miRTarBase - #MIRT594311


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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 Nr3c1   
Synonyms GR, Grl-1, Grl1
Description nuclear receptor subfamily 3, group C, member 1
Transcript NM_008173   
Expression
Putative miRNA Targets on Nr3c1
3'UTR of Nr3c1
(miRNA target sites are highlighted)		 
>Nr3c1|NM_008173|3'UTR
   1 CTGCCTTACTAAGAAAGGCTGCCTTAAAGAAAGTTGAATTTATAGCTTTTACTGTACAAACTTATCAACTTGTCTTGTAG
  81 ATGTTTTGTCGTTCTTTTTGTTTGTCTTGTTTGTTTTCTATACGCACTACATGTGGTCTCTAGAGGGCCAAGACTTGGCA
 161 ACAGAAGCAGATGAGCCATCACTTTTCAGTGACAGGAAAGCAGACAGTGATGTGCATTGGCTGGTGTATCACAGAAACTA
 241 GAACAGTTAGTGGAGACATGTCCACTATCAGAGAAGGACCGCACCTGAACCACCAGTGCCCAAAGTCCATGTGATCAACT
 321 TTCTGCTCAACTTTCAGTTGGCTGGATAACACTTTCTAGACTTTTCTGTTGGTGTATTTTTCCCATGTATAGTTAGGATA
 401 GCATTTTGATTTATGCATGGAAACCTGAAAAAAGTTTACACGTGTATATCAGAAAAGGGAAGTTGTGCCTTTTATAGCTA
 481 TTACTGTCTGGTTTTAACAATTTCCTTTATATTCAGTGAACTATGCTTGCTCGTTTTTCTTAAATAATTTTTGTATTCTA
 561 GTTATTGTATAGCTGTTTAAGATGGGCAGCTGCCTCACAGCTCTCCTAGACGCTAACATTAATTTCCGTGTGAAAATGGG
 641 TCGGTGCTCCTACCCTGATGGCACTCAGCTATCAGAAGACCACAGAAATTGACTCAGATCTCCAGTATTCTTGTCAAAAG
 721 CTCTTACTCTGTATATATCTGCTTCCATGGGGAATTATATAGGTTGTGCAGATTAACCGTCCTAACTGGTATAGAGCACC
 801 TAGTCCAGTGACCTGCTGGGTAAACTGTGGATGATGGTTACAAAAGACTAATTGTAAAACAGTGCCCACCAACAGGCCCC
 881 GTTTGCACCCAATGCACCATCTCTTCAGTGGTGCGATAGCAACAAAGTTTGTAACTCAGCTCTTTCAGGACCTTCGGGAG
 961 TAGTTTGTGTAACATTTTAAAATGTATTATTCCAGATAACCAGCTGTGATAAAGCCGAGAGATTGTTTTAATCAGACCAA
1041 GTAACTTCTCTCATTAAACGTTACCCTCAACTAAGTCTCTAATATGGCAAGAATGGCTAGACACCCATTTTCACATCCCA
1121 CCTGTCACCAATTGGTCTAGCTTTCCTGGTGGTACAGGAAAATCAGCTACTGATTTTTTGTTATTTAGAACTGAATGTCA
1201 GGCATCCATGTTTGTCCAACTATACATCCCTACATGTGCCATAGAATCTAACACAAGTCTTGTGAACTTCTTCACACTGA
1281 GAGTTATCATTTTAAACAAAACAGAAGCTGTAGTAGCCCTTTCTGTGTGCACCTTACCAACTTTCTGTGACTCAAAGCTT
1361 AACACACTTACTAAGCCACAAGAAATCTGATTTCTACTTAAGGTGGCCAAATTATTTGTGTAATAGAAAACTGAAAATCT
1441 AATATTAAAAATATGAAACTTCTAATATATTTTTATATTTAGTTCTAGTTTCAGATATATATCATATTGGTATTCACTAA
1521 TCTGGGAAGGGAAGGGCTACTGCAGCTGTACATGCAATTTATTAACATGATTGTAAAATAGCTGTATAGTGTAAAATAAG
1601 AATGATTTTTAGATGAGATTGTTTTATCATGACATGTTATATATTTTTTGTAGGGGTCAAAGAAATGTTGATGGATATCC
1681 TATAAGATTTATAGTATATAAGAGCATCCATACAGGCCTCAGTGGTCTTGGAAATTAAAACAGGTTTGCTCTAAGCTAGG
1761 GAGAGGGAGCTGGGACTGGCCCTGTGTGCAGTGCAGGTCCTGAGGGTTTGACCCGATCAGATCACAGGGGAACTAATTCC
1841 CTCCCATCTAACCATCCTCATCCGACCATGGCCCTGTCAGTGCAGGCTGGCTTTATTAAATCCAGGACAGAAAGGTGGCG
1921 CTTATGTACTTAGAGGCACCGTCCAGTAACAGGGTTGTTCCCACATGCAGCCTCCGCACGGGTTAACAGAAACAGAGGCT
2001 TTAGAAGTTTGGCAATAATGTGCATAGAGGTTCCAGCAATATGTAAATACTAAAGAATCGCATAGGAAGCCAATAATACA
2081 CTAATCCTCTCCATCCTACAAGAGTCCATTTCCAAGTAAGATGAGGACATGTTTATGTTTTCTTTGAATGCTTTTTGAAT
2161 GTTGTTATTTTCAGTATTTTGCAGAAATTATTTAATAAAAAAAAGTATAATCATTTGCTTTTTGAATTCTCTCTAAAAGG
2241 GAATGTTCAGTTTGTAATGGTTTAAATTGGTCTCAAAGTACTTTAAAATAATTGTAACCCAGCTGGATGTGAAATTTATG
2321 GTGCCTAAGAAATACCACTTGAAGATTATCAATGACAGTGTTAAGTTTCAAAATGAGCTTCTCAAAAATAGATTATTGTA
