pre-miRNA Information | |
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pre-miRNA | hsa-mir-3123 |
Genomic Coordinates | chr1: 241132272 - 241132346 |
Description | Homo sapiens miR-3123 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||
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Mature miRNA | hsa-miR-3123 | ||||||||||||||
Sequence | 49| CAGAGAAUUGUUUAAUC |65 | ||||||||||||||
Evidence | Experimental | ||||||||||||||
Experiments | Illumina | ||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | NR2E1 | ||||||||||||||||||||
Synonyms | TLL, TLX, XTLL | ||||||||||||||||||||
Description | nuclear receptor subfamily 2 group E member 1 | ||||||||||||||||||||
Transcript | NM_003269 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on NR2E1 | |||||||||||||||||||||
3'UTR of NR2E1 (miRNA target sites are highlighted) |
>NR2E1|NM_003269|3'UTR 1 GCTCACAAGATACCCACTTTTCAGGATGGGACAGTATCAGATGAACTTCAACCCATGGAGAACAAGCCTCAACTAACAAA 81 CCCTTCAGGAAGCATATACCGGGGAATGTGTAGCCTTCAGGAAAAAAATGCCAATTGACACAAAGCATTCCAGTAGCTAT 161 GACCTGCCGCCCTGACCAGGATAGGGCGGGTGGGAAGGAGAGGGGTGCAACAGGACCGCCTGCACTGAAAACTCACTGCT 241 GCCATGCCCTGGGAGGGGGCAAACTGGGGGTTGCCACAGGCCGTGCCATTCTGCCTCTTACCTGGAAGATCAGGCTGAAC 321 GATCAAAAGCTGAAACATAAGTAGTGCTTTCTCTTCCTTTTTAGCATACAAAGTTTGGTAACCAAATATAGCTCTGTGTA 401 TAACATCGTACTGCGGCCTTCAAAACTACGTTATGTTGGAGCATTTATTTTAAAAATAATGGTAGGTTTTAAATTAAAAG 481 TGTTATCAAAAGTTTCCCCTCTATTGTAATACATTATTAAGTGGCCTTCAGAACTGAGTTAATAAGTGAAAAGTAGCTTA 561 TGCCATGTGATTTGCTTTTTCTCTATCTTCTTTTTTCTTTTCTTTCTCTTTCTTTTGTTCTTTCTTCTTCTTTTTTAATA 641 CCATAGGCCAGGCAACCTTGTCAAAGGAATTGATGGACAAAATGAGATTCTCACCAGGACTTCAGGTTGGATAACATGTC 721 AAAAAGAGAAGAGCTTTACTAAAAGAACATAAGTCAAGGGAGGATGAATAAAAACAGCAAAACCAAATAAAGTGGAGATG 801 AGTGATTGAGTGAGGTAGATTGCTGTCCCGTTAACATAGTGCTGAAACCAAAGGCAGTGGGGGTCCAAACTCGTGGTGCA 881 GCAAGTCACACCAGACAGGAAACGAATATGGACGTAATTGCAGAAGGAACTTCAAGGAGATGAATGAATGCTAAAAGGGT 961 TCTTGACTGATCCATTGCTAACAGCCTGAGACTCTTCAATGCCTTTCCGAAAACTGGTTTCTAGTAAAGCCTTGAATGAA 1041 CACACACACACACACACACACACACACACACACACACACACACACACACCGTCCTACACTTTAAGCTGCTCCTTTGGTAT 1121 GACTCTATACTTATGGAAATGTAGAAACAAACATTTTTAAATAGCTGCTGTACTTTTCACATTTTGATTTATTAGGTACT 1201 AGCACTGAGGAAAAAAAATTCAGCACTTGGACTATCATAGGATGAGTAAAACTTTTCTTGTACAAAGTGAATTAACTGAT 1281 TTGTGAAGTTAAAAGGTTGTACTCATTGTATTTACAAAGAATAAAAATATATTGAATTTAAATGAAAAAAAAAAAAAA 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 | 7101.0 |
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 | ENST00000368986.4 | 3UTR | UAUCUUCUUUUUUCUUUU |
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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113 hsa-miR-3123 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT058369 | TBCEL | tubulin folding cofactor E like | ![]() |
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2 | 4 | ||||||
MIRT059816 | EFNA1 | ephrin A1 | ![]() |
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2 | 2 | ||||||
MIRT066850 | TMEM19 | transmembrane protein 19 | ![]() |
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2 | 2 | ||||||
MIRT071503 | CALM1 | calmodulin 1 | ![]() |
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2 | 6 | ||||||
MIRT073758 | NUBP1 | nucleotide binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT074324 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 10 | ||||||
MIRT094805 | LMNB1 | lamin B1 | ![]() |
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2 | 2 | ||||||
MIRT099173 | MAP3K4 | mitogen-activated protein kinase kinase kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT099545 | ID4 | inhibitor of DNA binding 4, HLH protein | ![]() |
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2 | 2 | ||||||
MIRT122643 | E2F3 | E2F transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT180918 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
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2 | 8 | ||||||
MIRT192844 | BLOC1S6 | biogenesis of lysosomal organelles complex 1 subunit 6 | ![]() |
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2 | 2 | ||||||
MIRT224984 | BAG4 | BCL2 associated athanogene 4 | ![]() |
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2 | 2 | ||||||
