miRTarBase - #MIRT594566


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pre-miRNA Information
pre-miRNA mmu-mir-208a   
Genomic Coordinates chr14: 54949060 - 54949142
Description Mus musculus miR-208a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-208a-5p
Sequence 15| GAGCUUUUGGCCCGGGUUAUAC |36
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol 4930563D23Rik   
Synonyms -
Description RIKEN cDNA 4930563D23 gene
Transcript NM_029252   
Expression
Putative miRNA Targets on 4930563D23Rik
3'UTR of 4930563D23Rik
(miRNA target sites are highlighted)		 
>4930563D23Rik|NM_029252|3'UTR
   1 GGGTGTCTGTTCCACAAAGCCCTGAGCTGTATGCTCTTTGCTGCTAACTGTGGAGTCTGATTCTGACTCACCATCACCAA
  81 AACCACACTCTAGGGGTGACCTTGAGGGATTACTGCCTCAACGGGGAGGTTCTTGAGGGCTACCAGCAAAGTCCTGGGGT
 161 TGACAGAGGCTCCATTAAAGTTTGTTGATAAGTACAGGGTATCAACTCTCATCTTGTGATGGCTACCCTGAGGACCACGT
 241 TTATGGGAGTTATTGGGAAGACTCTAGCACAGTGGAGGGTACTGGCGGGCAGGATTAAAGGATGTGTGATCAAAATTTAG
 321 GTCTAAGAAGAAAAGAGAACATCAACAACAAAAAAGAACACTCTGAATTAAATACTAAGCCAATAAACTTCAGGTTAAAT
 401 AATCCACAAGCATCCGCCTTGCCATGAGCAAGAGACACGTGCATACAGTGGTCCAGCCGGGGCTATCCCTCTGGGAGGTA
 481 GTGGTGGTGAGAGGCAACTGCGAGGTAGTCAAACCGCTCCATATGTCCAAGGCAAATGGGTGGGGCCAAAAGGGAGCCAT
 561 GGAGACATCAAAGGTTCAAGGGGTCTTAGGTCAAGTGGGGGATGGGAGGACGATGGAACCCACATATCCAACCTGCAAGA
 641 ATCCCATCCGGAGAGTCCAAAGGCTGCCACTGCGTCTATCTCAGGCCTCTGAGCTGAGCTACTGCAGTTGGCACAACACC
 721 CTGCTCAAGCCCCAGGGGGCGCTGTGGGCCGGAAGGGTCTGTGCTTGCACGTCTGCTACAGGAAAAGCCCGGCGCCTGTG
 801 AAACCGACCACAAAGCGCCTTTTTCCTTATGTATGCTCAAGCAATAACTTCACAACAGAAGTAGTTACTCTGAGGTGCAT
 881 AAAATGACAACCTACACAGGAAAATATGGACAGCCACGAGGCAGGAGCAGAAAGGGCACAAGAACTCTACTTGGTCTTCA
 961 GTTTTGCTGAACCTAGAAAAAAAAAAAAAGCTCTAAAGACAAGTCTGTAAAAAACTAGCGTATGAAGATGTCCACCAGCT
1041 CCCGGCGGATTTGACTGTGGGTGGAGTTGCGAAGCCAGGCCGCTGCCAAATGCAGACTGCTCCATATTCCAATCTTGTCC
1121 TCCTCTTCTCTGGAATCTTCCTGTGTTATTCAGAAAGAGGCCGTGGGATGAACAGAGCCACCTGGAGCGTTAATGCTCTT
1201 CAGGAGTAAGCGGTGGGTTCTGCAGTTTTCTCAAGTTGGAGAAAAGGGGATTTAACACACATCTTATCTAAAGGGTGCCG
1281 CACCCCAAACTGCCTATCACTTGGACCTACAAAGTTCACCTGTTGCAGATCCAACTCTTACACCGTGCTGTGTGAGCTGG
1361 TGGCTGCCGTATCAAAGGATTGCACATTTGGTGGCTGGAAGCAGCAATCCACTCTTTGCTATGCTGGCTATCGGGAGTCA
1441 GACATCAGTCTCACTGATGTGAATCAAGCTGTAAGCAGCATGGCTGTACTGCCGGGGGCTCTAGGGAAGGCTGCCACAAG
1521 TGTCTCCCAGGTTCTGATGGCCCACTTACCCTTGGCTAGAGTCATCTGCTGTCCAAGAAGCAGAACCTGATGAATAGGTT
1601 CCACAGGGCTCTGGTCTAGCCAGGAATGCCGGAAGTGTTAAAGGCCCTAGAAGAGAAGTGAGGAGGTTTGGGAGGCCTGC
1681 GCAGGACAGGTAGCAGAGGTCTCTTCCTGTGAATGGTCAGCTACGGCAGCATCGATAGCAACAGCCACAGTGGCAGCACC
1761 AGTGGCAGGTGCCACAGGGTCGGCAGCGTGAACCTGGCCAGCTAGGCAGGTCCAAGGTCTAGCGATGAATGTTTCCCAAG
1841 TGTGACAGCTCAGTAAAAACAGTCTCGGATGATCCTCGGT
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' cauauUGGGCC---C-GGUUUUCGAg 5'
               |:||||   | |||||:||| 
Target 5' atcccATCCGGAGAGTCCAAAGGCTg 3'
 641 - 666 145.00 -18.30
2 
miRNA  3' cauauugggcccggUUUUCGAg 5'
                        ||||||| 
Target 5' cctagaaaaaaaaaAAAAGCTc 3'
 972 - 993 140.00 -8.00
3 
miRNA  3' caUAUUGGGCCCGGUUUUCgag 5'
            ||:: : ||||||||||   
Target 5' aaATGGGTGGGGCCAAAAGgga 3'
 534 - 555 132.00 -19.62
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions CD4+ T cells (C57BL/6)
Disease MIMAT0017014
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 GSM1013576. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013588. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013593. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013594. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013595. RNA binding protein: AGO2. Condition:CD4+ T cells ...

