pre-miRNA Information | |
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pre-miRNA | hsa-mir-6715b |
Genomic Coordinates | chr10: 112299612 - 112299688 |
Description | Homo sapiens miR-6715b stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-6715b-3p | ||||||||||||||||||||||||
Sequence | 46| CUCAAACCGGCUGUGCCUGUGG |67 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | KLF2 | ||||||||||||||||||||
Synonyms | LKLF | ||||||||||||||||||||
Description | Kruppel like factor 2 | ||||||||||||||||||||
Transcript | NM_016270 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on KLF2 | |||||||||||||||||||||
3'UTR of KLF2 (miRNA target sites are highlighted) |
>KLF2|NM_016270|3'UTR 1 CCGGGACGCCCCCGCCCACCTGCGCGCGGCCGTGGCGGGTCCCACGCGCCGGGCGCGGCCCCCTCCCAAACTGTGACTGG 81 TATTTATTGGACCCAGAGAACCGGGCCGGGCACAGCGTGGCTACAGAGGGTCTCCCTCGATGACGACGACGACGACGCCA 161 CCACCCCAGCCCCCGTCTGTGACTGAAGGCCCGGTGGGAAAAGACCACGATCCTCCTTGACGAGTTTTGTTTTTCAAAAT 241 GGTGCAATAATTTAAGTGGCATCTTCTCTCCCACCGGGTCTACACTAGAGGATCGAGGCTTGTGATGCCTTGTGAGAAAT 321 AAGGGCCTTAATTTGTACTGTCTGCGGCATTTTTTATAATATTGTATATAGTGACTGACAAATATTGTATTACTGTACAT 401 AGAGAGACAGGTGGGCATTTTTGGGCTACCTGGTTCGTTTTTATAAGATTTTGCTGGGTTGGTTTTTTTTTTAATTAAAA 481 AGTTTTGCATCTTTTAAAAAAAATCACAGCACTGGTCTGGTTGCTTGGAACTGGGGCCTTGGGGCACTTGGGAGGAGGGG 561 GGAGCGGAGAGTTTGATGGAGGGCAGCCCCACTAAAGCATCGTGTGCAGTGGGTCCTGCGTCTGCCAGCACCGGGACTGC 641 CAGCTGCTGTGCCTGCCTGCCAGGAACCTGTGGGTTTTTCTGTAAATTTAGACACTGCATTTTAGGACTGAGGGAGGGTT 721 ATTTTAAGGTTGTTCTTTGAGCCATAAATTGCCTCTTTGCCCCACAGCTGGGGAAAGTGCTGGTCCCACTGACGTGGCCT 801 CCTCTACGTTGAAAAAAATAAAACTACTTACCTCTTCCTGGAAGCCTCTGAGGTTTTAGCCAAATTTCTGGAGTGCCAGC 881 TCTATATTTTTATTTTTATTTTTAAAGGGGGTTAACCTGCTGAGTTTCTGGCATGTTCTGCCCTTTACTCGTCTCGACAT 961 TTAGCAAGTCTTTTCTTAAGGGGTGAGTTCCCCATTCTGCTAGCGGAAAACAGTGAAACCTGCATTCGAGGGCCATGCAT 1041 GAAGCTCTTTTCCAGATGAGGAAACGGAGGCCCGGAGAGGTAGCGGCAGGGTGGTGGAGTTGGGTTGTTAGCCTGCTCTG 1121 TCTGCCTCCAAGGGTCCCTGAACCCCACTGGAAGGGAGTGGTAGCTTTCTACAATGACCCACCTGTTGTGTGCATTGGAA 1201 GGCTAGGAGAGCCTCCTCCCCTGTAGGTCTCCTGGTGCAAAAAATTCACTGCCTCAATGGTAGGAGGTGACCAGTCTGGA 1281 AACCCACCTGGAGAGCAGAGGAGACCCCTAAATCCCACCACCCCAAGTGTCTCAGGCAAGGAGGTATCTCTCCCCCCAGA 1361 TTTCACCTGCCACCCCTCACCTTCCCCATTCTCAGGGGCCCCGGGTAACCATGACCACCAACCATTGCACAAGTTTCCAG 1441 AAAGTGAAAATAGCTCGTAAGCAGCGCCTGCTTTAAAACACTCTCACCCCGTTGCGACAGAGGCTGGGATTTCCTCCCTC 1521 CCTGCATCCTTCCTCCTCCCCAACTACGGCAGCCCTGGAAACAGCTGAGAGGTGTTTGGTAATCCACGAAAAGCAGAAAT 1601 ACGATTTGACAATCTGATTCATTTTCCGAGAAAAAAAAAAAAAAAAAA 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 | 10365.0 | ||||||
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. |
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miRNA-target interactions (Provided by authors) |
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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 | ENST00000248071.5 | 3UTR | AGGUUUUAUUUUGUUUGGUUUGAGAUAGGGU |
