miRTarBase - #MIRT529062


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pre-miRNA Information
pre-miRNA hsa-mir-4653   
Genomic Coordinates chr7: 101159473 - 101159555
Description Homo sapiens miR-4653 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4653-5p
Sequence 10| UCUCUGAGCAAGGCUUAACACC |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs566953516 2 dbSNP
rs1307365749 4 dbSNP
rs1226652366 6 dbSNP
rs1216592229 12 dbSNP
rs1283699546 15 dbSNP
rs934609749 20 dbSNP
rs1377199291 21 dbSNP
rs1282994534 22 dbSNP
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B8DF7B miR-4653 Predictive Biomarker (PRD) Transcriptomic Data . . . .
Gene Information
Gene Symbol ZNF675   
Synonyms TBZF, TIZ
Description zinc finger protein 675
Transcript NM_138330   
Expression
Putative miRNA Targets on ZNF675
3'UTR of ZNF675
(miRNA target sites are highlighted)		 
>ZNF675|NM_138330|3'UTR
   1 TAATGATTTTGACAACACCTCAAATTTTTCTAAATATAAAGGAAATCATACTGGTGAAAAATTCTAGAAATGTAAAGAAT
  81 GTGTCAAAGACTTTAAATGGTTTTCACACTTCATTGTATGTAAGATAATTCATACTGGAGAAAACTACAAGTGTGAAGAA
 161 TTTGGCAATACTGTTAATTAAGGCTCAAACCTTATTGCACAGGAAAGCGTTTATACTTAAGAAAAATTGTACAAATATAA
 241 AGAGTGTAAAATAGCCATTAATATCTGTTGACATCTTAATATCAGAATGTTGGTACTTAATAAAAGCATTATAAATGCAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1 
miRNA  3' ccACAAUUCGGAACGAGUCUcu 5'
            |||||| :   ||||| |  
Target 5' acTGTTAATTAAGGCTCAAAcc 3'
 170 - 191 112.00 -7.36
2 
miRNA  3' ccACAAUU-CGGAA--CGAGUCUcu 5'
            ||||:|  :|||    |||||  
Target 5' tcTGTTGACATCTTAATATCAGAat 3'
 264 - 288 106.00 -7.90
3 
miRNA  3' ccACAAUUCGGAACGAGUCUCu 5'
            ||| |||  |   ||| || 
Target 5' aaTGTAAAGAATGTGTCAAAGa 3'
 69 - 90 96.00 -7.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31506087 15 COSMIC
COSN27006390 24 COSMIC
COSN31562331 33 COSMIC
COSN31486006 60 COSMIC
COSN24604933 62 COSMIC
COSN30114425 64 COSMIC
COSN31588929 85 COSMIC
COSN30531178 96 COSMIC
COSN30637643 99 COSMIC
COSN31479958 131 COSMIC
COSN31517524 158 COSMIC
COSN31601508 171 COSMIC
COSN17132216 215 COSMIC
COSN5436246 349 COSMIC
COSN2461736 426 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs758825330 2 dbSNP
rs561249526 4 dbSNP
rs754511317 6 dbSNP
rs1249427870 8 dbSNP
rs1038043076 13 dbSNP
rs199944113 14 dbSNP
rs1207528859 15 dbSNP
rs1239931059 18 dbSNP
rs761453646 20 dbSNP
rs755314843 23 dbSNP
rs1467242935 25 dbSNP
rs773703280 31 dbSNP
rs183364077 32 dbSNP
rs766524760 34 dbSNP
rs760640695 38 dbSNP
rs916362570 39 dbSNP
rs1278943872 40 dbSNP
rs774376505 43 dbSNP
rs763886992 45 dbSNP
rs1212153012 48 dbSNP
rs1191237325 50 dbSNP
rs1487817288 51 dbSNP
rs891848674 52 dbSNP
rs1173528626 53 dbSNP
rs1056601103 54 dbSNP
rs939218096 55 dbSNP
rs1179629474 66 dbSNP
rs923741518 70 dbSNP
rs1008189592 71 dbSNP
rs1367638670 74 dbSNP
rs1388167511 79 dbSNP
rs890414513 85 dbSNP
rs1339667914 89 dbSNP
rs751101122 94 dbSNP
rs1259967314 95 dbSNP
rs879697976 105 dbSNP
rs1425446436 107 dbSNP
rs968332353 116 dbSNP
rs755484468 123 dbSNP
rs574779691 125 dbSNP
rs1266131616 126 dbSNP
rs915158485 131 dbSNP
rs974774478 145 dbSNP
rs1262730691 149 dbSNP
rs964694112 150 dbSNP
rs1181011343 160 dbSNP
rs1019063127 166 dbSNP
rs556097202 171 dbSNP
rs770641788 182 dbSNP
rs879275119 182 dbSNP
rs548619092 184 dbSNP
rs1327908887 188 dbSNP
rs1349963621 202 dbSNP
rs950924247 203 dbSNP
rs1258388354 205 dbSNP
rs1296023312 208 dbSNP
rs1247650277 209 dbSNP
rs1173151130 210 dbSNP
rs1322782889 213 dbSNP
rs1353274087 216 dbSNP
rs73029757 221 dbSNP
rs368942724 230 dbSNP
rs1313344566 233 dbSNP
rs576923954 244 dbSNP
rs1236949655 246 dbSNP
rs940445464 254 dbSNP
rs899460277 261 dbSNP
rs1488758085 263 dbSNP
rs1312459509 267 dbSNP
rs1255865157 277 dbSNP
rs1451006138 279 dbSNP
rs1483091883 297 dbSNP
rs1183020060 304 dbSNP
rs1044615980 305 dbSNP
rs1416572243 305 dbSNP
rs1011894268 316 dbSNP
rs894793041 322 dbSNP
rs1299588638 323 dbSNP
rs1056230649 329 dbSNP
rs1321527166 330 dbSNP
rs1303412740 334 dbSNP
rs4402688 335 dbSNP
rs923801347 340 dbSNP
rs549894607 348 dbSNP
rs1165027883 351 dbSNP
rs1354432971 359 dbSNP
