pre-miRNA Information | |
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pre-miRNA | hsa-mir-4291 |
Genomic Coordinates | chr9: 93819357 - 93819421 |
Description | Homo sapiens miR-4291 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4291 | ||||||||||||
Sequence | 11| UUCAGCAGGAACAGCU |26 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | SOLiD | ||||||||||||
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 | ATF3 | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | activating transcription factor 3 | ||||||||||||||||||||
Transcript | NM_001040619 | ||||||||||||||||||||
Other Transcripts | NM_001030287 , NM_001674 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ATF3 | |||||||||||||||||||||
3'UTR of ATF3 (miRNA target sites are highlighted) |
>ATF3|NM_001040619|3'UTR 1 GGTATCTGAACTGCAGCTTCAGTATTAGCAGAGCCACAGGCCGCCTCTGTGGCATCACCAGGGTTTCTCTGAAGAAGAGG 81 GTCTGCATTTTCCTAAACCCAGTGCTGCTCTCCCATCTCCCATCTTCCTCTCGCAGCTTGATGAGCCCCGGTGTGTCCCA 161 GGTACACCCCTGCATCCAGGCAGCAGCCCAGGCCACCCCCTCCTCACTGGCCCTTGGCTCCTTTCTTGATGCCTCTGTTG 241 CTTGTCCCCCAGGAGTCGGAGAAGCTGGAAAGTGTGAATGCTGAACTGAAGGCTCAGATTGAGGAGCTCAAGAACGAGAA 321 GCAGCATTTGATATACATGCTCAACCTTCATCGGCCCACGTGTATTGTCCGGGCTCAGAATGGGAGGACTCCAGAAGATG 401 AGAGAAACCTCTTTATCCAACAGATAAAAGAAGGAACATTGCAGAGCTAAGCAGTCGTGGTATGGGGGCGACTGGGGAGT 481 CCTCATTGAATCCTCATTTTATACCCAAAACCCTGAAGCCATTGGAGAGCTGTCTTCCTGTGTACCTCTAGAATCCCAGC 561 AGCAGAGAACCATCAAGGCGGGAGGGCCTGCAGTGATTCAGCAGGCCCTTCCCATTCTGCCCCAGAGTGGGTCTTGGACC 641 AGGGCAAGTGCATCTTTGCCTCAACTCCAGGATTTAGGCCTTAACACACTGGCCATTCTTATGTTCCAGATGGCCCCCAG 721 CTGGTGTCCTGCCCGCCTTTCATCTGGATTCTACAAAAAACCAGGATGCCCACCGTTAGGATTCAGGCAGCAGTGTCTGT 801 ACCTCGGGTGGGAGGGATGGGGCCATCTCCTTCACCGTGGCTACCATTGTCACTCGTAGGGGATGTGGAGTGAGAACAGC 881 ATTTAGTGAAGTTGTGCAACGGCCAGGGTTGTGCTTTCTAGCAAATATGCTGTTATGTCCAGAAATTGTGTGTGCAAGAA 961 AACTAGGCAATGTACTCTTCCGATGTTTGTGTCACACAACACTGATGTGACTTTTATATGCTTTTTCTCAGATCTGGTTT 1041 CTAAGAGTTTTGGGGGGCGGGGCTGTCACCACGTGCAGTATCTCAAGATATTCAGGTGGCCAGAAGAGCTTGTCAGCAAG 1121 AGGAGGACAGAATTCTCCCAGCGTTAACACAAAATCCATGGGCAGTATGATGGCAGGTCCTCTGTTGCAAACTCAGTTCC 1201 AAAGTCACAGGAAGAAAGCAGAAAGTTCAACTTCCAAAGGGTTAGGACTCTCCACTCAATGTCTTAGGTCAGGAGTTGTG 1281 TCTAGGCTGGAAGAGCCAAAGAATATTCCATTTTCCTTTCCTTGTGGTTGAAAACCACAGTCAGTGGAGAGATGTTTGGA 1361 AACCACAGTCAGTGGAGCCTGGGTGGTACCCAGGCTTTAGCATTATTGGATGTCAATAGCATTGTTTTTGTCATGTAGCT 1441 GTTTTAAGAAATCTGGCCCAGGGTGTTTGCAGCTGTGAGAAGTCACTCACACTGGCCACAAGGACGCTGGCTACTGTCTA 1521 TTAAAATTCTGATGTTTCTGTGAAATTCTCAGAGTGTTTAATTGTACTCAATGGTATCATTACAATTTTCTGTAAGAGAA 1601 AATATTACTTATTTATCCTAGTATTCCTAACCTGTCAGAATAATAAATATTGGAACCAAGACATGGTAAACAAAAAAAAA 1681 AAAAA 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 | 467.0 | ||||||
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 | ENST00000366983.1 | 3UTR | gaaagugugaaugcugaacuga |
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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82 hsa-miR-4291 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT102445 | CALU | calumenin | ![]() |
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2 | 4 | ||||||
MIRT108677 | ZBTB33 | zinc finger and BTB domain containing 33 | ![]() |
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2 | 4 | ||||||
MIRT125969 | SHOC2 | SHOC2, leucine rich repeat scaffold protein | ![]() |
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2 | 6 | ||||||
MIRT179018 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 4 | ||||||
MIRT379033 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 6 | ||||||
MIRT442473 | CPEB4 | cytoplasmic polyadenylation element binding protein 4 | ![]() |
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2 | 2 | ||||||
MIRT442910 | PCBD2 | pterin-4 alpha-carbinolamine dehydratase 2 | ![]() |
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2 | 2 | ||||||
MIRT442979 | ZNF736 | zinc finger protein 736 | ![]() |
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2 | 2 | ||||||
MIRT445663 | TNFSF15 | TNF superfamily member 15 | ![]() |
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2 | 2 | ||||||
MIRT446237 | FZD6 | frizzled class receptor 6 | ![]() |
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2 | 2 | ||||||
MIRT448860 | FAM49B | family with sequence similarity 49 member B | ![]() |
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2 | 2 | ||||||
MIRT455559 | TRAF1 | TNF receptor associated factor 1 | ![]() |
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2 | 2 | ||||||
