pre-miRNA Information | |
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pre-miRNA | hsa-mir-500b |
Genomic Coordinates | chrX: 50010672 - 50010750 |
Description | Homo sapiens miR-500b stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Associated Diseases | ![]() |
Mature miRNA Information | |||||||
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Mature miRNA | hsa-miR-500b-3p | ||||||
Sequence | 51| GCACCCAGGCAAGGAUUCUG |70 | ||||||
Evidence | Experimental | ||||||
Experiments | Illumina | ||||||
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 | TNFRSF13C | ||||||||||||||||||||
Synonyms | BAFF-R, BAFFR, BROMIX, CD268, CVID4, prolixin | ||||||||||||||||||||
Description | TNF receptor superfamily member 13C | ||||||||||||||||||||
Transcript | NM_052945 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TNFRSF13C | |||||||||||||||||||||
3'UTR of TNFRSF13C (miRNA target sites are highlighted) |
>TNFRSF13C|NM_052945|3'UTR 1 CAGGGAGCCGGCAGGAGGTGGCCCCTGCCCTCCCTCTGGACCCCCAGCCAGGGGCTTGGAAATCAAATTCAGCTCTTCAC 81 TCCAGCATGCACATGCCCTCTTTCTGGGACCAGGCTAACTCTGCAGAAGCACAGACACTACAGACCACAGCATTCAGCCC 161 CCATGGAGTTTGGTGTGCTTGCCTTTGGCTTCAGACCTCACCATCTTTGACAGCCCTTGAAGGTGGTAGCCCAGCTCCTG 241 TTCCTGTGCCTTCAAAAGGCTGGGGCACTATGAGTAAAAGACCGCTTTTAAAATGGGGAAGGCACCATTAAGCCAAAATG 321 AATCTGAAAAAAGAC 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 | 115650.0 | ||||||
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 | ENST00000291232.3 | 3UTR | ACUGGACUAGGAGUCAGAAGGUGGAGUUCUGGGUGCUGU |
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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172 hsa-miR-500b-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT059905 | HDGF | heparin binding growth factor | ![]() |
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2 | 4 | ||||||
MIRT235394 | KDELR1 | KDEL endoplasmic reticulum protein retention receptor 1 | ![]() |
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2 | 4 | ||||||
MIRT442246 | PYGO1 | pygopus family PHD finger 1 | ![]() |
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2 | 2 | ||||||
MIRT443591 | ZNF439 | zinc finger protein 439 | ![]() |
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2 | 4 | ||||||
MIRT453280 | EFTUD2 | elongation factor Tu GTP binding domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT463540 | ZBTB7A | zinc finger and BTB domain containing 7A | ![]() |
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2 | 2 | ||||||
MIRT465589 | TNRC6B | trinucleotide repeat containing 6B | ![]() |
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2 | 2 | ||||||
MIRT469462 | REL | REL proto-oncogene, NF-kB subunit | ![]() |
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2 | 2 | ||||||
MIRT485449 | KCTD15 | potassium channel tetramerization domain containing 15 | ![]() |
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2 | 4 | ||||||
MIRT486682 | WDR81 | WD repeat domain 81 | ![]() |
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2 | 2 | ||||||
MIRT489078 | POLM | DNA polymerase mu | ![]() |
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2 | 2 | ||||||
MIRT493734 | GREM2 | gremlin 2, DAN family BMP antagonist | ![]() |
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2 | 2 | ||||||
MIRT494872 | DYNLL2 | dynein light chain LC8-type 2 | ![]() |
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2 | 2 | ||||||
MIRT496130 | RNF103-CHMP3 | RNF103-CHMP3 readthrough | ![]() |
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2 | 2 | ||||||
MIRT496489 | CHMP3 | charged multivesicular body protein 3 | ![]() |
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2 | 2 | ||||||
MIRT496924 | CLMN | calmin | ![]() |
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2 | 2 | ||||||
MIRT497297 | TMEM119 | transmembrane protein 119 | ![]() |
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2 | 2 | ||||||
MIRT499103 | AGRN | agrin | ![]() |
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2 | 2 | ||||||
MIRT508979 | CXorf38 | chromosome X open reading frame 38 | ![]() |
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2 | 2 | ||||||
MIRT509911 | NIPAL1 | NIPA like domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT512820 | ARRDC2 | arrestin domain containing 2 | ![]() |
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2 | 4 | ||||||
MIRT512827 | KBTBD6 | kelch repeat and BTB domain containing 6 | ![]() |
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2 | 4 | ||||||
MIRT515360 | MRPL52 | mitochondrial ribosomal protein L52 | ![]() |
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2 | 2 | ||||||
MIRT516610 | TRIM58 | tripartite motif containing 58 | ![]() |
