pre-miRNA Information | |
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pre-miRNA | hsa-mir-4318 |
Genomic Coordinates | chr18: 37657135 - 37657215 |
Description | Homo sapiens miR-4318 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||
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Mature miRNA | hsa-miR-4318 | |||||||||
Sequence | 55| CACUGUGGGUACAUGCU |71 | |||||||||
Evidence | Experimental | |||||||||
Experiments | SOLiD | |||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TAB1 | ||||||||||||||||||||
Synonyms | 3'-Tab1, MAP3K7IP1 | ||||||||||||||||||||
Description | TGF-beta activated kinase 1 (MAP3K7) binding protein 1 | ||||||||||||||||||||
Transcript | NM_006116 | ||||||||||||||||||||
Other Transcripts | NM_153497 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TAB1 | |||||||||||||||||||||
3'UTR of TAB1 (miRNA target sites are highlighted) |
>TAB1|NM_006116|3'UTR 1 GGCAGCCGGAGAATGCAGCCCAAGCAGGGCCTGGCATGGGGCAGGACAGGGTCCAGCCTTTTCCTAACATCTGCCTGTGC 81 CACAACGGCCAGCAGGTGCCCCATCCTCTGCCCACAGCAGACTCTGTCCCATGGCTCTCCGGGCAGTAGAGTGTGTGAGT 161 GCAGACTGGACCTGTGGTTCATACCTTGTCACCACCCGGGAAGCTGAAGGCCACTTCCTCCCAGATGGCCTCAGCCAGGA 241 CCATCGCCCTTTCTCAGAGCAGAGGGCCAGGTATAGAAACCGCAGTGGGCCTGCAAGCCGCCCGAGCCTCCCCAGCAGCC 321 TCCTACAGAGCAGGAAGAGGCGCCCTGTGAACCCTGAGTGTTGCAGGCCCAGCAGACCCTGCTGTCCCAAGCCCACCCCT 401 CCTCCCACCATCACCTCCCTCACCTCGGGACAGTAGCCCTCCACTTCTCCAGCCTCTCAGCCCTGTGCTCCTGCATCCAG 481 AGTGGAACCCAGGCTGGTGTCCGCATCTGTCCCTGGGCCCCACCCCTGGACCTGCCTTGGTTGTGTCATCTGTTGTAAAC 561 GTTCAGGAGGACCAGGGCAGCATCTGGGGCCTGGGATGGCCACAGAAGGGGCAGGCCAGGTGGAAAGGAGCCAGGGGGAA 641 GTGGTCTAAGAGACCTGGAACTGCCAGAGGATGGCGGCCTGGGCTTCCCCAGAGCCAGGCGTGCGGGAGAGGTGAGGACT 721 GGCCCCGGTGGGCTGAGGCAGGGGCCGCTGTCGTCAGGCCTGAGCCAGGGTGAGCTGGTGCCTGCCTTGCATTTTCCTTC 801 TGGTGCTGTGAAGACCATAGGCTGGCAGGCAGCTGAGATGAACTGTCTTTACCACTGATGAGGGGCCTCTGCCGGCTGAG 881 GGTAGCAAGCAGGGGTTGTGAGTCAGGCTGGGGGACTTGTTTGAAAGAAAGAGGAGTGGAAAATGGTTCCAGGAGGGAAG 961 AGGTTCTTTGAGACACAGTACCCTGGGAGGCATAGGAGAAGGGTCGGGCCAGCCCAGCCCAGGGCCTGAGTTAGACTATT 1041 TCCCACATGTTCTCTGCCTTCAGTGGGGAGGGGGTGCCACCAGGGCTGTCGGCCAGGATTGCCACTCCTGTTTCAGAGGA 1121 AGCAGGCCGAGAGACTTGCACCTTGGCCAAGCCACACAATCAGTGGGGCAGCCAGAGCTCAGACCTGAGCCATTTTGTCA 1201 GTATCCAGGACCCCCCGGATTCTCCACGCCCTCCCCATCTCCCAGTCTCCCTGCCCCCCATGCCCCAGACCGGCCCACCA 1281 GGGACTAGCCGCTGTCGCACAGCCTCTGGGGTGCTTGGTCTCTGCGAAGTCAAAGGCCTGACAGCTCTGTGGCCTGGGAA 1361 TCCATTTTCCTGCGGCAGAGCAGGGCCTGGTGTGGAACCAGGGAGCTGTGGGAAGCCACAGCAGAAATGGAAGAAAAACA 1441 GGTCTCAGCCCAGGGTCCTCGCTCACTCCCTCACTCCCCACTTTGAAGCCATCTCTGTTCTGCAGGTGAGAGGATTTAAA 1521 GTCAGTCACAAAGGCTTGGGAACAAAAGGAATTCTCTTCCAAGAATGCCTCTGTGGTGCTGTTTGGTCTCTAGAAACAGG 1601 GTCACTTTTTTAATGTAGTAAAGAAGTAATAAATGGTGGCATTACACATTGTGATATTAAAAAAAAAAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | hESCs (WA-09) |