MIRT459704 | ZNF641 | zinc finger protein 641 | ![]() |
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2 | 2 | ||||||
MIRT460608 | FEM1A | fem-1 homolog A | ![]() |
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2 | 2 | ||||||
MIRT462251 | LAMA4 | laminin subunit alpha 4 | ![]() |
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2 | 2 | ||||||
MIRT462469 | FIZ1 | FLT3 interacting zinc finger 1 | ![]() |
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2 | 2 | ||||||
MIRT466656 | TAF1D | TATA-box binding protein associated factor, RNA polymerase I subunit D | ![]() |
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2 | 6 | ||||||
MIRT466841 | STX6 | syntaxin 6 | ![]() |
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2 | 2 | ||||||
MIRT471403 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT471517 | PCGF3 | polycomb group ring finger 3 | ![]() |
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2 | 2 | ||||||
MIRT471681 | PABPN1 | poly(A) binding protein nuclear 1 | ![]() |
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2 | 2 | ||||||
MIRT472858 | MTHFD2 | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase | ![]() |
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2 | 2 | ||||||
MIRT474813 | KIAA0226 | RUN and cysteine rich domain containing beclin 1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT474931 | KCTD15 | potassium channel tetramerization domain containing 15 | ![]() |
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2 | 2 | ||||||
MIRT475814 | HDGF | heparin binding growth factor | ![]() |
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2 | 2 | ||||||
MIRT480434 | C17orf49 | chromosome 17 open reading frame 49 | ![]() |
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2 | 2 | ||||||
MIRT480903 | BCL2L2-PABPN1 | BCL2L2-PABPN1 readthrough | ![]() |
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2 | 2 | ||||||
MIRT481478 | ARL8B | ADP ribosylation factor like GTPase 8B | ![]() |
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2 | 2 | ||||||
MIRT484982 | UBE2V1 | ubiquitin conjugating enzyme E2 V1 | ![]() |
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2 | 8 | ||||||
MIRT485019 | TMEM189-UBE2V1 | TMEM189-UBE2V1 readthrough | ![]() |
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2 | 8 | ||||||
MIRT485036 | TMEM189 | transmembrane protein 189 | ![]() |
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2 | 8 | ||||||
MIRT495074 | HEYL | hes related family bHLH transcription factor with YRPW motif-like | ![]() |
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2 | 2 | ||||||
MIRT496004 | CD180 | CD180 molecule | ![]() |
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2 | 2 | ||||||
MIRT500675 | TRIM37 | tripartite motif containing 37 | ![]() |
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2 | 2 | ||||||
MIRT504544 | ZNF417 | zinc finger protein 417 | ![]() |
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2 | 6 | ||||||
MIRT506782 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 6 | ||||||
MIRT507256 | FGF2 | fibroblast growth factor 2 | ![]() |
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2 | 6 | ||||||
MIRT507386 | EN2 | engrailed homeobox 2 | ![]() |
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2 | 2 | ||||||
MIRT512505 | BTBD19 | BTB domain containing 19 | ![]() |
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2 | 2 | ||||||
MIRT516903 | CTSB | cathepsin B | ![]() |
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2 | 2 | ||||||
MIRT528124 | PPP1R10 | protein phosphatase 1 regulatory subunit 10 | ![]() |
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2 | 2 | ||||||
MIRT528874 | ATF3 | activating transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT536091 | MBOAT2 | membrane bound O-acyltransferase domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT541079 | RLIM | ring finger protein, LIM domain interacting | ![]() |
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2 | 2 | ||||||
MIRT541099 | RAF1 | Raf-1 proto-oncogene, serine/threonine kinase | ![]() |
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2 | 2 | ||||||
MIRT545360 | LIN7C | lin-7 homolog C, crumbs cell polarity complex component | ![]() |
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2 | 2 | ||||||
MIRT545831 | ZNF367 | zinc finger protein 367 | ![]() |
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2 | 4 | ||||||