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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75 hsa-miR-6715b-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT080245 | SMAD4 | SMAD family member 4 | 2 | 2 | ||||||||
MIRT142553 | TNRC6A | trinucleotide repeat containing 6A | 2 | 4 | ||||||||
MIRT384667 | MARCH9 | membrane associated ring-CH-type finger 9 | 2 | 2 | ||||||||
MIRT446660 | MXI1 | MAX interactor 1, dimerization protein | 2 | 4 | ||||||||
MIRT463754 | YTHDC1 | YTH domain containing 1 | 2 | 2 | ||||||||
MIRT476873 | FEM1B | fem-1 homolog B | 2 | 2 | ||||||||
MIRT478429 | DAZAP2 | DAZ associated protein 2 | 2 | 2 | ||||||||
MIRT495237 | SPRY3 | sprouty RTK signaling antagonist 3 | 2 | 4 | ||||||||
MIRT495945 | ANKRD52 | ankyrin repeat domain 52 | 2 | 2 | ||||||||
MIRT497116 | TYW3 | tRNA-yW synthesizing protein 3 homolog | 2 | 2 | ||||||||
MIRT497344 | RPP25L | ribonuclease P/MRP subunit p25 like | 2 | 2 | ||||||||
MIRT498133 | KLHL3 | kelch like family member 3 | 2 | 2 | ||||||||
MIRT502306 | GNA13 | G protein subunit alpha 13 | 2 | 2 | ||||||||
MIRT510854 | RAN | RAN, member RAS oncogene family | 2 | 8 | ||||||||
MIRT513323 | KCNMB1 | potassium calcium-activated channel subfamily M regulatory beta subunit 1 | 2 | 6 | ||||||||
MIRT523995 | DTX4 | deltex E3 ubiquitin ligase 4 | 2 | 4 | ||||||||
MIRT525837 | FAR2 | fatty acyl-CoA reductase 2 | 2 | 2 | ||||||||
MIRT527506 | MYD88 | myeloid differentiation primary response 88 | 2 | 2 | ||||||||
MIRT527668 | CIT | citron rho-interacting serine/threonine kinase | 2 | 2 | ||||||||
MIRT527996 | NDNF | neuron derived neurotrophic factor | 2 | 2 | ||||||||
MIRT528052 | MRS2 | MRS2, magnesium transporter | 2 | 2 | ||||||||
MIRT528257 | GPRIN2 | G protein regulated inducer of neurite outgrowth 2 | 2 | 2 | ||||||||
MIRT529401 | ICK | intestinal cell kinase | 2 | 2 | ||||||||
MIRT529558 | SNRNP48 | small nuclear ribonucleoprotein U11/U12 subunit 48 | 2 | 2 | ||||||||
MIRT530323 | TNFRSF10D | TNF receptor superfamily member 10d | 2 | 2 | ||||||||
MIRT532230 | KLF2 | Kruppel like factor 2 | 2 | 2 | ||||||||
MIRT534220 | SLC35G1 | solute carrier family 35 member G1 | 2 | 2 | ||||||||
MIRT536195 | MAML2 | mastermind like transcriptional coactivator 2 | 2 | 2 | ||||||||
MIRT538093 | DEPDC1 | DEP domain containing 1 | 2 | 2 | ||||||||
MIRT543159 | GTF2A1 | general transcription factor IIA subunit 1 | 2 | 2 | ||||||||
MIRT545840 | ZNF264 | zinc finger protein 264 | 2 | 4 | ||||||||
MIRT546401 | SRP9 | signal recognition particle 9 | 2 | 2 | ||||||||
MIRT550643 | SLC39A7 | solute carrier family 39 member 7 | 2 | 2 | ||||||||
MIRT558648 | CNKSR3 | CNKSR family member 3 | 2 | 2 | ||||||||
MIRT562208 | HMGN2 | high mobility group nucleosomal binding domain 2 | 2 | 2 | ||||||||
