miRTarBase - #MIRT605081


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pre-miRNA Information
pre-miRNA mmu-mir-3058   
Genomic Coordinates chr10: 95559231 - 95559321
Description Mus musculus miR-3058 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3058-5p
Sequence 14| UCAGCCACGGCUUACCUGGAAGA |36
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Dennd5b   
Synonyms 9330160C06Rik, AI852444, D030011O10Rik, Gm17524
Description DENN/MADD domain containing 5B
Transcript NM_177192   
Expression
Putative miRNA Targets on Dennd5b
3'UTR of Dennd5b
(miRNA target sites are highlighted)		 
>Dennd5b|NM_177192|3'UTR
   1 AGCAGCCGGCAGAAACTCTTCATCTACCCCTGGCTCCTGAAGCTTCCGTAACTATGGGGACCTATCTGGACCGGTCTGAC
  81 CATAGTGAGCACTGCCGGGGCAGTGCACTGGAAGCCCCAGTTTGAACAGTCTCCACTCTGCAGACAAGGCAAAGTGCTGT
 161 ATTGTAGTTCATTTGAACCTGAAATTTAGTATAAAATAGAGTATTTTCATGTGTTAGAAGTGTGTAAATATGCTATCTTT
 241 AAGAAATTATATTACTCTAATAAGATACTTTTCTTAGATTGAATATCCCTGTGACTTAAAATAAGTAGTTTAAAAATGTT
 321 GGGGGTGGGGAAAGCGGTGCTAGTCAGGAAGAAGCCAGTAAATGTGTACATAGTGCAACCCAGGAAGGCTTCTTTTTCCC
 401 TCCAGGTCTCACAAAGGAACCAGAATGCTTTGTCCTGAAGCAGCCATCCCTCCTGGAGTCCCATCCTGTGTGTGGTGAAT
 481 GTATACAGCTTTACATAGTGTACAGCAGTCCTCATTGTACCTTTTAAGTTATAAACCATTTAATACATTTGAATTATGAG
 561 TAATTTTTTTAGTTTTTGGGAACGTTTTTCATTGGCATAAGGAAAAGATAATTAAAGTATTTTAAATATCAGACCCCAGC
 641 AAGGCATAGTGGCGCACTCCCAGCACTAGGGAGGCAGGGGCAGGTGCATCTGAGTTGCAGACCAGACAGAGCTACATAGC
 721 AAGACCCTATCTCAACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCAAATACCAGATCC
 801 CAAGAGCTTGGCTAATTGGAAAGCAAACACAAGAAGCCCTGAGAAGCATGGGACTTTAACTTCTTTACTTTTGAAAGATT
 881 AGCCTGGAGGCTTCGTTCTTGGAATTTTTATTACTGTTCTTTGATAGGGCTTTTGAGATAATGAATTTTAGTATCAATCA
 961 TATAGCCATAACTGTAAGAAACAGTGTGACTTTTAACTTGGCCATCTAAACTCTTTAAGTGGAGCTAAACTACCAGCCCA
1041 GTCTTTGTTAGGTTCCAGCCACTCCCTCTGTCCGCCCCATCCCCCCTCTCAGGAAATAAAAGGAATGTGGGAGAAGGAGG
1121 AGGTCTCAGTGTGATTTGGAATGCTTTTGTGAAGGTATTTGTTGACCATGATAATGCAAATAACAGAAGCTGAGAGAAAG
1201 AATGAAGCCTTTCTGGGTGTTTCAGGGAAATGTAAAGCAATTGTCCCAGAGAAGTTAAAAGCCACTGTGGCAGACTGAGG
1281 AGTGAATTTGACTCAAGAGACAATTTAGGAACTCCTGAAACCTTTCTAGTTTGATAGCTTATTTATTTTTTTGTTAAGCA
1361 AATGTTAGCAACTACATAAATCTTTATCTTTTGGTGAGTAAGTTTCGGAACTCTAATTAGGCACCGATACCTTGTTAGTA
1441 GCAAAATTGCCTCGGCAGAGCTCCAGGTTTTATTCCCTGTTGTAGCTGAAAACCCAAGCCATGGCCTCTCAGGATCCGTG
1521 TGCAATCTCAGGGCCCTGGGCTCTTGCCAGCAGTGCTGTTTTCCTGTTTACTGGAGGAAGGGACTAATAGATCAAGTACC
1601 TCATGCCCTTTATCAGAAACTCTGAAGAAAAGGGTTGCTGAGGATACATTTACACACCCATGGAAAGAAAGGGCTTAGAA
1681 CATGTCTCTAGATGACCTGTGTAACCCAGTGGTTTGTTTACTTAGAATAAGGGTGTTTATAGTAGAATGAGAGTATTCTA
1761 GAGACCAATCTACTTACTATAGGAAACATCCACAAATTAAGATACAGTCCATCCCAGGGTTTTATTGCTGTCTTTTCCCA
1841 TGGGGCCATCCTGATGCTGAGCGCTTGGTGGACTTTTAAGTCAGTGTTCCACAGTTGAGTCCCAACAGCAAGTACAGCCT
1921 CTTCATTTTATAGGTGAAAATAGGACACTTCAAATCAAAGACTTTGTATTCTTGCCCTCTCCCCCTTGACAACACAAGGG
