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 Emx2   
Synonyms Pdo
Description empty spiracles homeobox 2
Transcript NM_010132   
Expression
Putative miRNA Targets on Emx2
3'UTR of Emx2
(miRNA target sites are highlighted)
>Emx2|NM_010132|3'UTR
   1 AAGTCCAAACCCAATCCTACAAAAATGGACAGCACAGAGCAAGAAAGACAGGGAGAGGAGGGGAAGAAAAACCCTACAAA
  81 ACAAAAACAAACTGCACACACATCCACCGAGAAAGGGAGAGAGGGAATCAGAGCAGTGACGCTCGCAGCAGACTTTGGAC
 161 AGCGAGGGCACTGGACCGGGAACCGGCGCCGGGCCGGGCACCGCTTACAGGACAGCAGAGGACGGAGGCCCGATCATCAA
 241 CATGCAACCCTCGTCTAAAGAGGCAGCTGAGTGAGTGAGAGAGACAGAGACTGGGAGGGAGAGAGAGGAATGAGAGAGAG
 321 AGAGAGAGAGAATGAATGATCCTTGTGAGGCAAAGGCACATTCTGACAAGGGGAGCTGTCAGTCAAATGCCAAACCAGGG
 401 AAACAAGATGATTGGCGGGTATTCCGCTTATCGAAGTCCATTTAGAAATGATAATGATTTTTTTTTTTGGAAAAAAAAAG
 481 GCACAGGACTTTTAATTTTGCACTTCACAGTGTTTCCCCCTCATCTTTAATTAGAAATAACATACAAAATTCCATGTCTA
 561 GCCCCATCCTACACCTGTTTCAAAACTTGAATTGCATGTAGCAGTTGTCGGGCGAATGGTGTCTAAAAACTGAATTGTAA
 641 TTTTATTCCTCTTTTAAAGACAGGTTCTGTGTATTTTTATTTTTTATTTTTTTTCTGAGAAATGTTCAGTCTGTAAAAAC
 721 ACTTTTTTGATACCTTCTATTGTCAAAGTGATTGTGAAAGCTAAACGAAGTAGGCTCGGAGATAGTGGTCCTCTGACAGA
 801 GAAATGAGGGAGCAGGACTGGGATGGAGGGCGGGGGAGGGTGCCCCTGAGAAGAATCAGGACTCATGCTAGGGGTAAAAA
 881 CAACCCACGATAAAAGACCCAAATTAATTCTATTTCTTGGATATTTCCTTTCCTAACATTCTGATACTTTAAATCACCAA
 961 GTCAACTTTTCCTTTTAGTGGTTGGAGAGATTGACTGCATCCAGCCACTCATCATAATGGCCATTCAGAACTTTTAAGTC
1041 TGTCTATTGCAAAAGTGGAAGGAAGGACTGTATTTAATGGGGTGATGGTGGCGTGGCCAAGGACATGGGAGTTTTCAAGC
1121 ACTGAGTTTCTCTTCCAAGACCATAGACTTACTAAAGAGGGTTACAAATGCTTCCTTAGTGTCTTCTATACCAGATTGTA
1201 AATATTTTTGTGTTTTGTGTTAATTTGTTAGAATTCTAACACACTATATACTTCCAAGAAGTATGTCAATGTCAATATTT
1281 TGTCAATAAAGATTTATCAATATGCCCTCA
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' agagagaGAGAGAGAATGAATg 3'
317 - 338 155.00 -9.90
2
miRNA  3' auccgacCCCUC-AUUUACUUAu 5'
                 || || |:|:|||:| 
Target 5' ctaaagaGGCAGCTGAGTGAGTg 3'
255 - 277 123.00 -15.90
3
miRNA  3' auCCG---ACCCCUCA--UUU-ACUUAu 5'
            |||   ||| |  |  ||| ||||| 
Target 5' cgGGCGAATGGTGTCTAAAAACTGAATt 3'
609 - 636 122.00 -7.50
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 GSM622573. RNA binding protein: AGO2. Condition:KO1 ...

- 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' auccgacCCCUCAUUUACUUAu 5'
                 | ||| :||||||| 
Target 5' agagagaGAGAGAGAAUGAAU- 3'
21 - 41
2
miRNA  3' auCCGACCCCUCAUUUACUUau 5'
            ||   | ||| :|||||:  
Target 5' -gGGAGAGAGAG-GAAUGAGag 3'
1 - 20
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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