Disease | 10454.0 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
"PAR-CLIP data was present in SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine
... - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development. |
Article |
- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al. - Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
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CLIP-seq Support 1 for dataset SRR359787 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
Location of target site | ENST00000216160.6 | 3UTR | CAGUACCCUGGGAGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22012620 / SRX103431 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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60 hsa-miR-4318 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT068761 | RB1 | RB transcriptional corepressor 1 | 2 | 2 | ||||||||
MIRT094193 | THAP6 | THAP domain containing 6 | 2 | 2 | ||||||||
MIRT166771 | PAPD7 | poly(A) RNA polymerase D7, non-canonical | 2 | 2 | ||||||||
MIRT185495 | SRP9 | signal recognition particle 9 | 2 | 2 | ||||||||
MIRT347687 | LSM14A | LSM14A, mRNA processing body assembly factor | 2 | 2 | ||||||||
MIRT441948 | PEX2 | peroxisomal biogenesis factor 2 | 2 | 2 | ||||||||
MIRT443293 | TAF8 | TATA-box binding protein associated factor 8 | 2 | 4 | ||||||||
MIRT447126 | DUSP16 | dual specificity phosphatase 16 | 2 | 2 | ||||||||
MIRT447428 | MED21 | mediator complex subunit 21 | 2 | 2 | ||||||||
MIRT447971 | MSH6 | mutS homolog 6 | 2 | 2 | ||||||||
MIRT450693 | RPN2 | ribophorin II | 2 | 2 | ||||||||
MIRT465671 | TNPO2 | transportin 2 | 2 | 2 | ||||||||
MIRT477011 | FAM60A | SIN3-HDAC complex associated factor | 2 | 2 | ||||||||
MIRT479898 | CCDC117 | coiled-coil domain containing 117 | 2 | 2 | ||||||||
MIRT488681 | ELP2 | elongator acetyltransferase complex subunit 2 | 2 | 2 | ||||||||
MIRT490349 | PEX10 | peroxisomal biogenesis factor 10 | 2 | 2 | ||||||||
MIRT491108 | NARS | asparaginyl-tRNA synthetase | 2 | 2 | ||||||||
MIRT494804 | ALG9 | ALG9, alpha-1,2-mannosyltransferase | 2 | 2 | ||||||||
MIRT512730 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | 2 | 2 | ||||||||
MIRT518098 | UGT2B4 | UDP glucuronosyltransferase family 2 member B4 | 2 | 4 | ||||||||
MIRT518113 | RPS7 | ribosomal protein S7 | 2 | 2 | ||||||||
MIRT528967 | FAM19A3 | family with sequence similarity 19 member A3, C-C motif chemokine like | 2 | 2 | ||||||||
MIRT529796 | AP4S1 | adaptor related protein complex 4 sigma 1 subunit | 2 | 2 | ||||||||
MIRT530503 | FADS6 | fatty acid desaturase 6 | 2 | 2 | ||||||||
MIRT530797 | SNRPD1 | small nuclear ribonucleoprotein D1 polypeptide | 2 | 2 | ||||||||