MIRT246065 | NRAS | NRAS proto-oncogene, GTPase | ![]() |
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2 | 2 | ||||||
MIRT357085 | PRRC1 | proline rich coiled-coil 1 | ![]() |
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2 | 2 | ||||||
MIRT378170 | C5ORF51 | chromosome 5 open reading frame 51 | ![]() |
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2 | 2 | ||||||
MIRT441636 | KDM5A | lysine demethylase 5A | ![]() |
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2 | 2 | ||||||
MIRT441802 | BCAS1 | breast carcinoma amplified sequence 1 | ![]() |
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2 | 2 | ||||||
MIRT443019 | C21orf91 | chromosome 21 open reading frame 91 | ![]() |
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2 | 2 | ||||||
MIRT443445 | SERPINB4 | serpin family B member 4 | ![]() |
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2 | 2 | ||||||
MIRT443661 | SERPINB3 | serpin family B member 3 | ![]() |
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2 | 2 | ||||||
MIRT443776 | STS | steroid sulfatase | ![]() |
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2 | 2 | ||||||
MIRT444663 | TSPAN14 | tetraspanin 14 | ![]() |
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2 | 2 | ||||||
MIRT444924 | KIAA1522 | KIAA1522 | ![]() |
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2 | 2 | ||||||
MIRT445378 | FOXO1 | forkhead box O1 | ![]() |
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2 | 2 | ||||||
MIRT447920 | PAIP2B | poly(A) binding protein interacting protein 2B | ![]() |
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2 | 2 | ||||||
MIRT449202 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT449713 | TSPYL1 | TSPY like 1 | ![]() |
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2 | 2 | ||||||
MIRT450403 | TMEM47 | transmembrane protein 47 | ![]() |
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2 | 2 | ||||||
MIRT450787 | PAPOLG | poly(A) polymerase gamma | ![]() |
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2 | 2 | ||||||
MIRT451381 | C19orf43 | telomerase RNA component interacting RNase | ![]() |
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2 | 2 | ||||||
MIRT452507 | WDR1 | WD repeat domain 1 | ![]() |
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2 | 2 | ||||||
MIRT453264 | PARP11 | poly(ADP-ribose) polymerase family member 11 | ![]() |
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2 | 2 | ||||||
MIRT454642 | FAM83H | family with sequence similarity 83 member H | ![]() |
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2 | 2 | ||||||
MIRT455513 | C6orf106 | chromosome 6 open reading frame 106 | ![]() |
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2 | 2 | ||||||
MIRT456709 | LDB1 | LIM domain binding 1 | ![]() |
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2 | 2 | ||||||
MIRT457231 | AP3D1 | adaptor related protein complex 3 delta 1 subunit | ![]() |
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2 | 2 | ||||||
MIRT459235 | MRPS21 | mitochondrial ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT460553 | IFNAR1 | interferon alpha and beta receptor subunit 1 | ![]() |
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2 | 4 | ||||||
MIRT461424 | CTSL2 | cathepsin V | ![]() |
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2 | 3 | ||||||
MIRT462869 | CYP51A1 | cytochrome P450 family 51 subfamily A member 1 | ![]() |
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2 | 2 | ||||||
MIRT467178 | SPTY2D1 | SPT2 chromatin protein domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT469233 | RHOBTB3 | Rho related BTB domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT474125 | LIPC | lipase C, hepatic type | ![]() |
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2 | 2 | ||||||
MIRT475509 | HSP90B1 | heat shock protein 90 beta family member 1 | ![]() |
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2 | 4 | ||||||
MIRT478134 | DHX36 | DEAH-box helicase 36 | ![]() |
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2 | 2 | ||||||