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2 | 2 | ||||||
MIRT517053 | TLDC1 | TBC/LysM-associated domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT517637 | ZNF491 | zinc finger protein 491 | ![]() |
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2 | 2 | ||||||
MIRT518270 | LEAP2 | liver enriched antimicrobial peptide 2 | ![]() |
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2 | 2 | ||||||
MIRT518625 | STAR | steroidogenic acute regulatory protein | ![]() |
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2 | 2 | ||||||
MIRT518887 | N4BP2L2 | NEDD4 binding protein 2 like 2 | ![]() |
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2 | 2 | ||||||
MIRT519026 | PAICS | phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase | ![]() |
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2 | 2 | ||||||
MIRT520365 | UBE2G2 | ubiquitin conjugating enzyme E2 G2 | ![]() |
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2 | 2 | ||||||
MIRT521106 | SLC1A5 | solute carrier family 1 member 5 | ![]() |
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2 | 2 | ||||||
MIRT521943 | PHC3 | polyhomeotic homolog 3 | ![]() |
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2 | 2 | ||||||
MIRT522253 | NPEPPS | aminopeptidase puromycin sensitive | ![]() |
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2 | 2 | ||||||
MIRT522853 | KIAA1551 | KIAA1551 | ![]() |
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2 | 2 | ||||||
MIRT522868 | KIAA1549 | KIAA1549 | ![]() |
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2 | 2 | ||||||
MIRT524207 | DDX19B | DEAD-box helicase 19B | ![]() |
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2 | 2 | ||||||
MIRT526004 | ARHGAP27 | Rho GTPase activating protein 27 | ![]() |
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2 | 2 | ||||||
MIRT527769 | RRAD | RRAD, Ras related glycolysis inhibitor and calcium channel regulator | ![]() |
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2 | 2 | ||||||
MIRT527827 | TMEM74B | transmembrane protein 74B | ![]() |
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2 | 2 | ||||||
MIRT527861 | SMOC1 | SPARC related modular calcium binding 1 | ![]() |
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2 | 2 | ||||||
MIRT528040 | WT1 | Wilms tumor 1 | ![]() |
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2 | 2 | ||||||
MIRT529802 | ZDHHC8 | zinc finger DHHC-type containing 8 | ![]() |
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2 | 2 | ||||||
MIRT531723 | TARS | threonyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT531996 | BARD1 | BRCA1 associated RING domain 1 | ![]() |
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2 | 2 | ||||||
MIRT533338 | UNC119B | unc-119 lipid binding chaperone B | ![]() |
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2 | 2 | ||||||
MIRT533621 | TNFRSF13C | TNF receptor superfamily member 13C | ![]() |
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2 | 2 | ||||||
MIRT533652 | TMOD2 | tropomodulin 2 | ![]() |
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2 | 2 | ||||||
MIRT534397 | SENP3 | SUMO1/sentrin/SMT3 specific peptidase 3 | ![]() |
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2 | 2 | ||||||
MIRT538686 | CCDC80 | coiled-coil domain containing 80 | ![]() |
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2 | 2 | ||||||
MIRT540444 | RBM43 | RNA binding motif protein 43 | ![]() |
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2 | 2 | ||||||
MIRT542586 | ZC3H12C | zinc finger CCCH-type containing 12C | ![]() |
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2 | 8 | ||||||
MIRT542796 | PLEKHA3 | pleckstrin homology domain containing A3 | ![]() |
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2 | 4 | ||||||
MIRT542991 | ERC1 | ELKS/RAB6-interacting/CAST family member 1 | ![]() |
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2 | 2 | ||||||
MIRT544424 | ZNF460 | zinc finger protein 460 | ![]() |
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2 | 4 | ||||||
MIRT545740 | ESF1 | ESF1 nucleolar pre-rRNA processing protein homolog | ![]() |
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2 | 4 | ||||||
MIRT552618 | ZBTB8A | zinc finger and BTB domain containing 8A | ![]() |
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2 | 2 | ||||||
MIRT554456 | SAMD8 | sterile alpha motif domain containing 8 | ![]() |
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2 | 2 | ||||||
MIRT569663 | PRIM1 | DNA primase subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT569924 | PCSK9 | proprotein convertase subtilisin/kexin type 9 | ![]() |