- Loeb GB; Khan AA; Canner D; Hiatt JB; et al., 2012, Molecular cell.

Article - Loeb GB; Khan AA; Canner D; Hiatt JB; et al.
- Molecular cell, 2012
MicroRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3' untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA-miR-155-in a genetically controlled manner. We found that approximately 40% of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these noncanonical sites feature extensive complementarity to the miRNA seed with one mismatch. These noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. Thus, noncanonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
LinkOut: [PMID: 23142080]
CLIP-seq Support 1 for dataset GSM4656405
Method / RBP HITS-CLIP / AGO
Cell line / Condition mouse liver / e125
Location of target site NM_029252 | 3UTR | CUAGAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE153876
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1013576
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, 155KO, biological rep2
Location of target site NM_029252 | 3UTR | CUAGAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1013588
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep2
Location of target site NM_029252 | 3UTR | CCUAGAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1013593
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep7
Location of target site NM_029252 | 3UTR | ACCUAGAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1013594
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep8
Location of target site NM_029252 | 3UTR | ACCUAGAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1013595
Method / RBP HITS-CLIP / AGO2
Cell line / Condition CD4+ T cells (C57BL/6) / CD4+ T cells, WT, biological rep9
Location of target site NM_029252 | 3UTR | ACCUAGAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23142080 / GSE41285
CLIP-seq Viewer Link
30 mmu-miR-208a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577883 Qpct glutaminyl-peptide cyclotransferase (glutaminyl cyclase) 2 2
MIRT579319 B3galnt1 UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 2 2
MIRT579650 2510002D24Rik RIKEN cDNA 2510002D24 gene 2 2
MIRT579796 Zfp300 zinc finger protein 300 2 2
MIRT580636 Suz12 suppressor of zeste 12 homolog (Drosophila) 2 4
MIRT581361 Reep3 receptor accessory protein 3 2 6
MIRT581857 Pik3r1 phosphoinositide-3-kinase regulatory subunit 1 2 2
MIRT583433 Frmd6 FERM domain containing 6 2 4
MIRT584342 Cdyl2 chromodomain protein, Y chromosome-like 2 2 2
MIRT586902 Hist2h2be histone cluster 2, H2be 2 2
MIRT589714 Kitl kit ligand 2 2
MIRT591273 Lars2 leucyl-tRNA synthetase, mitochondrial 2 4
MIRT593811 Lztfl1 leucine zipper transcription factor-like 1 2 2
MIRT593895 Edaradd EDAR (ectodysplasin-A receptor)-associated death domain 2 2
MIRT594222 Trim8 tripartite motif-containing 8 2 2
MIRT594501 Clmn calmin 2 2
MIRT594507 Cd99l2 CD99 antigen-like 2 2 2
MIRT594522 Bicd2 bicaudal D homolog 2 (Drosophila) 2 2
MIRT594566 4930563D23Rik RIKEN cDNA 4930563D23 gene 2 2
MIRT594769 Tmem132c transmembrane protein 132C 2 2
MIRT594821 Pknox1 Pbx/knotted 1 homeobox 2 2
MIRT594967 Tmem255a transmembrane protein 255A 1 1
MIRT595117 Prtg protogenin 2 2
MIRT595124 Maml3 mastermind like 3 (Drosophila) 2 2
MIRT595307 Gpr35 G protein-coupled receptor 35 2 2
MIRT595351 Fgfr1op2 FGFR1 oncogene partner 2 2 2
MIRT595874 Csmd1 CUB and Sushi multiple domains 1 2 2
MIRT596155 Opn5 opsin 5 2 2
MIRT604065 Eno2 enolase 2, gamma neuronal 2 2
MIRT604938 Gprc5b G protein-coupled receptor, family C, group 5, member B 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-208a (S)-3,5-dihydroxyphenylglycine (DHPG) NULL 443586 Quantitative real-time PCR mouse brain 22309833 2012 up-regulated
miR-208a Tert-butyl hydroperoxide (t-BHP) NULL 6410 Microarray mouse auditory cells 20510889 2010 down-regulated
miR-208a Sulfonyl-hydrazone-1 (SHZ) NULL NULL Quantitative real-time PCR Murine broblast-derived Induced pluripotent stem cells 21445862 2011 up-regulated
miR-208a 1,2,6-Tri-O-galloyl-beta-D-glucopyranose NULL NULL Microarray HepG2 hepatocarcinoma cells. 22506400 2011 down-regulated

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