MIRT481326 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | ![]() |
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2 | 2 | ||||||
MIRT482003 | AMOTL2 | angiomotin like 2 | ![]() |
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2 | 2 | ||||||
MIRT482230 | AHCYL2 | adenosylhomocysteinase like 2 | ![]() |
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2 | 2 | ||||||
MIRT483436 | RHOXF2B | Rhox homeobox family member 2B | ![]() |
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2 | 2 | ||||||
MIRT483824 | ZC3H12B | zinc finger CCCH-type containing 12B | ![]() |
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2 | 2 | ||||||
MIRT492051 | TNFSF9 | TNF superfamily member 9 | ![]() |
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2 | 2 | ||||||
MIRT494114 | DLX6 | distal-less homeobox 6 | ![]() |
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2 | 2 | ||||||
MIRT498882 | ZNF12 | zinc finger protein 12 | ![]() |
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2 | 10 | ||||||
MIRT499674 | NPHP3 | nephrocystin 3 | ![]() |
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2 | 2 | ||||||
MIRT506932 | IGDCC4 | immunoglobulin superfamily DCC subclass member 4 | ![]() |
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2 | 6 | ||||||
MIRT509461 | ZNF587 | zinc finger protein 587 | ![]() |
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2 | 6 | ||||||
MIRT510048 | AKR1B10 | aldo-keto reductase family 1 member B10 | ![]() |
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2 | 4 | ||||||
MIRT514807 | NWD1 | NACHT and WD repeat domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT515217 | CRCP | CGRP receptor component | ![]() |
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2 | 2 | ||||||
MIRT515486 | INCENP | inner centromere protein | ![]() |
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2 | 4 | ||||||
MIRT517765 | ZNF366 | zinc finger protein 366 | ![]() |
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2 | 4 | ||||||
MIRT518216 | TRMT10B | tRNA methyltransferase 10B | ![]() |
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2 | 2 | ||||||
MIRT519602 | ZNF805 | zinc finger protein 805 | ![]() |
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2 | 2 | ||||||
MIRT523570 | GGCX | gamma-glutamyl carboxylase | ![]() |
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2 | 4 | ||||||
MIRT525795 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 2 | ||||||
MIRT533055 | ZBTB37 | zinc finger and BTB domain containing 37 | ![]() |
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2 | 2 | ||||||
MIRT534218 | SLC37A3 | solute carrier family 37 member 3 | ![]() |
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2 | 4 | ||||||
MIRT535633 | NR2E1 | nuclear receptor subfamily 2 group E member 1 | ![]() |
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2 | 2 | ||||||
MIRT535863 | MRPL17 | mitochondrial ribosomal protein L17 | ![]() |
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2 | 2 | ||||||
MIRT536344 | LEFTY1 | left-right determination factor 1 | ![]() |
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2 | 2 | ||||||
MIRT537923 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 | ||||||
MIRT543114 | SKA2 | spindle and kinetochore associated complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT544717 | ZNF529 | zinc finger protein 529 | ![]() |
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2 | 2 | ||||||
MIRT544847 | BASP1 | brain abundant membrane attached signal protein 1 | ![]() |
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2 | 4 | ||||||
MIRT545536 | ARF3 | ADP ribosylation factor 3 | ![]() |
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2 | 2 | ||||||
MIRT547124 | PHLPP2 | PH domain and leucine rich repeat protein phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT548070 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 2 | ||||||
MIRT548446 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | ![]() |
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2 | 2 | ||||||
MIRT548626 | DAZAP1 | DAZ associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT550259 | FAM120AOS | family with sequence similarity 120A opposite strand | ![]() |