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2 | 2 | ||||||
MIRT570140 | IL1RL2 | interleukin 1 receptor like 2 | ![]() |
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2 | 2 | ||||||
MIRT573558 | TMEM120B | transmembrane protein 120B | ![]() |
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2 | 2 | ||||||
MIRT574282 | OPRD1 | opioid receptor delta 1 | ![]() |
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2 | 2 | ||||||
MIRT575335 | Fbxo6 | F-box protein 6 | ![]() |
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2 | 2 | ||||||
MIRT607057 | IDS | iduronate 2-sulfatase | ![]() |
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2 | 2 | ||||||
MIRT607078 | POM121L7 | POM121 transmembrane nucleoporin like 7 pseudogene | ![]() |
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2 | 2 | ||||||
MIRT607500 | HEBP2 | heme binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT607530 | ABL2 | ABL proto-oncogene 2, non-receptor tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT607808 | RHBDL2 | rhomboid like 2 | ![]() |
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2 | 2 | ||||||
MIRT608079 | ZFP14 | ZFP14 zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT609119 | NUDT3 | nudix hydrolase 3 | ![]() |
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2 | 2 | ||||||
MIRT609745 | PTCH1 | patched 1 | ![]() |
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2 | 2 | ||||||
MIRT612904 | HIF1AN | hypoxia inducible factor 1 alpha subunit inhibitor | ![]() |
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2 | 2 | ||||||
MIRT618720 | PCSK2 | proprotein convertase subtilisin/kexin type 2 | ![]() |
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2 | 2 | ||||||
MIRT618778 | HLA-E | major histocompatibility complex, class I, E | ![]() |
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2 | 2 | ||||||
MIRT619015 | SLC2A6 | solute carrier family 2 member 6 | ![]() |
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2 | 2 | ||||||
MIRT623223 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
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2 | 2 | ||||||
MIRT623819 | GEMIN6 | gem nuclear organelle associated protein 6 | ![]() |
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2 | 2 | ||||||
MIRT625704 | OPTN | optineurin | ![]() |
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2 | 2 | ||||||
MIRT626437 | CHDH | choline dehydrogenase | ![]() |
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2 | 2 | ||||||
MIRT628087 | KAT7 | lysine acetyltransferase 7 | ![]() |
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2 | 2 | ||||||
MIRT628936 | APOB | apolipoprotein B | ![]() |
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2 | 2 | ||||||
MIRT633543 | PGBD5 | piggyBac transposable element derived 5 | ![]() |
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2 | 2 | ||||||
MIRT634348 | SGOL1 | shugoshin 1 | ![]() |
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2 | 2 | ||||||
MIRT634611 | KIAA1919 | major facilitator superfamily domain containing 4B | ![]() |
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2 | 2 | ||||||
MIRT635243 | QPRT | quinolinate phosphoribosyltransferase | ![]() |
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2 | 2 | ||||||
MIRT636681 | BTLA | B and T lymphocyte associated | ![]() |
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2 | 2 | ||||||
MIRT636923 | ZNF845 | zinc finger protein 845 | ![]() |
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2 | 2 | ||||||
MIRT637606 | ZNF554 | zinc finger protein 554 | ![]() |
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2 | 2 | ||||||
MIRT639242 | RANGAP1 | Ran GTPase activating protein 1 | ![]() |
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2 | 2 | ||||||
MIRT640835 | POLR3A | RNA polymerase III subunit A | ![]() |
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2 | 2 | ||||||
MIRT642098 | FBXL2 | F-box and leucine rich repeat protein 2 | ![]() |
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2 | 2 | ||||||
MIRT643087 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT643934 | C17orf104 | meiosis specific with coiled-coil domain | ![]() |
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2 | 2 | ||||||
MIRT644353 | FXN | frataxin | ![]() |
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2 | 2 | ||||||
MIRT645628 | SF3A3 | splicing factor 3a subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT645754 | FAM213A | family with sequence similarity 213 member A | ![]() |
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2 | 2 | ||||||
MIRT646329 | MVB12B | multivesicular body subunit 12B | ![]() |
