miRTarBase - #MIRT598550


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pre-miRNA Information
pre-miRNA mmu-mir-1906-1   
Genomic Coordinates chr12: 109544541 - 109544620
Description Mus musculus miR-1906-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA mmu-mir-1906-2   
Genomic Coordinates chrX: 88759474 - 88759553
Synonyms mmu-mir-1906, Mir1906
Description Mus musculus miR-1906-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-1906
Sequence 48| UGCAGCAGCCUGAGGCAGGGCU |69
Evidence Experimental
Experiments Microarray
Putative Targets

Gene Information
Gene Symbol Isoc1   
Synonyms 2610034N03Rik
Description isochorismatase domain containing 1
Transcript NM_025478   
Expression
Putative miRNA Targets on Isoc1
3'UTR of Isoc1
(miRNA target sites are highlighted)		 
>Isoc1|NM_025478|3'UTR
   1 GAGACTTGAAGGATCAGGGTCCTCCTTCCCTCCAGGCGATGAGACTGCAAACCACACAAGCCCTTGTCTCCACTAGAACT
  81 ACTATGTCAAGTCAACAGCTCCTTCTTTGCGGCTCTTAGTAACCCTTACCTGGCTAGACCGTTGTGTACAAGTGTTTAGT
 161 TCCAATGTCGAGGCTTCAGGTGCTGCTTCTCTTCTTCTTAACGAGCTTTTAGTTATTAAGACAAATTACCATGGAGGTGC
 241 CTGTCTCGTCTATACTGCATACTCTGACCATATCTTTCCAAAGTGCACCCTCTGGTGAAGTATTCTTAAATTGTGCACTT
 321 TAATGGGAGAAAAACAAAAAAAAACAAACAAACAAACAAAAAAACCCACGTACCACAATGATTTGACCTTTCTTTTGTTG
 401 TGAAGCATCCCTTGTCATGTCAGTGTATACCCAGTGATTTTGCTTCTCAGGCTGACTGGCCAATGACTCCTGGGTGAGAA
 481 TTGAGAACCAGGACTCTGGCTCGTGTATCTCCTCCTCTCTCAGTGTTGGAGTCGCTGACTGAGTGAGGTGCATTGGCTTA
 561 AGGAGCGCAAATTATCTTCAATATTGTGTATCTGTCTTGATTGCATTAATTTTCTTATTCCTGTTACGGTCTTTGTGGAT
 641 GCTCTTCCTATGGATAACAGTCTATGTTAACATTTTTCTTCCACTGAATGTTTTCCTTGCTCCTTGGTTATTTTAAACTT
 721 GTAAACAGATGGGAGTGGTTTGCAGTGCTGGGTCATTGACAGAGGTTTGCCCAAACATACAGTCTTTTTGAGTGCATCTT
 801 TTACTATACACAGGAATTGGTGGAGAAAGAAACACTAGGTAAAATGTACCCATATTCCCCTCCAAACATTGTTATGGCTG
 881 ACATCATCAACCAGACTCATAGGGGTAATACTGTGGTCATTGTTAACCAATCAATAAACTTATTTCCATTTCATACTGAT
 961 AATTACTCAAACATCTTTTTAATGTCTGTTGTGATATGTGGAACTATGTGGAACATTACTCTCTTTGTATAAAATTAAAG
1041 AAAATGTATAATGTGGGTGAAATTGTTTTGTTTTCCATGACTCCATGAATATTAGTCAATGAATTGTAATGAGTTCTCAA
1121 AGGTAACAGATTTGCTGTTTGTTTAAAATCATTGGAACCTTCAAAGGAGGGGAATCCTCTGCAGGCCCAGACTGATAGCG
1201 TTCCTGCAGGGTTTTCCTGTTAGCACTGTAGAAATGTGTTCTGTTATTTGAGCCTTGGTAAGGCACCATTGCCTAGTGTT
1281 CTTCTTGGTGTGCTCAGTTGTTCTCAGCCTCTGGGCTGTGACCACAGATATATCACATATCAGATATATCACATATCAGA
1361 TATATCACATATCAGATATTTGCATTAAAATTCATGACAGTAGCAAAATTACAGTTATGAAGTAGCAACAAAAATAATTT
1441 TATGGCTAGGGAGTCACCACAAATGAGGAACGGAATTAAAGGGTTGCAGCATTAGGAAGGTTGAGAGCTGCTGCCTAGAA
1521 GATGAGTCCAGAAAGAAGCATCATATTGTTATCCACGTTTTAAAATAATTTCTAATAAATGTAAGCTAGTGTTTTTCAAA
1601 CTTTTATTATCTGGAGTGCTTGCTAAAATACTGAGTTTAGCTTCTTCCTCTCCCTTCGT
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' ucgggaCGGAGUC-CGACGACGu 5'
                | :| || |||||||| 
Target 5' taggaaGGTTGAGAGCTGCTGCc 3'
 1493 - 1515 152.00 -17.20
2 
miRNA  3' ucgggaCGGAGUC--CGACGACGu 5'
                ||:||||  |||||| | 
Target 5' gtcgagGCTTCAGGTGCTGCTTCt 3'
 167 - 190 134.00 -22.30
3 
miRNA  3' ucGGGACG--GAGUCCGAC-GACgu 5'
            :::|||  ||||||||| |||  
Target 5' gaTTTTGCTTCTCAGGCTGACTGgc 3'
 436 - 460 126.00 -22.40
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 GSM622570. RNA binding protein: AGO2. Condition:WT1A HITS-CLIP data was present in GSM622571. RNA binding protein: AGO2. Condition:WT1B HITS-CLIP data was present in GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011, Nature structural & molecular biology.

