miRTarBase - #MIRT598042


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pre-miRNA Information
pre-miRNA mmu-mir-486a   
Genomic Coordinates chr8: 23142555 - 23142682
Description Mus musculus miR-486a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-486a-5p
Sequence 33| UCCUGUACUGAGCUGCCCCGAG |54
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Nkain3   
Synonyms C530048M05, E130310K16Rik
Description Na+/K+ transporting ATPase interacting 3
Transcript NM_172987   
Expression
Putative miRNA Targets on Nkain3
3'UTR of Nkain3
(miRNA target sites are highlighted)		 
>Nkain3|NM_172987|3'UTR
   1 GAAGACAAAAGATTTGTATTTGTTAAGCATAGATCTCATGCAGTGGTGTAGAGTATGGAATGTATAATGAGACCCAGACA
  81 TGAGGGAAGTGAAATACAAAGCTATTTTAAAGGCCCCAAACAAGAGAAAAAAAAATGGCACAGGAGGTGGGAGGTGAGGG
 161 GTGGTGGGGATACAAGGAAAAATGCCTTGTCTGAGAAACAAGATCTGTAGGCTCCATTGAAATAGGTTGAAGATGAGCAA
 241 CTAAGAGTTCTATGTCACCTTGGGAGACTGTTCTGAGAGTTACATGGCCAGGTGATTTCATACTTATACTTCGGAAAAAG
 321 CCAAGCTACCTGTCACTTCCTGCTGGCCTTAAACTACAAACCTGAATGTCTTATTATAAGCAATTGTGACATAATGATAA
 401 TTGTTTGTGCATCTAAACATATCTGGCTATGAAAAAGATCCAGTACTAATTAGATGATATGAAATTGTTTTAGTTCTGTT
 481 TGTAATATTAGGGGACTACAATCTTCCTGTGGTTTATTCTTAACTAAAACACCATTATGAATAATATAACTGTAGTTGAT
 561 AGTAACATTGTGATCCATGATTGAGAATACAAAGTAGGATTAGGAGAAAACCGGCATGAATGTGAGGTTTAAACGTCTTA
 641 AATTACCTACAATTACCAACTCAGAACTAAAGTATAATCTATTGCTTCTAGCCTGAGATTCCCGTGTGCCACAGAGTGAT
 721 GAGAATATGACCAAACATCAAACTTTAAATTTAGTTAAAACCATATGAGGTATGTTTGCATCTTTTTTGTTGTTGTTGTT
 801 GTTTAATTGCACAGTTCTCAAGTGTCAACTTTCAAGTTTTCCTATAGTGATGTTGTGTCACAATGTCCAAAGCCTAGACA
 881 TACTGGAAATAAGGAAAAAGACAAGACCACATGAGCCAATTCATTAAGGTATTAATTCAAAAGTCACTAGGTAAAACGCA
 961 ATCAGCAGAGGCAAAAGAAGAGTCATCCAGAAGCCTAAGGAAACAGGGAGAACTCAGGGAGTCCTTGGTAATGAGAAACT
1041 GGTGTGTTGCATGACTCTAACATCCATGAAGACGAAGCCTGGATGAGCAAATACAAACACAAGTATACACAGTTAAATAA
1121 TGAGAAGCAATCTGAGCTTACAAAGCTTTTATTTTTGCCTTGTTTCCTGCTTGTTTGTATTCTCCTGAACCTATAACGGG
1201 CATAATTATAAGCAAGAGTACTTCAAAGAATGCTCATTGTGTTAAACTTTGAGATATTTACAAGATTCAAAGCCTAAATT
1281 ATCTTTGTGGGAATGAGCTTTGAGCTTTTCATTTCTTTAAAATGAAAACAGAGTTCAGAATGATATTAAATATTTTCTTC
1361 TCTAACGTTTTTTCCTTCTTTATTGATAGTATACAATTCTTTTTATCCTGTGCCTGGCAAATTCATTAACAAATATTTCA
1441 CTGTCAAACAGATGACAATCTGTAGCCCAGCTTAACCCTCGTCATTCATTAGAAGAGAGATGGGAAATGGGGAACTTCAA
1521 TTTCTCTCTTACTGTATCAAGTCTGAAATCTTACCTCCACATCAAAGGTTAGCTTTAACACTCAAAAAAGAATGCCTTTC
1601 GTGTCATTAGGAAAGTGTCTGTCATGAAGATTCTCAACCTTGGAAAGAGAACAGGACATGGACTGTTCACCAGTGCTCCA
1681 CATCAGTGAAATAGGTACATTCATAAGAAACAATAAGGACTTTTGCAACAAGAAACAGAATTTTGGAAATAGCATCCTTA
1761 GTTCACTTTTAATTGTCAATTTCAGTGACTATAAATTCCTATATCATATGCTAGCAGATACATATATGTGCCATGAGGTA
1841 CATCTTTAGCTCAGGTAATCAAATATCAGTTGACATTATAAAACTTGCTAAGAACTTTATATGCCCCAGTACAGGGGAAC
1921 ACCAGGGCCAAAAAGGGGGAGTGGGTGGGCAGGGGAGTGGGGGTGGGTGGATATGGGGGACTTTTGGTATAGCATTGGAA
2001 ATGTAAATGAGCTAAATACCTAATAAAAAATGGAAAAAAAAAAAAAAAAAAA
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' gagccccgucGAGUCAUGUCCu 5'
                    | ||||||||| 
Target 5' ctttatatgcCCCAGTACAGGg 3'
 1895 - 1916 152.00 -15.70
2 
miRNA  3' gaGCCCCGU-CGAGUCAUGUCcu 5'
            :|||| |  :|::|||:||  
Target 5' taTGGGGGACTTTTGGTATAGca 3'
 1972 - 1994 124.00 -16.20
3 
miRNA  3' gagcCCCGUCGAGUCAUGUCCu 5'
              ||  ||   || ||||| 
Target 5' ccttGGAAAG---AGAACAGGa 3'
 1638 - 1656 115.00 -14.60
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 GSM622570. RNA binding protein: AGO2. Condition:WT1A HITS-CLIP data was present in GSM622571. RNA binding protein: AGO2. Condition:WT1B HITS-CLIP data was present in GSM622572. RNA binding protein: AGO2. Condition:WT2 HITS-CLIP data was present in GSM622573. RNA binding protein: AGO2. Condition:KO1 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]
16 mmu-miR-486a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT003527 Pten phosphatase and tensin homolog 5 2
MIRT003791 Pax7 paired box 7 4 1
MIRT004586 Foxo1 forkhead box O1 5 1
MIRT578874 Fam129c family with sequence similarity 129, member C 1 1
MIRT581056 Shc4 SHC (Src homology 2 domain containing) family, member 4 1 3
MIRT590827 Zcchc9 zinc finger, CCHC domain containing 9 1 1
MIRT592961 Tns3 tensin 3 1 1
MIRT597071 Tbc1d8b TBC1 domain family, member 8B 1 1
MIRT598042 Nkain3 Na+/K+ transporting ATPase interacting 3 1 1
MIRT598358 Maoa monoamine oxidase A 1 1
MIRT598720 H2-Q4 histocompatibility 2, Q region locus 4 1 1
MIRT598800 Gm7609 predicted pseudogene 7609 1 1
MIRT599803 Aim2 absent in melanoma 2 1 1
MIRT601041 Cnnm3 cyclin M3 1 1
MIRT606321 Ms4a6c membrane-spanning 4-domains, subfamily A, member 6C 1 1
MIRT736452 Igf2bp3 insulin-like growth factor 2 mRNA binding protein 3 4 0

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