miRTarBase - #MIRT592390


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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 Trp53i11   
Synonyms Tp53i11
Description transformation related protein 53 inducible protein 11
Transcript NM_001025246   
Expression
Putative miRNA Targets on Trp53i11
3'UTR of Trp53i11
(miRNA target sites are highlighted)		 
>Trp53i11|NM_001025246|3'UTR
   1 CAGGCTGGGACCTGCCTGGGCCTGGACCTGGGCCCGAGCAGCTGGGGACTTCACTGTCCATGGGTCCTAGACAGGCCTGC
  81 AGGCAGGCAGGGTGCACACGCCTTCCTTCCCTCCCAGGCACTCCACGGAGTCATCTTGGGTCTCCTGGGATTCTAGGAGT
 161 GACAGACCAGGCTGTGGCCTCTGCACCCCACCCCTCACCCTTGTGCAGGGACAACTCCTTGCCCTGTGTTTCTTGGCCTC
 241 TAGACTCTAACAGGCAGAGTCTAGAGTAAGTTTTAGGGTCTGGGCTGAGTCAAGGTGAGTTCCTCTGCCAGGAAGCCCTT
 321 TCTAGGAGGTTGTGTCGGCCCCAGCAGGGGCTCTCAGCTTCTCCCCATCCAGAAACCCGATGTGTGAGTCCCTCATCACA
 401 CACGCACACACACACACACACACACACACACACACACACACACACACACACACACGGTGTTTCTAGAGATCCAGTTGAGG
 481 ACATCTAGCAAGGGGAGTGACTGCCTCCCTTGGGCCAAGTTCCCCAGCCTCAGCCTGCACATCTCTCTCTTTGGCCTGCT
 561 GGAGGGTACTCTGATTCTCTGGCTGGCCGCCTGCGTCCCAGAGCACCAGAGTCCCTTCCCGACAGGCTAGGGTTAGGCAA
 641 TGTACCACAGGCCTGATAGTCCCTGGCTCCTAGCTGCCCATAGGCTCCTAGTGCATGAGGAATTCTGAGGAGAGGACAAG
 721 TGGGGACATTTCCTCGGCATGGCCTCCAAGGCCTGCATGGCTACACACCTGGCTCAGTGCCTCCTCCAGATCCCCTCCTG
 801 AGGCTGCCCCAAGGCCTACGGGTTAAAGCCAATAGCTGCTCACATGCAACAACGGAAGGAGATTCAAGAGTCTGCCATCC
 881 CTTAGCAGCCCCTAAGTGGGCCTCTAGAGCTGAAGACACACCCCTGGTGCCACCAGCCTGTGTGGCCCCTCCCCTTGGCC
 961 CTAGCTCCCAGCACCTCCCTACCCTTCAGCAGCAAGCACACTAAGAGATTTGGCCCGAGGCTTCTCCCTTCTGCAAGGGG
1041 GTGGTCCCCTATACCCGAGGAATCTTTCTCTAGGGCACCTGGGCTCACAGCCTCCCTGGGCTCGGTTGTTCCTGCTGCCA
1121 AGTGCTCTGTGACCATGGCCTTTGCCTAGTGGAGGGAACTCAGTGGAGGATGTGCCCAGCAGTGGCCGGGGCTGCTTCTG
1201 TAACCAAGGTCTGGCAGAGTAGCGATTCCCTGCGTGTTCAGGAAGGGCCCATTGTGTATACCTGCCTCTTGTCACTGGCT
1281 TGGTGCCAGTCCCTCAGTCCCACCTCTTTACTCGGACCATGGACCCTGCCACTGCCAGCTCTTAGTACAGTCCCAACTAC
1361 CGTAGACCAGGTGACATTTGTTGACACCATTCTCAGAGGTGTTGAAGATTTATCATCTTGAATCCTCCACAAATACAGAT
1441 ACAGTCCCAAGGGAGGTAGTCGTAGAAATGGAAGACGCCAGCCCTGCGCAGCCTGCAGGGACATCCGCCAGGCTTCCCCT
1521 CAGCAGCAGGAGCCCAGGTCACCCTGGTTAAACTGCAGTGATACATTTAGGTGGGTGGGGTCAAGGCATATGTGGCCTCC
1601 GGGAGACACCTGCTTGGAAGGAGGCAGTGATGGAGATAGAGCCCCACTCTGAGTCTGGGCTCAGAGTGCCCTGACTGCTC
1681 TCCCCCACCCCATCCCCAGCTCCTCTTGTCATGCTTCTGCCTGGCCCCCAAGACTGCCTCTGTCATGGTCACTATTTATT
1761 CTTGGTCCCTTTTTCTTTTTGTAAGAAACAGTCACAAGAAAACAACAACAACAACAAAAAACAACCAATGAGAAACAAAA
1841 AAAAAAAAAAAAAAAAAAAAAAA
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' auGUGUGUUCGU-GUACGUGUGu 5'
            || :||:|||  :||||||| 
Target 5' tgCAGGCAGGCAGGGTGCACACg 3'
 78 - 100 164.00 -23.90
2 
miRNA  3' auGUGUGUUCGUGUACGUGUGu 5'
            | ||: | |||| |||||| 
Target 5' ccCTCATCA-CACACGCACACa 3'
 390 - 410 135.00 -15.40
3 
miRNA  3' auguGUGUUCGUGU---ACGUGUGu 5'
              | ||: | ||   ||||||: 
Target 5' gttcCCCAGCCTCAGCCTGCACATc 3'
 519 - 543 134.00 -9.10
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Brain (Mouse neocortex)
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 Chi_BrainC_130_50. RNA binding protein: AGO. Condition:Brain C 2A8 P13 130 KD ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' auGUGUGUUCGUGUACGUGUGu 5'
            | ||: | |||| |||||| 
Target 5' ccCUCAUCA-CACACGCACACa 3'
 		7 - 27
Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
Experimental Support 2 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 GSM622572. RNA binding protein: AGO2. Condition:WT2 ...

- 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' auguguguucguguaCGUGUGu 5'
                         |||||| 
Target 5' -------------acGCACACa 3'
 		1 - 9
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]
Experimental Support 3 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 ERR266286. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 1h 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.

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]
CLIP-seq Support 1 for dataset Chi_BrainC_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition Brain (Mouse neocortex) / Brain C 2A8 P13 130 KD
Location of target site NM_001025246 | 3UTR | GUGAGUCCCUCAUCACACACGCACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_001025246 | 3UTR | ACGCACACACACACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset ERR266286
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / A_Liver partial hapatectomy 1h
Location of target site NM_001025246 | 3UTR | CACGCACACACACACACACACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset ERR266298
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Liver / A_Untreated
Location of target site NM_001025246 | 3UTR | ACACGCACACACACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23597149 / E-MTAB-1612
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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