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 GSM622570
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1A
Location of target site NM_025478 | 3UTR | AGCAUUAGGAAGGUUGAGAGCUGC
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 GSM622571
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1B
Location of target site NM_025478 | 3UTR | AUUAGGAAGGUUGAGAGC
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 GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_025478 | 3UTR | AGCAUUAGGAAGGUUGAGAGCUGCU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
27 mmu-miR-1906 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT578439 Irgq immunity-related GTPase family, Q 2 10
MIRT578971 Dhdh dihydrodiol dehydrogenase (dimeric) 2 4
MIRT580446 Tln2 talin 2 2 2
MIRT582494 Mbtps2 membrane-bound transcription factor peptidase, site 2 2 2
MIRT587588 Cox15 cytochrome c oxidase assembly protein 15 2 2
MIRT589524 Mtf1 metal response element binding transcription factor 1 2 2
MIRT591281 Klc1 kinesin light chain 1 2 4
MIRT591935 Ddx19b DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b 2 2
MIRT592084 Sorcs2 sortilin-related VPS10 domain containing receptor 2 2 2
MIRT592206 Mapkap1 mitogen-activated protein kinase associated protein 1 2 4
MIRT592349 Armcx6 armadillo repeat containing, X-linked 6 2 4
MIRT592351 Angel1 angel homolog 1 2 2
MIRT592365 4930444A02Rik protein-O-mannose kinase 2 2
MIRT592427 Spsb4 splA/ryanodine receptor domain and SOCS box containing 4 2 2
MIRT592671 Itgav integrin alpha V 2 2
MIRT592712 Fbxo21 F-box protein 21 2 4
MIRT593155 Itsn1 intersectin 1 (SH3 domain protein 1A) 2 2
MIRT593662 Spen SPEN homolog, transcriptional regulator (Drosophila) 2 2
MIRT593976 Cdc14b CDC14 cell division cycle 14B 2 2
MIRT597931 Pacsin2 protein kinase C and casein kinase substrate in neurons 2 2 2
MIRT597949 Opa1 OPA1, mitochondrial dynamin like GTPase 2 2
MIRT598550 Isoc1 isochorismatase domain containing 1 2 2
MIRT599017 Fgd4 FYVE, RhoGEF and PH domain containing 4 2 2
MIRT600307 Tacc1 transforming, acidic coiled-coil containing protein 1 2 2
MIRT603647 Otop1 otopetrin 1 2 2
MIRT605000 Fam168b family with sequence similarity 168, member B 2 2
MIRT606275 Oxsm 3-oxoacyl-ACP synthase, mitochondrial 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-1 Anthocyanin NULL 145858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Caffeic acid NULL 689043 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Catechin approved 9064 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Curcumin NULL 969516 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Ferulic acid NULL 445858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Quercetin NULL 5280343 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Galactose NULL 6036 Quantitative real-time PCR lens 22736950 2012 up-regulated
miR-1 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Quantitative real-time PCR myocardial differentiation of mouse ES cells 19521018 2009 down-regulated
miR-1 Sulfonyl-hydrazone-1 (SHZ) NULL NULL Quantitative real-time PCR Murine broblast-derived Induced pluripotent stem cells 21445862 2011 up-regulated
miR-1 Cocaine NULL 446220 Next-generation sequencing ventral striatum 21708909 2011 up-regulated
miR-1 Atorvastatin approved 60823 Quantitative real-time PCR Cardiomyocyte 23860036 2013 down-regualted
miR-1 Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-1 Docosahexaenoic acid NULL 445580 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 Palmitic acid approved 985 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miR-1 Essential amino acids (EAA) NULL NULL Quantitative real-time PCR skeletal muscle of young adults 19828686 2009 up-regulated
miR-1 Hydrogen peroxide (H2O2) NULL 784 Quantitative real-time PCR Human umbilical vein endothelial cells 21527937 2011 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Microarray apoptosis-resistant breast cancer cells 21971930 2011 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR acute promyelocytic leukemia 22072212 2012 up-regulated
miR-1 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-1 Bicalutamide approved 2375 Microarray prostate 22674191 2012 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR cardia 22889704 2012 up-regulated
miR-1 Perfluorooctane sulfonate NULL 74483 Microarray zebrafish embryos 20878907 2011 up-regulated
miR-1 Quinidine approved 441074 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 up-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 down-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR post-infarction rat cardiomyocytes 21220930 2011 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 down-regulated
miR-1 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 up-regulated

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