGGCGUCUUAGAGUCGAGGUUa 5'
             || |||  |:||  |||||| 
Target 5' ctaCCTCAGTCTTTC-CCTCCAAa 3'
 134 - 156 132.00 -15.80
2 
miRNA  3' uagggCGUCU-UAGAGU-CGAGGUUa 5'
               |:||: : || : |||:||| 
Target 5' agaagGTAGGTGGCTGGTGCTTCAAc 3'
 3590 - 3615 131.00 -12.60
3 
miRNA  3' uaGGGC-GUCUUAGAGUCGAGGUUa 5'
            ||:|  ||: |||  |||::|| 
Target 5' gtCCTGAAAGGTTCTATGCTTTAAg 3'
 3680 - 3704 130.00 -15.40
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 GSM1013581. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013582. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013583. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013585. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013586. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013588. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013589. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013592. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013594. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013595. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013598. 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 GSM1013581
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep7
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1013582
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep8
Location of target site NM_172925 | 3UTR | CCUCCAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1013583
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep9
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1013585
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep11
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1013586
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep12
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1013588
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep2
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1013589
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep3
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM1013592
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep6
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM1013594
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep8
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM1013595
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep9
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1013598
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep12
Location of target site NM_172925 | 3UTR | CCCUCCAAAAAAAAAAA
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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