MIRT532654 | TAB1 | TGF-beta activated kinase 1 (MAP3K7) binding protein 1 | 2 | 2 | ||||||||
MIRT533417 | TXLNG | taxilin gamma | 2 | 2 | ||||||||
MIRT536327 | LGSN | lengsin, lens protein with glutamine synthetase domain | 2 | 2 | ||||||||
MIRT537611 | ERMP1 | endoplasmic reticulum metallopeptidase 1 | 2 | 2 | ||||||||
MIRT540738 | FN3KRP | fructosamine 3 kinase related protein | 2 | 2 | ||||||||
MIRT545780 | ZNF805 | zinc finger protein 805 | 2 | 2 | ||||||||
MIRT549884 | GINS4 | GINS complex subunit 4 | 2 | 2 | ||||||||
MIRT550618 | MTHFR | methylenetetrahydrofolate reductase | 2 | 2 | ||||||||
MIRT551451 | SULT1B1 | sulfotransferase family 1B member 1 | 2 | 2 | ||||||||
MIRT554858 | RDH11 | retinol dehydrogenase 11 (all-trans/9-cis/11-cis) | 2 | 2 | ||||||||
MIRT556558 | LIMS1 | LIM zinc finger domain containing 1 | 2 | 2 | ||||||||
MIRT572893 | ADCY2 | adenylate cyclase 2 | 2 | 2 | ||||||||
MIRT576517 | Slc35e2 | solute carrier family 35, member E2 | 2 | 2 | ||||||||
MIRT609005 | PYGO1 | pygopus family PHD finger 1 | 2 | 2 | ||||||||
MIRT614782 | SEC63 | SEC63 homolog, protein translocation regulator | 2 | 2 | ||||||||
MIRT633849 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | 2 | 2 | ||||||||
MIRT634841 | APOOL | apolipoprotein O like | 2 | 2 | ||||||||
MIRT638838 | CRTAP | cartilage associated protein | 2 | 2 | ||||||||
MIRT639980 | POU5F1B | POU class 5 homeobox 1B | 2 | 2 | ||||||||
MIRT640263 | ALDOA | aldolase, fructose-bisphosphate A | 2 | 2 | ||||||||
MIRT641538 | SNW1 | SNW domain containing 1 | 2 | 2 | ||||||||
MIRT656540 | MACC1 | MACC1, MET transcriptional regulator | 2 | 2 | ||||||||
MIRT667590 | LONRF2 | LON peptidase N-terminal domain and ring finger 2 | 2 | 2 | ||||||||
MIRT667732 | KIAA1456 | KIAA1456 | 2 | 2 | ||||||||
MIRT667911 | ING1 | inhibitor of growth family member 1 | 2 | 2 | ||||||||
MIRT669865 | BROX | BRO1 domain and CAAX motif containing | 2 | 4 | ||||||||
MIRT675877 | ATP1B4 | ATPase Na+/K+ transporting family member beta 4 | 2 | 2 | ||||||||
MIRT676868 | ZNF451 | zinc finger protein 451 | 2 | 2 | ||||||||
MIRT683211 | MBNL1 | muscleblind like splicing regulator 1 | 2 | 2 | ||||||||
MIRT704515 | COL4A1 | collagen type IV alpha 1 chain | 2 | 2 | ||||||||
MIRT710184 | DYRK3 | dual specificity tyrosine phosphorylation regulated kinase 3 | 2 | 2 | ||||||||
MIRT712036 | TRIP13 | thyroid hormone receptor interactor 13 | 2 | 2 | ||||||||
MIRT716586 | BRAP | BRCA1 associated protein | 2 | 2 | ||||||||
MIRT724189 | MMP16 | matrix metallopeptidase 16 | 2 | 2 | ||||||||
MIRT724205 | MED7 | mediator complex subunit 7 | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||
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