miRTarBase - #MIRT596728


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pre-miRNA Information
pre-miRNA mmu-mir-664   
Genomic Coordinates chr1: 185242975 - 185243043
Synonyms mmu-mir-664, Mir664
Description Mus musculus miR-664 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-664-3p
Sequence 38| UAUUCAUUUACUCCCCAGCCUA |59
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Wdr59   
Synonyms 5430401O09Rik, Cdw12
Description WD repeat domain 59
Transcript NM_001170742   
Other Transcripts NM_001170743 , NM_176923   
Expression
Putative miRNA Targets on Wdr59
3'UTR of Wdr59
(miRNA target sites are highlighted)		 
>Wdr59|NM_001170742|3'UTR
   1 ACTTAAAGGACAGTGGCACTTCCGGAAATCCCAGAGGACTCCATAAGTGCTGGAGAAGGCTCTCTGCTGCTGCTGGTGGA
  81 AAGTCCTAGAACCAGGGCCATCCTCGTGATTTAGGATGGAGAGTATCCTCTCACAGACTGTCACAGCATCCGCTCGTGAT
 161 CCTGTGTGTTCCCTTCTCCTTGGCTGCCGGGCACGGATGGTGCTGGAAGAAGGGAGGGGGACGCACAGAGCTGACCCTCC
 241 TGTACTGTCTGTTGAGTCCACAGTGGATGTTTTCATGAGGAAAAGCACCTGTTTCCAGAGCCATCAGAGCTAGCATCAGC
 321 CTTCAAGATTCTGTCCTTGAACCAGGAATGGACCCTCCAGATGCCAGTACAAAGGCACACAGCAGCTGCAAAACAGACTC
 401 CTGAGCCAGAAGACGCTGGCTCTTAGTGCCATCCACAAGTGAGCTATGGTATCTGTGACTTAGAAGTTGGCACCTTGATG
 481 ATGGCCTTATAAAATACAATACTAAAGTGTAATATATGATGGACATATATTCAGCATTCTTTTTCTTGGTACAGGGCTGG
 561 AACTCAGCGCCTTGCACATACTGGTGAGCAGCCATACCACTGAGTTACATTCCAGCCCCATAAGAAACTTAAGATGTATA
 641 TGTTTTCTGTTTCTCTTCATCTGCTTTCCTTTAACTAATAGAAGTTTGTACTTGTGTGTGTGTGTGTGTGTGTGTGTGTG
 721 TGTGTGTGTGTGTGTGTGTGAGTGAGTGAGTGAGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGAGAGAGAGAGGATG
 801 AATAAGGAAAGTGACCGTCTTAGTGACTCATTTTGCATTGTACTTCTGGTTGAAGGGAACTGTTTTGGACCGGACTAGAA
 881 TTAGTCTCATGACTTGTAAAGGAAATGCCATTTGACTTTGATCATCTGACAGAGGAAACGGAATCTGACATTAAGGTTCT
 961 CTCTAGCCGCAAGAGTCTCATAATTATTTCTTCTAGCACAGGGGAAATGAGATTGCATTTCAGCACTGATACCAGAGTCT
1041 CTCTCTGCCTCTGGGCAGGCTGGCTGGGCTCCAGGGGTACTTTTTACTTGAACTCCCTTGCAAACTCATCATGATTTTCA
1121 GGGGTTTCACTTGTCTATACCAGGGAAGAGAGTTTAAAAAAAAAAACAAGACCCACTATACTGAAATCTCTCTCTCTTAG
1201 AAATTTAAATTCCTTGGGCCTGTCATAAGGCTCAGTGGGCAGAGGTGCCTGCCACTAAGCTTACTAACCTCAGTTTTCTC
1281 CCTCGCATGAGCCACCATAGAAGAACTGACTCCTAAGAGTTGTCCTCTGACTTCCACATGTGTGCTTTGATATGTGAATG
1361 TACACACACACATACAAAAAATGTAATTTAACAATTTTATGATTCCAAACTAATTAACCGGAGACACATAAGTAATTTGT
1441 GTCATTGGATTATGGTTGCACGTGTTTGTAGTCCCTTCACTCACGGGGCTGAGGTAAGAGGGTTTCAAGTTTGAGACCAT
1521 CCTGGGCTACACAGTGAGGTGATGGCCAGCCTCACTTATATATGAAGACACTTACAAGCAAACGTCATAAAGAAGATCTG
1601 GAGAGATCGCTTAGTAATCAAATGCTTGGCTAGCATACAGGAGGTGATGTGTTTGATCCTCAGCAACACACACACTGACA
1681 CTCAAACTAAAACAAAACAAAATACTACATGTTCCATAATAGGTAAGTGTTGTATATCACTTTGTTTGAAACTATGATTT
1761 AAGACTCATGAATGGATTAGGAAATCAGTCTCGTAGATAAAAACCAACACTTTCTATTTTCAAGGATTACTTTGTGTGTG
1841 TAAATCTCTGTGTCTTCAAGTGTATGTTGTGTGGGACAGAAGAGGCCATCTGGTTCCTTGGTGCTAGGATTATCAGTCTT
1921 TTCAGGACACCTTGTGTCATGTGTGTTCAGGGATCCTAACTTGGATCTTCATGATTGCAAAGTCAGAACTGTTTTGTCTC
2001 CAGCCCCCAAACTGTCATATAAAGAAAGTAAAATAATGTGGGTGAGAGACAATCGTGTAC