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2 | 2 | ||||||
MIRT551940 | AKAP8 | A-kinase anchoring protein 8 | ![]() |
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2 | 4 | ||||||
MIRT552511 | ZIK1 | zinc finger protein interacting with K protein 1 | ![]() |
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2 | 4 | ||||||
MIRT554015 | SPIRE1 | spire type actin nucleation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT556647 | KPNA2 | karyopherin subunit alpha 2 | ![]() |
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2 | 4 | ||||||
MIRT559744 | ACOX1 | acyl-CoA oxidase 1 | ![]() |
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2 | 2 | ||||||
MIRT560393 | TMEM254 | transmembrane protein 254 | ![]() |
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2 | 2 | ||||||
MIRT562234 | HMGB2 | high mobility group box 2 | ![]() |
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2 | 2 | ||||||
MIRT563325 | ORC4 | origin recognition complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT563697 | RPS26 | ribosomal protein S26 | ![]() |
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2 | 2 | ||||||
MIRT565066 | USP25 | ubiquitin specific peptidase 25 | ![]() |
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2 | 2 | ||||||
MIRT565349 | TMED2 | transmembrane p24 trafficking protein 2 | ![]() |
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2 | 2 | ||||||
MIRT565624 | SLC31A1 | solute carrier family 31 member 1 | ![]() |
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2 | 2 | ||||||
MIRT566379 | PNISR | PNN interacting serine and arginine rich protein | ![]() |
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2 | 2 | ||||||
MIRT567575 | FEM1C | fem-1 homolog C | ![]() |
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2 | 2 | ||||||
MIRT569383 | DDX20 | DEAD-box helicase 20 | ![]() |
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2 | 2 | ||||||
MIRT570037 | FAM228A | family with sequence similarity 228 member A | ![]() |
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2 | 2 | ||||||
MIRT573269 | DCAF10 | DDB1 and CUL4 associated factor 10 | ![]() |
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2 | 2 | ||||||
MIRT573912 | PARP1 | poly(ADP-ribose) polymerase 1 | ![]() |
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2 | 2 | ||||||
MIRT620034 | ST6GALNAC3 | ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT635606 | ZWILCH | zwilch kinetochore protein | ![]() |
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2 | 2 | ||||||
MIRT644413 | FRMD6 | FERM domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT652528 | TM9SF4 | transmembrane 9 superfamily member 4 | ![]() |
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2 | 2 | ||||||
MIRT656238 | MFSD6 | major facilitator superfamily domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT661373 | DYRK4 | dual specificity tyrosine phosphorylation regulated kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT662530 | PNPLA4 | patatin like phospholipase domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT675551 | MALL | mal, T-cell differentiation protein like | ![]() |
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2 | 2 | ||||||
MIRT693650 | ACBD7 | acyl-CoA binding domain containing 7 | ![]() |
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2 | 2 | ||||||
MIRT696348 | SLC35D2 | solute carrier family 35 member D2 | ![]() |
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2 | 2 | ||||||
MIRT705815 | AKNA | AT-hook transcription factor | ![]() |
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2 | 2 | ||||||
MIRT707632 | TARDBP | TAR DNA binding protein | ![]() |
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2 | 2 | ||||||
MIRT717902 | COPS8 | COP9 signalosome subunit 8 | ![]() |
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2 | 2 | ||||||
MIRT723626 | SOBP | sine oculis binding protein homolog | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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