miRTarBase - #MIRT585311


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pre-miRNA Information
pre-miRNA mmu-mir-466h   
Genomic Coordinates chr2: 10514891 - 10514971
Description Mus musculus miR-466h stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-466h-5p
Sequence 11| UGUGUGCAUGUGCUUGUGUGUA |32
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Zfp248   
Synonyms 2810037F07Rik, E130106N01Rik
Description zinc finger protein 248
Transcript NM_028335   
Expression
Putative miRNA Targets on Zfp248
3'UTR of Zfp248
(miRNA target sites are highlighted)		 
>Zfp248|NM_028335|3'UTR
   1 GTGTTTAGCTTTCGCATGCCTGTCAAGTCCATTGTAGTTTTAAAAATGAGCTTAGAGCCTGCCAAAGAATACCACAGAGT
  81 ACTAGAAAATACCATCGTGTTGGAATGCATGGAAGCTTTCAAGAAAAGAAGAAACTTTCATTTGAAAGATTGTATTGAAG
 161 GGAAATTATTCATATAAATAATATGGTAATAAACTTAGAAATTAAATTGTATAATGTCTTCCAAATCTGTCTTTTAAATA
 241 TAATGGTTAATATTAATTTTACTTGTATTCATAGGAAAGTATGAAACTTAAAAATGAGCGTCTACAGCATTGACCATACA
 321 TGTAAAGACAGCCGGTGTTTATAGACCTTGTGTGAGTATGTTAATGTAACAGAAGTCTAGGAAACCCTGGATTTATGATT
 401 TATTGGAACCCAGAAAGGATGTGAGGAAGATGAGCCCTTAGTTTAGCAACTGTTATGGAATACTTTCACACTAAATACCA
 481 CCAGCGTTTTTATAGGTTGATAGGATTATGTACGCTTCTGAACATATTTGTGAATGTGATCTAGATGTGTGAATATGTAA
 561 ATATACCTGTATGCATGTACCTGTACACAAATGGTGTTGTCACAAAGGCAGCTCACACCATTTAAAAGTGCTGATGATTG
 641 TTAAAATGTCAGGATTTTTGTGGCTCAATTGTCTAATATTACATGAAATTGCAGCTCAATTATACTGAGAGCAAAGGAAA
 721 TAAACAACACTTGTCATTCCTAACACTCTGCTGTATCTCACTGCTGTCTTGGCTGTGTACCATCGGTCTCCATGCTGAGA
 801 GTGCTGTAGAGTGGTTCACTATTGTATATCTCCTTCAGTTACCTCCCATGTGTGCGTGCACACACACACACACACACACA
 881 CACACACACACACACACACACACACACACGCCATTGCTCCGCTCATGTTGGTAGCTTGCCCTTAGGACGTTTATACTGTA
 961 GGAACTGATAAAGCATGTGTCAGAGCTTGATTTTCTCAGAGAAGCCGTGTGTATATAAACTATGTGGTAGATTTAAAATA
1041 TAAACTGCCCCTCTTTGTATTTCCTAAAATAAATAAATGGCTCTGGCCATCATTGTCAAATTGCCTCTATAGTAAAGAAG
1121 CCAAAGATGGTTTACTGAGCCTTTTAATTACCTCAGAACTATCCAGTTCTAAATACTACCAGTCTCGATAGCTTGGTCAG
1201 TATATGCTTCAAGTAACATTATTATATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
1281 CTCTCTCTCCCCCCCCCCCCTTCCCCTCTCTCTCACACACACATATATTATCACAGACTTTTCACTATTTTGGACCATGA
1361 ATAAGTATGGCCATTATTACCAAACTACCCATTTGGTGAGGAAATGAAACAGTATATTTCTGAGAGTTTTTCTTAGCTAC
1441 CTCTATGTCAATCATATAGATGCTGTTAATAAAAGTGATATTTACATGACTTAACTCGAGTTGTCAATGGTAATGCTACA
1521 CTCTACAAATTTAAAGATGGTAGTATATAATAAAATGTTCATATTATACCCTTGGAAAAAAAAAAAAAAAAAAAAAAA
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' auGUGUGUUCGUGUACGUGUGu 5'
            | ||:: |::|:||||||| 
Target 5' ctCCCATGTGTGCGTGCACACa 3'
 843 - 864 164.00 -18.70
2 
miRNA  3' auGUGUGUUCGUGUACGUGUGu 5'
            :|::|| |:|| ||:|||| 
Target 5' tgTATGCATGTACCTGTACACa 3'
 568 - 589 152.00 -16.40
3 
miRNA  3' augugUGUUCGUGUACGUGUGu 5'
               |:|:|  :|||:||:| 
Target 5' ggttgATAGGATTATGTACGCt 3'
 495 - 516 125.00 -12.50
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 ERR266298. RNA binding protein: AGO2. Condition:A_Untreated ...

