miRTarBase - #MIRT601744


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pre-miRNA Information
pre-miRNA mmu-mir-690   
Genomic Coordinates chr16: 28599935 - 28600043
Synonyms Mirn690, mmu-mir-690, Mir690
Description Mus musculus miR-690 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-690
Sequence 83| AAAGGCUAGGCUCACAACCAAA |104
Evidence Experimental
Experiments MPSS
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B6MEZ5 miR-690 Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Serum Microarray
Gene Information
Gene Symbol Rbm34   
Synonyms 4930547K05Rik, 6330444B11, D8Ertd233e
Description RNA binding motif protein 34
Transcript NM_172762   
Expression
Putative miRNA Targets on Rbm34
3'UTR of Rbm34
(miRNA target sites are highlighted)		 
>Rbm34|NM_172762|3'UTR
   1 TAACTGAGGTTGCCTCCTTTCTGTGGTGAAACCTTGCAATGAGTGTCTGGGTTTTTTATGGATTATGTAGAAAATGTGGA
  81 GGCATCCACGGTGTCTGGTTTTTGTTTTTGTTTTTTTTTTAATTCATGCTATATGTAAGGCTTCTTTGAAGCCTTGTTCT
 161 TAGAAATGTATTTAAAGAAAAATAATAAACATTAATACTCTGTGTTTAGGATAAGTGTTCAAATGGTCACTGTGAGAATA
 241 CTGATTCCAGGTATAGTCACAGTCCCTAAGAAAGACTTGTGAGCTGTGTAAAACACACACGCACATTCTTCACTTCTCAT
 321 TTTTCTTTCTCTTGCAATTGTAGTATAGATCTACATTTCTTATCCCATATATCTAATAATTGCTAACCAATAAGACTGAT
 401 AGGATAAGAGTGACTATCTTCTAATTCGTTGCCAGTGACTACAGTGGTCAATGATGTCCTTGGCTATTAGGTGTGTGTGT
 481 GTGTGGAGGGGGGGGTGCTCATAAGAAAAATACTCTTCCAGGAAAATGTGATGCTTAAATTAGTATCACTCAGAATGAAA
 561 CAGCTGTCCCAGAAAGTTTAAAGACAGCATCTAATAAATGATGTTAATTAAACTGCAGTCTTTAAAGTTGAATGACATGA
 641 CAACATGGTGCTGCATTCCCTAAGTTCCAGACACATCTTACCAAGCTGGGGCTGGATCCAGGATGAAGTGGGGGAAGCAG
 721 GAAGCCAAGGCTGATTCAGGCAGGCAGAGTCCAGTAGGCAAGAGGGTAGGATAAGTTTTCACTCTTTTAGTTGTAAAAGT
 801 TCTGTCTTTGGGAAATGCCATGTAGAAAACCTAATGAGGTCTTTAAAACATAGCTCTAGGGGCTGGAGAGATGGCTCAGC
 881 AGTTAAGAATACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCTCAGCAACCACATAGTAGCTCGCAACCATCCGTAA
 961 TGAGATCTGATGCCCTCTTCTGTTGTTTGTTTGTTTGAGACAGGGTTTCTCTGTATAGCCTTGGCTGTCCTGGAACTCAC
1041 TTTGCAGACCAGGCTGACCTTGAACTCAGAAATCCGCCTGCCTCTGCCCCCCAAGTGCTGGGATTAAAGGCGTGCGCCAC
1121 CATGCCTGGCTGATGCTCTCTTCTGGAATGTCTGGATACAACTACAGTGTACTTACACATAAATAAATCTTAAACAAAAA
1201 ACAAACAAACCCCATAGCTCTAGAGGCTGGAGAGTTGGTTTCTTGGTTAAGAGCATGCACTGCTCTTCAGAGTACCTAAG
1281 TTCAATTCCTAGTACCCACGTCAAGCAGTTCACAACTGTCTGTAACTTGAGCTCCTAGGTCCAACTCCTCTAGTCTCCCC
1361 AGACTTTGTGCACTTTTTCACTAACATAACCTACACACACATATATACAAGTAAAAAATAAAAGTGTGGGGCTGGAGAGA
1441 TGGCTCAGTGGTTAAGAGCACTGACTGTTCTTCTAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAAC
1521 CATCTGTCCGATGCACTCTTCTGCTGTGTGTCTGAAGTCAGCTACCGTGTACTCACATTAAATAAATATTAAAAAATAAA
1601 TAAAAGTGTGTAGCTTTTACAGCAGAGAAAGCTCTATTTCCTGTATCCAAGACTGGATAATTTATGGTTGGTTTTCCTTA
1681 CAGTATTTAGAACCTTTTCAGTTAAATTTCAGCAATTTTACCTGATCACTCTGGAGCATTTTTGCATAAACTATATAAAG
1761 ATGTAACATTAGATTGTGCGTGCATATATAATCTATGTACAACTTACAGCTCCTGTGAGTGAGCAGGTTATATACATGCA
1841 TAGATGTAACTTTATTTAATATGTGTATGATGTGAATGTGGAGGCCAGAAGAAAACTCTGGAGTTTTCTCCTTCCAAAGC
1921 ATGGACTCACTCAGCCATCTCACTGGCCCTAGATACTTTGGAATTCGGTACTGTGTAACTGTTGAAATTCCTCCTTTAGA
2001 ATGTGTGTGCTACTATGATTGTGTAAATCATTAAAAAATGTATTTTGTAGGAAATTTTCTAAAAAAAAAAAAAAAA
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' aaaCCAACACUCGGAUCGGAAa 5'
             | || |  |: ||||||| 
Target 5' aggGTTTCTCTGTATAGCCTTg 3'
 1002 - 1023 151.00 -11.30
2 
miRNA  3' aaaccaaCACUCGGAUCGGAAa 5'
                 ||| |  ||||:|| 
Target 5' aataaaaGTGTG--TAGCTTTt 3'
 1599 - 1618 131.00 -8.50
3 
miRNA  3' aaaccaacacucggaUCGGAAa 5'
                         |||||| 