2001 TTAGAATTTATGCTTTTTACCACACCCGAGAGCATGAAACCAACCTCGGAGACATTCTTACTCAGGATCATTTCTTCTGT
2081 TGAATCTTCAGTCAACTGTACAGATAGGAAGCTATGTTTCTGTGATGCAGAATAATAAGGACTGAAGCTTGCCTTGCCGC
2161 GTTAGATTGTTTTGTTGTTGTTTGTGAAACAGGATCTCACTGTATATCCCTGGCTGGCCCTGGAACTTCATTTGTAGACC
2241 AGGCTCACCTGGAGAGATCTACCTCCTAAGTGAGGGATTCATGTGAGAGCCCTGCCTACCAAACTGTTCTTAATCTCTTA
2321 GGCATTACATCTGTGGTTAAAAAATGGGAGCAGAGTTGCATTCCAGCTTAAGTTTAAAACTGTTACTTAAAGTAGTACCA
2401 AAAAAACAAAAAATTACCTATAAAGTTTTTTGTTCCACATGATGTCCTTTGGATGAGCTAATGGCTAGCCTTATGCCTTG
2481 CTCAGACAGCTGGGCCTCGTGGGAGCTGCTTAACTGACCCATAGCCCATTCCTTTGAATTTCCCACTGGCGATAGATCTT
2561 AGCCGTACAGGATAAATTTAATATGTAGAAACACTGTAAAGACCTTAGGGTGTGATAAAAAAGAAAAATGTTTCCACTGA
2641 ATTTGGGGTTACCCATTGCAAATGATAAAGAAGTAAGGCTTCTTATGTGACCTATAACAAACTGAATCAATATGGGAAAT
2721 GCATCACAATGGTAACATTGCTCAAAACAGATGCATATAATCGTACAAGCTGACTTCTGTAAGGACCATACAACAGGCAT
2801 CCTTCGTGCTGTGCTATTTAAAAACAAACAGACAAAAAACTTAGTACAAAGCTTTAGAATCACCGCATAGAAAATGAAAA
2881 TCAAAACTTTATTTGCGTGTGTGCAAATAAATTTAAAGCAAATACCTGGGACCAAGATTAATATCCTACGTAGTAACTAA
2961 AGTTAAATTGGCAAGGAGAGGTAGCTAAGCAGTTAAGAGCACTGGCTGCTCTTGCAGAAGACCCAGGTTCATTGCCAGCA
3041 CCCACATGGTACCTCACACCCACCTATTACTACAGTTCCAGAGGATCGGATGAACTCTTCTAACCACCTTGGGCACCCAG
3121 CATAGTGAACATACATTCGTGTAGGCAAAACTCTCATGAAATAAAACAAATCTTTTTTTAAATATCTTATTAAATGTGCA
3201 GTGGCTGGGGATGTAGCTCAGTGGTAGAATGCCTGTGTAGTAAATACAAAACCTTGGGTTCTGTCCTCAGCACAAATAAA
3281 ATTGCCAAATTTTTAACTTCTTCAAAAGCTTGTTCTCCAAGTCTTTGTTTTGAGTAATAAAATCTCTAATCTTAACCTTC
3361 ATGTCACATTTCTGGTGGCCTTACAGTGGCTTGCATATTATATGTGAAAAGCTCTCAATGCTTTAAGAAGGAAGTACTTT
3441 GGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCAAAGGTCCAAAGTTCAAATCCCAGCAACCACAT
3521 GGTGGCTCACAACCATCCGTAACGAGATCTGACTCCCTCTTCTGGAATGTCTGAAGACAGCTACAATGTACTTACATATA
3601 ATAAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGGAAGTACTTTAGTACTTCACAATGACTGAG
3681 CTTCTCCATGTGAGGTAGGGTTGTGAGTCAGAAAGCAGGCTGCCAGGAACAAGTGAAGACCCCTGACTTGACCCTGTTTC
3761 CCCTGGGAATGAAAATCTGATGGAGGAAACCTAAAATTTGCAACTGTTGAATTTCATCTAAAATTCATTTTAAATGTTCA
3841 TATTTATTGTACCTTTTCTAGCTCTGTAGGATTTATTTAACATGACTTTTAAAATTTTTATTTTAATGAACTTCTATAGC
3921 ACTGTATGAGTAATAAACATTTGTTTCTACTTCCTTTTCTGACAGTAAGCACATGTATAAGTGTAATGAAAAACAGATTA
4001 AGGCTATACATAGGACTTTGTGTCTGACATGTGTCAATATCTCTAAAATAGGAAGTAGTAGACAAGGCCAGGGAAATATT
4081 TGACAGTATTGGGAAGAGAGTTCTTTACAATGTGAAATATCTTCTAAGAATAATGGCTTTTCAATAGAGTATTCATTTAG
4161 GAAATTGTTTTTTCTCTGAAGTTTACAGAAGCTAGTCTACCCTTTTCATGGTGTTGAAAGGGTGTTCTAAACTTATATAT
4241 TTCAGTATTAGCACATCTTTATTGATTGACAACAGAGTACTCTACTGCTTTGATAGAGTAAATGGTATCTCTAAGCCTCT
4321 GTGTCTTTTGTTTGGTTTAGTTTTGCTTTTTTTTTTTTTTTTTTTTTTAAGAGTCCTCAAAGAGGCCTTGGCTGTCCTAG
4401 AATTCACTCTATAGACCAACCATGCTGGCCTTGAACTCACAGACATCCACCTGCCTTTGCCTCCCAAGTGCTGGAATCAA
4481 AGGCATACACCACCACACCTGGCAAGCATCAGTGTCTTTAGAAATCTTTGTTTCTTTCTCTCTCCTCTTTTAAAGATTTA