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2 | 2 | ||||||
MIRT646817 | COX19 | COX19, cytochrome c oxidase assembly factor | ![]() |
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2 | 2 | ||||||
MIRT647019 | ADCY2 | adenylate cyclase 2 | ![]() |
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2 | 2 | ||||||
MIRT647621 | IGSF9B | immunoglobulin superfamily member 9B | ![]() |
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2 | 2 | ||||||
MIRT648517 | PIGG | phosphatidylinositol glycan anchor biosynthesis class G | ![]() |
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2 | 2 | ||||||
MIRT648871 | ABCA6 | ATP binding cassette subfamily A member 6 | ![]() |
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2 | 2 | ||||||
MIRT649620 | ITPKC | inositol-trisphosphate 3-kinase C | ![]() |
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2 | 2 | ||||||
MIRT650062 | CCDC134 | coiled-coil domain containing 134 | ![]() |
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2 | 2 | ||||||
MIRT650734 | TNFSF8 | TNF superfamily member 8 | ![]() |
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2 | 2 | ||||||
MIRT652389 | TMEM55A | phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT654352 | RBM27 | RNA binding motif protein 27 | ![]() |
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2 | 2 | ||||||
MIRT655796 | NOVA2 | NOVA alternative splicing regulator 2 | ![]() |
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2 | 2 | ||||||
MIRT657329 | HNRNPK | heterogeneous nuclear ribonucleoprotein K | ![]() |
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2 | 2 | ||||||
MIRT657734 | GOSR1 | golgi SNAP receptor complex member 1 | ![]() |
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2 | 2 | ||||||
MIRT660613 | ANO6 | anoctamin 6 | ![]() |
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2 | 2 | ||||||
MIRT661243 | ARL17B | ADP ribosylation factor like GTPase 17B | ![]() |
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2 | 2 | ||||||
MIRT662245 | PGBD4 | piggyBac transposable element derived 4 | ![]() |
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2 | 2 | ||||||
MIRT662921 | MED18 | mediator complex subunit 18 | ![]() |
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2 | 2 | ||||||
MIRT662963 | JPH2 | junctophilin 2 | ![]() |
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2 | 2 | ||||||
MIRT663347 | ZNF74 | zinc finger protein 74 | ![]() |
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2 | 2 | ||||||
MIRT663528 | MASTL | microtubule associated serine/threonine kinase like | ![]() |
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2 | 2 | ||||||
MIRT663547 | CCR6 | C-C motif chemokine receptor 6 | ![]() |
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2 | 2 | ||||||
MIRT663977 | ZNF786 | zinc finger protein 786 | ![]() |
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2 | 2 | ||||||
MIRT664084 | METTL2B | methyltransferase like 2B | ![]() |
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2 | 2 | ||||||
MIRT664358 | C16orf45 | chromosome 16 open reading frame 45 | ![]() |
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2 | 2 | ||||||
MIRT664421 | TIGD6 | tigger transposable element derived 6 | ![]() |
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2 | 2 | ||||||
MIRT664476 | ZYG11B | zyg-11 family member B, cell cycle regulator | ![]() |
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2 | 2 | ||||||
MIRT664979 | TDRD1 | tudor domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT665128 | PYCRL | pyrroline-5-carboxylate reductase 3 | ![]() |
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2 | 2 | ||||||
MIRT666259 | SLC31A1 | solute carrier family 31 member 1 | ![]() |
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2 | 2 | ||||||
MIRT666321 | SLC16A10 | solute carrier family 16 member 10 | ![]() |
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2 | 2 | ||||||
MIRT666881 | POLQ | DNA polymerase theta | ![]() |
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2 | 2 | ||||||
MIRT668469 | FADS6 | fatty acid desaturase 6 | ![]() |
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2 | 2 | ||||||
MIRT669554 | ALG14 | ALG14, UDP-N-acetylglucosaminyltransferase subunit | ![]() |
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2 | 2 | ||||||
MIRT669835 | ISCA2 | iron-sulfur cluster assembly 2 | ![]() |
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2 | 2 | ||||||
MIRT670185 | CCDC142 | coiled-coil domain containing 142 | ![]() |
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2 | 2 | ||||||
MIRT672020 | PXMP4 | peroxisomal membrane protein 4 | ![]() |
