miRTarBase - #MIRT587942


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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 Atl2   
Synonyms 2010110I21Rik, AA407293, AV334690, Aip-2, Arl6ip2
Description atlastin GTPase 2
Transcript NM_019717   
Other Transcripts NM_178050   
Expression
Putative miRNA Targets on Atl2
3'UTR of Atl2
(miRNA target sites are highlighted)		 
>Atl2|NM_019717|3'UTR
   1 CAGTTCATCTGCTCATGGACTCCACTCTCCCTTGTTCATGCTTGCTGTACAATGAGAACTCAGATAAAATAAACCAAAGT
  81 TTACAATCAACTGTAGAAGTAGTTTAGTGTAACTGGCTTCACAGATGGCCGCCACAGAGTGTGAACGTTGTTTGTTGGTT
 161 TGCAGCCTTCTTTGCTGTCTCCTTAGACTCGGTGACTGCCTGAGGAGCATCAGGTTATCATGCACACTTGTGCCATGGTT
 241 AATTCTTTTCTTTCTTTTTACCGAATTCAATGTTAGTGAAATTTGTCTTATGTAAAAGGATATTTCAGGGAAATATTTTA
 321 AGAAATCTATTTAGAGTCTCTTTAATATAGTGTCCCATTGAAATTTTAATTTTTAGAGAATTTATGAATCACTGTATCAA
 401 GAATCAGATGGGAATGACAATGAAGCCTTTACCGAGCCACTACATTAAAAGTGTATATTGCTTTACTGCCTTCAATTGCC
 481 AGTATTACATAAATGCATGTTTCAGAAACTTCACACAAATCACATGAGAACTCTTGTAGCTGAGAAGGTAATTCTGAGGT
 561 GTACATTTGTCTTGCCTTTTTAAATTTGTAAACCTGCCCTGAAAGGAGATGCATTATCTGGGAAACTGAACTGTCTTTTT
 641 GCAGTTTAGCCTTCATGTACATAAAATATGCCATTAATTTTATTGGGGGAAAAATTCCATCCAAAAATGTTGCCTACAGC
 721 TATGAGTTAAGAGTGTCTACAGCGTGTAGCTTTCATTTTCTAAAGATTACAGGTAGGGCATGTATATGAATTATAAATAT
 801 ATAAATACAATTTTGTATTAAAAGTTTTGTAGTTTATGGCAAAACCTGGTTCTGTGGTAGGCTACTGAGTCCAGTCCTGT
 881 GACAGGAGTGTTTGTGGCTCGTGTCACTGTGTGAACGCATAGACAGTGTGAAGTTTTGATATATTTGTGATATTTATCTT
 961 CCCTGAGCACTGCAGTCTCACCCCCAAGAGAATTCAATGGGAATGTTTTATTGTGACTTGTCCTCTGTTGCATTTTAAAG
1041 TTATTTCCTGTAATTTATTTTCAGTACATAATTAAAAATTTGTTGTATATATAAAACGAAAGTTGTGATTCTTTTTTAAG
1121 GAATTCTTTCAAGTGTGTATCTCACCATATAACATTGTTCATGCTGAAAGAGGGTGGGTCAGGGTGCACCGAGTTAGAGC
1201 TCAAGGTATTGTACTTTAAAGCTGAGCGTGTAAAAAGTTATTTTTCGTGTCTTTTTATGTAAGGGATATTTTTTGTGATA
1281 ATCTATCTGGGGATTTAATAATTTTAATCTTTTCTCCATCTCTTCCCCCACTCCCATCGTGTGTGTGTGTGTGTGTGTGT
1361 GTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAATATGTGTGTGTTTGCGTGTGGGCTATA
1441 TATGTAAAGCTACCATTTTTCCAGTACTTATAACCTCCTTTACAGAGACCTATTAAATCGCTCCTATTTGGTTTTTAAGA
1521 GAATTCAGATGTTGAGTTGCATGCATGAAGGTCTGAGTTTGCTTTGATTGGCACACTTCCCTCCCACTCTGACCCAGTCC
1601 TACTTTATATGGATTGTATTTGTTTCCGTCTGTGGTAAGCAGCTGCCTTCTCATCTGTTCCTACACAGAACGAATCCATC
1681 CGAACAGTCTCTCTTTCTCTGACCACTTTGTTTTATGAATGCTGTAAATTGTTTTTATGAATGAAAAATAAAAAGTTTGT
1761 TGTATACTAAAAAAAAAAAAAAAAAAAAAA
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' agagagaGAGAGAGAATGAATa 3'
 1394 - 1415 155.00 -10.00
2 
miRNA  3' auCCGACCCCU-CAUUUACUUAu 5'
            ||: ||| | ||| |||||| 
Target 5' caGGTAGGGCATGTATATGAATt 3'
 770 - 792 140.00 -15.50
3 
miRNA  3' aucCGACCCCU-CAUUUACUUau 5'
             | |||| | |  ||||||  
Target 5' tcaGATGGGAATGACAATGAAgc 3'
 404 - 426 135.00 -7.00
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Liver
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 ERR266281. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 48h HITS-CLIP data was present in ERR266292. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 48h ...

- Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' auccgacCCCUCAUUUACUuau 5'
                 | ||| :|||||   
Target 5' agagagaGAGAGAGAAUGA--- 3'
 		18 - 36
Article - Schug J; McKenna LB; Walton G; Hand N; et al.
- BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions C2C12
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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast ...

- Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell.

Article - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al.
- Cell, 2014
MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.
LinkOut: [PMID: 25083871]
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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