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' auCCGACCCCUCAUUUACUUAu 5'
            ||   | ||| ::|||||| 
Target 5' agGGAGAGAGAGAGGATGAATa 3'
 783 - 804 140.00 -12.40
2 
miRNA  3' auccgAC-CCCUCAUUUACUUAu 5'
               || | ||||:|:|||:| 
Target 5' gtgtgTGTGTGAGTGAGTGAGTg 3'
 730 - 752 133.00 -15.10
3 
miRNA  3' auccgaccccucAUUUACUUAu 5'
                      |:||||:|| 
Target 5' atttaagactcaTGAATGGATt 3'
 1757 - 1778 130.00 -5.60
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 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]
34 mmu-miR-664-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577936 Prl5a1 prolactin family 5, subfamily a, member 1 1 1
MIRT578554 Hopx HOP homeobox 1 1
MIRT579006 Cyp19a1 cytochrome P450, family 19, subfamily a, polypeptide 1 1 1
MIRT579669 1200011I18Rik GPALPP motifs containing 1 1 1
MIRT580267 Trim12c tripartite motif-containing 12C 1 1
MIRT580632 Sycp2 synaptonemal complex protein 2 1 1
MIRT580981 Slc12a2 solute carrier family 12, member 2 1 1
MIRT581678 Ppp1r3d protein phosphatase 1, regulatory subunit 3D 1 1
MIRT582092 Ogdh oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 1 1
MIRT582126 Nr2c1 nuclear receptor subfamily 2, group C, member 1 1 1
MIRT583126 Heca hdc homolog, cell cycle regulator 1 1
MIRT583594 Fam78b family with sequence similarity 78, member B 1 1
MIRT583662 Fam160b2 family with sequence similarity 160, member B2 1 5
MIRT584399 Cdc27 cell division cycle 27 1 1
MIRT584815 Arid4b AT rich interactive domain 4B (RBP1-like) 1 1
MIRT585915 Slc16a9 solute carrier family 16 (monocarboxylic acid transporters), member 9 1 1
MIRT586057 Rnmt RNA (guanine-7-) methyltransferase 1 1
MIRT586080 Rgs4 regulator of G-protein signaling 4 1 1
MIRT587942 Atl2 atlastin GTPase 2 1 2
MIRT590595 Atp2a2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 1 1
MIRT590735 Ado 2-aminoethanethiol (cysteamine) dioxygenase 1 1
MIRT591492 Aqp3 aquaporin 3 1 2
MIRT594084 Scoc short coiled-coil protein 1 1
MIRT594733 Zfp62 zinc finger protein 62 1 1
MIRT595057 Aldh1l2 aldehyde dehydrogenase 1 family, member L2 1 1
MIRT595113 Rgs17 regulator of G-protein signaling 17 1 1
MIRT595239 Rhbdl1 rhomboid, veinlet-like 1 (Drosophila) 1 1
MIRT595762 Otud6b OTU domain containing 6B 1 1
MIRT595778 Mc1r melanocortin 1 receptor 1 1
MIRT596728 Wdr59 WD repeat domain 59 1 1
MIRT598239 Mlph melanophilin 1 1
MIRT600005 4930563E22Rik RIKEN cDNA 4930563E22 gene 1 1
MIRT602439 Emx2 empty spiracles homeobox 2 1 1
MIRT736865 Smad4 SMAD family member 4 4 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-664 Acarbose Approved 444254 Microarray diabetic rats cells 24260283 2014 up-regulated
miR-664 Sorafenib approved 216239 Quantitative real-time PCR hepatocellular carcinoma 21530512 2011 up-regulated
miR-664 Ginsenoside Rh2 NULL 119307 Microarray NSCLC cell line A549 23152132 2013 up-regulated

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