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2 | 2 | ||||||
MIRT672070 | KIAA0930 | KIAA0930 | ![]() |
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2 | 2 | ||||||
MIRT672475 | RTTN | rotatin | ![]() |
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2 | 2 | ||||||
MIRT672851 | ICOSLG | inducible T-cell costimulator ligand | ![]() |
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2 | 2 | ||||||
MIRT673090 | AK1 | adenylate kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT673581 | KDELC2 | KDEL motif containing 2 | ![]() |
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2 | 2 | ||||||
MIRT674586 | SLC35B4 | solute carrier family 35 member B4 | ![]() |
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2 | 2 | ||||||
MIRT675001 | STRN3 | striatin 3 | ![]() |
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2 | 2 | ||||||
MIRT679018 | MTMR10 | myotubularin related protein 10 | ![]() |
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2 | 2 | ||||||
MIRT679680 | STAT3 | signal transducer and activator of transcription 3 | ![]() |
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2 | 2 | ||||||
MIRT682833 | FLG2 | filaggrin family member 2 | ![]() |
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2 | 2 | ||||||
MIRT682886 | SAR1A | secretion associated Ras related GTPase 1A | ![]() |
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2 | 2 | ||||||
MIRT683442 | AP3B2 | adaptor related protein complex 3 beta 2 subunit | ![]() |
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2 | 2 | ||||||
MIRT687040 | RNF115 | ring finger protein 115 | ![]() |
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2 | 2 | ||||||
MIRT691957 | RHOH | ras homolog family member H | ![]() |
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2 | 2 | ||||||
MIRT694625 | ZFPM1 | zinc finger protein, FOG family member 1 | ![]() |
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2 | 2 | ||||||
MIRT695637 | SLC26A2 | solute carrier family 26 member 2 | ![]() |
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2 | 2 | ||||||
MIRT697640 | WRN | Werner syndrome RecQ like helicase | ![]() |
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2 | 2 | ||||||
MIRT702009 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT702034 | MOGAT1 | monoacylglycerol O-acyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT704789 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 2 | ||||||
MIRT705728 | AMMECR1L | AMMECR1 like | ![]() |
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2 | 2 | ||||||
MIRT705879 | ADM | adrenomedullin | ![]() |
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2 | 2 | ||||||
MIRT706220 | ACOT9 | acyl-CoA thioesterase 9 | ![]() |
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2 | 2 | ||||||
MIRT708418 | CERS4 | ceramide synthase 4 | ![]() |
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2 | 2 | ||||||
MIRT709114 | C3orf18 | chromosome 3 open reading frame 18 | ![]() |
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2 | 2 | ||||||
MIRT709595 | ITPA | inosine triphosphatase | ![]() |
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2 | 2 | ||||||
MIRT710945 | MRPL45 | mitochondrial ribosomal protein L45 | ![]() |
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2 | 2 | ||||||
MIRT712345 | NLN | neurolysin | ![]() |
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2 | 2 | ||||||
MIRT712530 | CYTH2 | cytohesin 2 | ![]() |
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2 | 2 | ||||||
MIRT714019 | ASCC1 | activating signal cointegrator 1 complex subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT717287 | ARMC12 | armadillo repeat containing 12 | ![]() |
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2 | 2 | ||||||
MIRT717733 | FGF1 | fibroblast growth factor 1 | ![]() |
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2 | 2 | ||||||
MIRT718083 | CLIC5 | chloride intracellular channel 5 | ![]() |
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2 | 2 | ||||||
MIRT718562 | MUC20 | mucin 20, cell surface associated | ![]() |
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2 | 2 | ||||||
MIRT721639 | MYLK3 | myosin light chain kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT722632 | C8A | complement C8 alpha chain | ![]() |
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2 | 2 | ||||||
MIRT723177 | CDCA4 | cell division cycle associated 4 | ![]() |
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2 | 2 | ||||||
MIRT725523 | FAM229B | family with sequence similarity 229 member B | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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