MIRT562886 | NACA2 | nascent polypeptide associated complex alpha subunit 2 | 2 | 2 | ||||||||
MIRT566786 | MKL2 | MKL1/myocardin like 2 | 2 | 2 | ||||||||
MIRT567508 | FOXC1 | forkhead box C1 | 2 | 2 | ||||||||
MIRT570235 | CPNE5 | copine 5 | 2 | 2 | ||||||||
MIRT576823 | Tgfbr3 | transforming growth factor, beta receptor III | 2 | 2 | ||||||||
MIRT610704 | GPX6 | glutathione peroxidase 6 | 2 | 2 | ||||||||
MIRT611141 | CRISP1 | cysteine rich secretory protein 1 | 2 | 4 | ||||||||
MIRT618100 | PPP5D1 | PPP5 tetratricopeptide repeat domain containing 1 | 2 | 2 | ||||||||
MIRT619086 | OMA1 | OMA1 zinc metallopeptidase | 2 | 2 | ||||||||
MIRT619716 | FCF1 | FCF1, rRNA-processing protein | 2 | 2 | ||||||||
MIRT620953 | POLR2D | RNA polymerase II subunit D | 2 | 2 | ||||||||
MIRT624645 | ASXL3 | additional sex combs like 3, transcriptional regulator | 2 | 2 | ||||||||
MIRT624655 | ARMC10 | armadillo repeat containing 10 | 2 | 2 | ||||||||
MIRT630778 | KLHL42 | kelch like family member 42 | 2 | 4 | ||||||||
MIRT635596 | ATP9A | ATPase phospholipid transporting 9A (putative) | 2 | 2 | ||||||||
MIRT637122 | MKX | mohawk homeobox | 2 | 2 | ||||||||
MIRT645527 | ZWINT | ZW10 interacting kinetochore protein | 2 | 2 | ||||||||
MIRT647249 | PTGDR2 | prostaglandin D2 receptor 2 | 2 | 2 | ||||||||
MIRT651508 | WNT9A | Wnt family member 9A | 2 | 2 | ||||||||
MIRT658721 | ELK4 | ELK4, ETS transcription factor | 2 | 2 | ||||||||
MIRT658804 | EFNA5 | ephrin A5 | 2 | 2 | ||||||||
MIRT659319 | CSRNP3 | cysteine and serine rich nuclear protein 3 | 2 | 2 | ||||||||
MIRT664605 | UGT3A1 | UDP glycosyltransferase family 3 member A1 | 2 | 2 | ||||||||
MIRT666047 | STON2 | stonin 2 | 2 | 2 | ||||||||
MIRT672228 | PDE7B | phosphodiesterase 7B | 2 | 2 | ||||||||
MIRT683243 | WFDC6 | WAP four-disulfide core domain 6 | 2 | 2 | ||||||||
MIRT686565 | TPM3 | tropomyosin 3 | 2 | 2 | ||||||||
MIRT697560 | ZBTB10 | zinc finger and BTB domain containing 10 | 2 | 2 | ||||||||
MIRT699294 | SLC5A3 | solute carrier family 5 member 3 | 2 | 2 | ||||||||
MIRT707134 | TRA2B | transformer 2 beta homolog | 2 | 2 | ||||||||
MIRT712255 | PTPRN2 | protein tyrosine phosphatase, receptor type N2 | 2 | 2 | ||||||||
MIRT713896 | IGF2R | insulin like growth factor 2 receptor | 2 | 2 | ||||||||
MIRT716186 | UBN2 | ubinuclein 2 | 2 | 2 | ||||||||
MIRT716525 | KSR2 | kinase suppressor of ras 2 | 2 | 2 | ||||||||
MIRT716968 | CNOT6 | CCR4-NOT transcription complex subunit 6 | 2 | 2 | ||||||||
MIRT717154 | LRRC3C | leucine rich repeat containing 3C | 2 | 2 | ||||||||
MIRT718669 | LSM10 | LSM10, U7 small nuclear RNA associated | 2 | 2 | ||||||||
MIRT722100 | PTBP3 | polypyrimidine tract binding protein 3 | 2 | 2 | ||||||||
MIRT723569 | GEMIN4 | gem nuclear organelle associated protein 4 | 2 | 2 | ||||||||
MIRT724703 | CRAMP1L | cramped chromatin regulator homolog 1 | 2 | 2 |