- 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' auguguguucGUGUACGUGUGu 5'
                    ::|:||||||| 
Target 5' ----------UGCGUGCACACa 3'
 		1 - 12
2 
miRNA  3' auGUGUGUUCGUGUACGUGUGu 5'
            ||||||  ||||  ||||| 
Target 5' caCACACACACACACACACACa 3'
 		15 - 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]
CLIP-seq Support 1 for dataset ERR266298
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / A_Untreated
Location of target site NM_028335 | 3UTR | UGCGUGCACACACACACACACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1385342
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_GM_Ago2_CLIP-Seq_myoblast
Location of target site NM_028335 | 3UTR | UGCGUGCACACACACACACACACACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
87 mmu-miR-466h-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577339 Zfp157 zinc finger protein 157 2 2
MIRT577488 Tns4 tensin 4 2 6
MIRT578067 Oxsm 3-oxoacyl-ACP synthase, mitochondrial 2 2
MIRT578343 Ltf lactotransferrin 2 2
MIRT578743 Gm4841 predicted gene 4841 2 4
MIRT578822 Fermt1 fermitin family member 1 2 2
MIRT579127 Chrnd cholinergic receptor, nicotinic, delta polypeptide 2 2
MIRT579135 Chrna1 cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) 2 2
MIRT579305 BC021785 major facilitator superfamily domain containing 4B5 2 4
MIRT579417 Agtrap angiotensin II, type I receptor-associated protein 2 2
MIRT579732 Zfp92 zinc finger protein 92 2 4
MIRT579978 Wrn Werner syndrome RecQ like helicase 2 4
MIRT581035 Sim1 single-minded homolog 1 (Drosophila) 2 4
MIRT581532 Pten phosphatase and tensin homolog 2 2
MIRT582312 Nab1 Ngfi-A binding protein 1 2 4
MIRT582843 Itga9 integrin alpha 9 2 4
MIRT582976 Igf2 insulin-like growth factor 2 2 4
MIRT583470 Foxk1 forkhead box K1 2 4
MIRT584662 B4galt6 UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6 2 4
MIRT585220 Zfp488 zinc finger protein 488 2 4
MIRT585299 Zfp26 zinc finger protein 26 2 2
MIRT585311 Zfp248 zinc finger protein 248 2 4
MIRT585835 Slc6a17 solute carrier family 6 (neurotransmitter transporter), member 17 2 4
MIRT586077 Rhobtb1 Rho-related BTB domain containing 1 2 2
MIRT586329 Pgm5 phosphoglucomutase 5 2 4
MIRT587381 Dzip3 DAZ interacting protein 3, zinc finger 2 2
MIRT587611 Cml2 N-acetyltransferase 8 (GCN5-related) family member 2 2 2
MIRT587631 Clec7a C-type lectin domain family 7, member a 2 8
MIRT587725 Cd28 CD28 antigen 2 2
MIRT587758 Cd200r1 CD200 receptor 1 2 2
MIRT588012 Akap7 A kinase (PRKA) anchor protein 7 2 2
MIRT588296 1700019G17Rik N-acetyltransferase 8 (GCN5-related) family member 4 2 2
MIRT588555 Uhrf1bp1l UHRF1 (ICBP90) binding protein 1-like 2 2
MIRT588689 Tet2 tet methylcytosine dioxygenase 2 2 2
MIRT588893 Slc1a2 solute carrier family 1 (glial high affinity glutamate transporter), member 2 2 4
MIRT589021 Rnf11 ring finger protein 11 2 2
MIRT589101 Rasal2 RAS protein activator like 2 2 4
MIRT590106 Etv3 ets variant 3 2 2
MIRT590170 Elovl6 ELOVL family member 6, elongation of long chain fatty acids (yeast) 2 4