Target 5' gtaaggcttctttgaAGCCTTg 3'
 135 - 156 120.00 -11.20
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 GSM622571. RNA binding protein: AGO2. Condition:WT1B HITS-CLIP data was present in GSM622572. RNA binding protein: AGO2. Condition:WT2 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' aaaccaacacucggAUCGGAAa 5'
                        ||||||| 
Target 5' -------------aUAGCCUUg 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]
CLIP-seq Support 1 for dataset GSM622571
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1B
Location of target site NM_172762 | 3UTR | GUUUGUUUGAGACAGGGUUUCUCUGUAUAGCCUUGGCUGUCCUGGAACUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
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_172762 | 3UTR | GUUUGUUUGAGACAGGGUUUCUCUGUAUAGCCUUGGCUGUCCUGGAACUCACUUU
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 GSM622573
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO1
Location of target site NM_172762 | 3UTR | AUAGCCUUGGCUGUCCUGGAACUCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
29 mmu-miR-690 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT054611 Vcan versican 3 1
MIRT054612 Ctnnb1 catenin (cadherin associated protein), beta 1 3 1
MIRT438463 Cebpe CCAAT/enhancer binding protein (C/EBP), epsilon 2 1
MIRT580328 Tnrc6a trinucleotide repeat containing 6a 2 2
MIRT587416 Dnase2a deoxyribonuclease II alpha 2 4
MIRT588924 Shroom3 shroom family member 3 2 2
MIRT593056 Madd MAP-kinase activating death domain 2 2
MIRT593335 Cebpa CCAAT/enhancer binding protein (C/EBP), alpha 2 2
MIRT593667 Smarcc1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 2 2
MIRT594943 Fnta farnesyltransferase, CAAX box, alpha 2 2
MIRT595735 Apcdd1 adenomatosis polyposis coli down-regulated 1 2 2
MIRT596853 Ttc26 tetratricopeptide repeat domain 26 2 2
MIRT596914 Trim27 tripartite motif-containing 27 2 2
MIRT597246 Slc39a1 solute carrier family 39 (zinc transporter), member 1 2 2
MIRT597547 Ranbp3l RAN binding protein 3-like 2 2
MIRT600400 Sgms2 sphingomyelin synthase 2 2 2
MIRT600700 Lpp LIM domain containing preferred translocation partner in lipoma 2 2
MIRT600812 Gpcpd1 glycerophosphocholine phosphodiesterase 1 2 2
MIRT601006 Cst6 cystatin E/M 2 2
MIRT601281 2010107G23Rik RIKEN cDNA 2010107G23 gene 2 2
MIRT601474 Tnfaip6 tumor necrosis factor alpha induced protein 6 2 2
MIRT601744 Rbm34 RNA binding motif protein 34 2 2
MIRT603545 Ptchd2 dispatched RND transporter family member 3 2 2
MIRT603901 Htr5a 5-hydroxytryptamine (serotonin) receptor 5A 2 2
MIRT605244 Soga1 suppressor of glucose, autophagy associated 1 1 1
MIRT605502 Siglece sialic acid binding Ig-like lectin E 2 2
MIRT605746 Fgfr1 fibroblast growth factor receptor 1 2 2
MIRT735810 Map2k3 mitogen-activated protein kinase kinase 3 2 0
MIRT735811 Map3k7 mitogen-activated protein kinase kinase kinase 7 2 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-690 Glucose NULL 5793 Microarray pancreatic {beta} cells 19096044 2009 down-regulated
miR-690 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-690 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse liver 19270793 2009 up-regulated
miR-690 Phenethyl isothiocyanate(PEITC) NULL 16741 Microarray neonatal mice liver 20145010 2010 up-regulated
miR-690 Tert-butyl hydroperoxide (t-BHP) NULL 6410 Microarray mouse auditory cells 20510889 2010 up-regulated

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