4561 TTTATTTTTTATGTGTACATCATTCTGGCTGCATGTATGCCTGCAGAGCAGAAGCTTATTAGAGATGTTATTACATATCT
4641 CATTACAGATGGTTGTGAGCCGCCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGATGAGCAGTCAGTCAGTGCTC
4721 TTAACCGCTGAGCCATCTCTCCAGCCTGAAATCTTTGTTTCTTATGTAGCTATTTTTTTTTCAATATCATTTAGAATAAC
4801 TGGGAGACTTTCTGTCTCTTTTAACTTATGTCCCTTTTTTAAAAAAATACATGTACAATTTTGCTCAATCCAATGGACCG
4881 TTGAGCTTTGTAAAGAAGTTTGCTTTTGCGGTATGATAAAAGGCATCCAAGGAGGGGCTGGAGTGAGTTCAGTGTTAGAT
4961 GTGCTTAACATACTTACACAAGGCCCTGAGCAGCACTCCAGCAAAAGAAAATAAACTCAAGGATGATTATAGCCGCCCTC
5041 CCCCCCAAGTCTGATGTCTCTCTCCCTCTCTCAAGGATAAGATCAAAATTGATTTCAGAAAGACACATTGAGGTGTTCAT
5121 ATTTATATCAGACTGAAGAAAAGTTCATCAAATAAACTTCCCCCTCTTGGAAGGGTTCTGTCATGTCCTTAGTGATTTAG
5201 GAAGTAGCCATGCTTGCTTGGTCCAATTACTTGTGTGTTGGATCCAAGATGTATTTTAAACAAATATTGGCATAGATAGT
5281 AAGGAGTTTCTGTTGTCAGTCAAATGAGGATATAAAACATAGAAAAAAAAATCTTATGCTACACTTGAGCCTCATATAAA
5361 GATAGCCTGTGTTTTGTTGTTGTTGTTGTTGGTTTTGTTTTTAATTACTATTTCTGCATTTAAATTATACACTGTTTTCC
5441 TTTGTATTATTAACAATGTATGTCAGAACTGGAGTTTTCTCCCCTCCCCCATCTGAACATAATATAAAATCTGAAAAGTA
5521 TTGTGACAAGCACTTTAACATATCAGACAAACTGACATGGGTTTTCAGGTTTTGGAGTACATTTAAATATGACTTTTCAT
5601 GCTTTGTTCTTTACAATAAAACTGTGGGGTTGATACT
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' agAAGGUCCAUUCGGCACCGACu 5'
            | ::|  |: || ||||||| 
Target 5' ctTATTAAATGTGCAGTGGCTGg 3'
 3186 - 3208 153.00 -14.13
2 
miRNA  3' agAAGGUC------CAUUCGG-----CACCGACu 5'
            || |||      ||:||||     ||||:|| 
Target 5' caTTACAGATGGTTGTGAGCCGCCATGTGGTTGc 3'
 4641 - 4674 143.00 -18.40
3 
miRNA  3' agAAGGUCCAUUCGG-----CACCGAcu 5'
            ||:| ||| :|||     ||||||  
Target 5' caTTTCTGGT-GGCCTTACAGTGGCTtg 3'
 3367 - 3393 140.00 -18.20
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 ...

- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011, Nature structural & molecular biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' agaagguccauucggCACCGACu 5'
                         ||||||| 
Target 5' --------------aGUGGCUGg 3'
 		1 - 9
2 
miRNA  3' agaaggUCCAUUCGG-CACCGACU--- 5'
                | |||: :| ||||: ||   
Target 5' cuggggAUGUAGCUCAGUGGUAGAAUG 3'
 		6 - 32
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]
14 mmu-miR-3058-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT582584 Lsm6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated 1 2
MIRT596389 Ulk1 unc-51 like kinase 1 1 2
MIRT597024 Thap2 THAP domain containing, apoptosis associated protein 2 1 1
MIRT598064 Nif3l1 Ngg1 interacting factor 3-like 1 (S. pombe) 1 1
MIRT598727 H2-D1 histocompatibility 2, D region locus 1 1 1
MIRT598925 Gjc3 gap junction protein, gamma 3 1 1
MIRT600197 Vsig10 V-set and immunoglobulin domain containing 10 1 1
MIRT601407 Uba1y ubiquitin-activating enzyme, Chr Y 1 1
MIRT603601 Pigv phosphat