2401 CATTTATGGAATGTTATATGGTTAAACCCAAAAAGCACATCACACATAAATCTGCTTTCAGTTCCAACCAGCTTGGCTTT
2481 CAAAAATAGAGCTCCAAAAAAAAAAAAGGAAAAAAAAGATATATATGCTTTGTTATTAACAGAAGGCAGCAGACATTCAT
2561 AAAACTACTATCGGAAGTTTTCCATTAGATGTATAAAGAGCTATCCTTTGGTATGTGGGAAAGAAGAAAGCTGTCATAAT
2641 TCTGATTGAGTATAAGTGAGAGAGATACGGTACTGTTTGAGAGCAGCTCCTTTTCTGCGTGTGGCTTCATACCGTTCCAA
2721 ACTATGTAGATTTTATAATAGCTTCAGTGAGAATTGGTAACATGCCTGTATGACTCACAACAGATCTTGAAAACTATCTT
2801 TAATTACTGGTAGGACAAAAAGGGACATTCTGGTTATTTTAGGCACTGGCTTGGAACACTGTATATGCAGAAGAAAGAAG
2881 ACAGGCAATCTGGGGAAAGGAAGGGGACCTGGGAAGCACTGCCTTCTTTAAGGAAAGACACACCAATAGATGAGATCATC
2961 CCAAAGGCACAGGGACCACAGAGTGTGAGTCCTTAGTGACGAGTCAGGTGAGCTCTGGTGAGCTTGGAGAAGCCAGCCCC
3041 ACCAGCAGAGCAGGCACGGCAGGGATGGGACAAGCAGGGACGACAATTCCAGCTGGACACTGGTCCCAGTATTTTGCTCC
3121 CTCTTATATACCGTGAGGCAGTATCACCGTGGGATGAACCATGGTAGCACGTTTTGATCTGTCAGCACTCAAGGATCATG
3201 GTAGCCTTCGGGAGCTTTAGGTTTTGGTTGGTCACCCCAACGATCAGCTGTAGTTGAATGTGTTTCTTATGTGCCTGGTT
3281 TCAGTGTTAGAAGGTGAAATAGAGTGTGCAAAGGACACTGCAAACCACTTCGGATGGAAGTTTTCTCATTTTCCAGACTA
3361 TTTTCGGTCAGCCTGGTCTATCAAGATCGGTAACCAGGTCTTCAGGAAAGGGTTGGCTTCTATCTAGGACATGCCTGAAA
3441 GGATTTTATTTTCTGATAAATGGCTGTATGAAAATACCCTCCTAAATACCCTGCTTAACTACATATAGATTTCAGTGTGT
3521 CAATATTCTATTTTGTATATTAAACAAATGCTATATAATGGGGACAAATCTATATTATACTGTGTATGGCATTATTAAGA
3601 AGCTTTTTCATTATTTTTTATCACAGTAATTTTTAAATGTGTAAAAATTAAAAACCAGTGACTCCTGTTTAAAAATAAAA
3681 GTTGTAGTTTTTTATTCATGCTGAATAACCTGTAGTTTAAAAACCTGTCTTTCTACTACACAGTGAGATGTCAGACTGTA
3761 AAGTTTTGTGTGGAAATGTTTAACTTTTATTTTTCATTTCAATTTGCTGTTCTGGTATTACCAAACCACACATTTGTAAT
3841 GAATTGGCAGTAAATGTTAGTCAGCCATTTACAGCAATGCCAAATATGGATAAACATCATAATAAAAGTATCTGCTTTTT
3921 CATTATGTGACTCCCAAAAAAAAAAAAAAAAAA
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' ggCTTTCAAAAATAGAGCTCCAAa 3'
 2475 - 2498 158.00 -10.60
2 
miRNA  3' uaGGGCGUCUU------AGAGUCGAGGUUa 5'
            | | || ||      |:||||:||||| 
Target 5' atCACACATAAATCTGCTTTCAGTTCCAAc 3'
 2439 - 2468 148.00 -18.60
3 
miRNA  3' uaGGGCGUCUUAGAGU--CGAGGUUa 5'
            | :|::|  || :|  |:||||| 
Target 5' tgCGTGTGGCTTCATACCGTTCCAAa 3'
 2696 - 2721 136.00 -12.80
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 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 GSM1013594. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013595. 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_008173 | 3UTR | AGCUCCAAAAAAAAAAA
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 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_008173 | 3UTR | AGCUCCAAAAAAAAAAA
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 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_008173 | 3UTR | AGCUCCAAAAAAAAAAAA
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 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_008173 | 3UTR | AGCUCCAAAAAAAAAAAA
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 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_008173 | 3UTR | AGCUCCAAAAAAAAAAA
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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