MIRT547115 | PHLPP2 | PH domain and leucine rich repeat protein phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT547312 | NPTN | neuroplastin | ![]() |
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2 | 2 | ||||||
MIRT547959 | HIGD1A | HIG1 hypoxia inducible domain family member 1A | ![]() |
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2 | 4 | ||||||
MIRT549943 | RPL7L1 | ribosomal protein L7 like 1 | ![]() |
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2 | 2 | ||||||
MIRT550749 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | ![]() |
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2 | 2 | ||||||
MIRT565145 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT571050 | POLQ | DNA polymerase theta | ![]() |
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2 | 2 | ||||||
MIRT571361 | ZNF45 | zinc finger protein 45 | ![]() |
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2 | 2 | ||||||
MIRT610133 | FOXI2 | forkhead box I2 | ![]() |
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2 | 2 | ||||||
MIRT613145 | DSE | dermatan sulfate epimerase | ![]() |
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2 | 2 | ||||||
MIRT613379 | ABCC12 | ATP binding cassette subfamily C member 12 | ![]() |
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2 | 2 | ||||||
MIRT615752 | C6 | complement C6 | ![]() |
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2 | 2 | ||||||
MIRT616460 | ADRA2B | adrenoceptor alpha 2B | ![]() |
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2 | 2 | ||||||
MIRT616719 | FEM1B | fem-1 homolog B | ![]() |
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2 | 2 | ||||||
MIRT618312 | IPP | intracisternal A particle-promoted polypeptide | ![]() |
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2 | 2 | ||||||
MIRT631491 | RASSF4 | Ras association domain family member 4 | ![]() |
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2 | 2 | ||||||
MIRT643134 | PLCXD2 | phosphatidylinositol specific phospholipase C X domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT643482 | DISC1 | disrupted in schizophrenia 1 | ![]() |
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2 | 2 | ||||||
MIRT649715 | TWSG1 | twisted gastrulation BMP signaling modulator 1 | ![]() |
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2 | 2 | ||||||
MIRT653542 | SLC38A7 | solute carrier family 38 member 7 | ![]() |
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2 | 2 | ||||||
MIRT666307 | SLC22A3 | solute carrier family 22 member 3 | ![]() |
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2 | 2 | ||||||
MIRT692005 | NAP1L4 | nucleosome assembly protein 1 like 4 | ![]() |
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2 | 2 | ||||||
MIRT696838 | ARL2BP | ADP ribosylation factor like GTPase 2 binding protein | ![]() |
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2 | 2 | ||||||
MIRT698204 | TMEM248 | transmembrane protein 248 | ![]() |
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2 | 2 | ||||||
MIRT703316 | GDPD5 | glycerophosphodiester phosphodiesterase domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT709376 | FAM13A | family with sequence similarity 13 member A | ![]() |
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2 | 2 | ||||||
MIRT710112 | MED23 | mediator complex subunit 23 | ![]() |
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2 | 2 | ||||||
MIRT711975 | HOMER2 | homer scaffolding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT712275 | PPIP5K2 | diphosphoinositol pentakisphosphate kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT714108 | TMED9 | transmembrane p24 trafficking protein 9 | ![]() |
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2 | 2 | ||||||
MIRT719113 | MAML1 | mastermind like transcriptional coactivator 1 | ![]() |
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2 | 2 | ||||||
MIRT719727 | SLC39A11 | solute carrier family 39 member 11 | ![]() |
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2 | 2 | ||||||
MIRT720018 | TFAP2C | transcription factor AP-2 gamma | ![]() |
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2 | 2 | ||||||
MIRT720358 | ZBTB8B | zinc finger and BTB domain containing 8B | ![]() |
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2 | 2 | ||||||
MIRT720372 | NUDT3 | nudix hydrolase 3 | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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