MIRT590929 Tacr2 tachykinin receptor 2 2 2
MIRT591061 Ptpre protein tyrosine phosphatase, receptor type, E 2 4
MIRT591144 Nsun3 NOL1/NOP2/Sun domain family member 3 2 2
MIRT591210 Mdm2 transformed mouse 3T3 cell double minute 2 2 2
MIRT591429 Car10 carbonic anhydrase 10 2 4
MIRT591502 Acot2 acyl-CoA thioesterase 2 2 4
MIRT591557 Zfp449 zinc finger protein 449 2 2
MIRT591632 Ubtf upstream binding transcription factor, RNA polymerase I 2 4
MIRT591952 Ceacam1 carcinoembryonic antigen-related cell adhesion molecule 1 2 2
MIRT591973 Ap1ar adaptor-related protein complex 1 associated regulatory protein 2 2
MIRT592040 Tnfrsf13c tumor necrosis factor receptor superfamily, member 13c 2 2
MIRT592091 Smo smoothened, frizzled class receptor 2 2
MIRT592109 Slc25a12 solute carrier family 25 (mitochondrial carrier, Aralar), member 12 2 2
MIRT592174 Oxtr oxytocin receptor 2 2
MIRT592217 Map3k7 mitogen-activated protein kinase kinase kinase 7 2 2
MIRT592224 Magee2 melanoma antigen, family E, 2 2 6
MIRT592250 Lcp2 lymphocyte cytosolic protein 2 2 4
MIRT592267 Kcnj16 potassium inwardly-rectifying channel, subfamily J, member 16 2 2
MIRT592390 Trp53i11 transformation related protein 53 inducible protein 11 2 6
MIRT592420 Stxbp5l syntaxin binding protein 5-like 2 2
MIRT592441 Snx12 sorting nexin 12 2 2
MIRT592515 Npr3 natriuretic peptide receptor 3 2 2
MIRT592626 Mbnl3 muscleblind like splicing factor 3 2 4
MIRT592703 Gfra2 glial cell line derived neurotrophic factor family receptor alpha 2 2 2
MIRT592746 Epas1 endothelial PAS domain protein 1 2 2
MIRT592765 Dmd dystrophin, muscular dystrophy 2 4
MIRT592843 Akap2 A kinase (PRKA) anchor protein 2 2 2
MIRT592989 Cacna2d2 calcium channel, voltage-dependent, alpha 2/delta subunit 2 2 2
MIRT593003 Bend4 BEN domain containing 4 2 2
MIRT593228 Fndc3a fibronectin type III domain containing 3A 2 2
MIRT593415 Neurod2 neurogenic differentiation 2 2 4
MIRT593453 Rab11fip1 RAB11 family interacting protein 1 (class I) 2 2
MIRT593482 Havcr2 hepatitis A virus cellular receptor 2 2 2
MIRT593517 Csf2ra colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) 2 2
MIRT594037 2810006K23Rik RIKEN cDNA 2810006K23 gene 2 2
MIRT594129 Fam104a family with sequence similarity 104, member A 1 1
MIRT595670 Rxrb retinoid X receptor beta 2 2
MIRT595701 Fndc7 fibronectin type III domain containing 7 2 2
MIRT596268 Bnc2 basonuclin 2 2 2
MIRT596281 Slc6a8 solute carrier family 6 (neurotransmitter transporter, creatine), member 8 2 2
MIRT598763 Gpr68 G protein-coupled receptor 68 2 2
MIRT601111 Btrc beta-transducin repeat containing protein 2 2
MIRT601202 Arhgef9 CDC42 guanine nucleotide exchange factor (GEF) 9 2 2
MIRT603151 Ubxn8 UBX domain protein 8 2 2
MIRT603192 Trim65 tripartite motif-containing 65 2 2
MIRT604581 Trim71 tripartite motif-containing 71 2 2
MIRT605447 St18 suppression of tumorigenicity 18 2 2
MIRT605591 Ncam1 neural cell adhesion molecule 1 2 2

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