rs1042653420 362 dbSNP
rs1242596536 363 dbSNP
rs1459393558 370 dbSNP
rs959692054 372 dbSNP
rs1257024220 375 dbSNP
rs1368917042 376 dbSNP
rs1479959922 388 dbSNP
rs1178511552 390 dbSNP
rs1237043094 400 dbSNP
rs1188409663 403 dbSNP
rs946523386 403 dbSNP
rs915190971 404 dbSNP
rs974638846 409 dbSNP
rs1439701447 413 dbSNP
rs1160149519 418 dbSNP
rs528621043 421 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 171392.0
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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ccACAAU--UCGGAACG-AGUcucu 5'
            | |||  ||::  || |:|    
Target 5' uuUUUUAUUAGUUGGGCAUUAug-- 3'
 		16 - 38
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]
CLIP-seq Support 1 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000359788.4 | 3UTR | GAGAUAGGAGAAUUUUUUUUUAUUAGUUGGGCAUUAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
78 hsa-miR-4653-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT118186 ZNF544 zinc finger protein 544 2 2
MIRT332935 PRKAB2 protein kinase AMP-activated non-catalytic subunit beta 2 2 2
MIRT442166 ARL10 ADP ribosylation factor like GTPase 10 2 2
MIRT442387 CLVS2 clavesin 2 2 2
MIRT442595 SIX1 SIX homeobox 1 2 2
MIRT448014 HLA-DOA major histocompatibility complex, class II, DO alpha 2 2
MIRT448061 MMP15 matrix metallopeptidase 15 2 2
MIRT489017 C1QTNF6 C1q and TNF related 6 2 2
MIRT494456 BTG2 BTG anti-proliferation factor 2 2 2
MIRT495650 SLC35B2 solute carrier family 35 member B2 2 2
MIRT504016 ACSL6 acyl-CoA synthetase long chain family member 6 2 2
MIRT506777 KLHL15 kelch like family member 15 2 4
MIRT507229 FOXN2 forkhead box N2 2 4
MIRT512550 MFN2 mitofusin 2 2 6
MIRT512842 A1CF APOBEC1 complementation factor 2 6
MIRT513944 DDX3X DEAD-box helicase 3, X-linked 2 8
MIRT516103 GADL1 glutamate decarboxylase like 1 2 4
MIRT519831 ZFP69B ZFP69 zinc finger protein B 2 4
MIRT523210 HIST1H3E histone cluster 1 H3 family member e 2 2
MIRT525008 ACTN4 actinin alpha 4 2 6
MIRT528858 PKP1 plakophilin 1 2 2
MIRT529062 ZNF675 zinc finger protein 675 2 2
MIRT531719 TARS threonyl-tRNA synthetase 2 2
MIRT534039 STK4 serine/threonine kinase 4 2 2
MIRT543848 APIP APAF1 interacting protein 2 2
MIRT545866 ZNF264 zinc finger protein 264 2 4
MIRT556037 MXD1 MAX dimerization protein 1 2 2
MIRT557081 HOXB3 homeobox B3 2 2
MIRT561345 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT562705 ZNF415 zinc finger protein 415 2 2
MIRT563223 ZNF286A zinc finger protein 286A 2 2
MIRT563860 ZNF616 zinc finger protein 616 2 4
MIRT563879 PAGR1 PAXIP1 associated glutamate rich protein 1 2 2
MIRT564652 ZNF487P zinc finger protein 487 1 1
MIRT566595 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT570878 ZFP1 ZFP1 zinc finger protein 2 2
MIRT573067 TRIB1 tribbles pseudokinase 1 2 2
MIRT573941 ZNF708 zinc finger protein 708 2 2
MIRT575966 Slfn5 schlafen 5 2 5
MIRT607293 CD300E CD300e molecule 2 4
MIRT608187 ERBB2 erb-b2 receptor tyrosine kinase 2 2 2
MIRT609537 ADPRH ADP-ribosylarginine hydrolase 2 2
MIRT610152 PRMT8 protein arginine methyltransferase 8 2 4
MIRT611571 SLFN5 schlafen family member 5 2 7
MIRT613335 AGO2 argonaute 2, RISC catalytic component 2 4
MIRT616560 ZNF512B zinc finger protein 512B 2 2
MIRT617240 SPATS2 spermatogenesis associated serine rich 2 2 2
MIRT618011 SLC9A3R2 SLC9A3 regulator 2 2 2
MIRT618478 IL17REL interleukin 17 receptor E like 2 2
MIRT619099 IFI44L interferon induced protein 44 like 2 2
MIRT622265 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT623080 NME6 NME/NM23 nucleoside diphosphate kinase 6 2 2
MIRT625621 LILRB2 leukocyte immunoglobulin like receptor B2 2 2
MIRT627844 PLEKHA6 pleckstrin homology domain containing A6 2 2
MIRT630459 GMPS guanine monophosphate synthase 2 2
MIRT630524 BAZ2A bromodomain adjacent to zinc finger domain 2A 2 4
MIRT631502 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT634537 MRPS17 mitochondrial ribosomal protein S17 2 2
MIRT638807 DCTN3 dynactin subunit 3 2 2
MIRT641303 SLAMF1 signaling lymphocytic activation molecule family member 1 2 2
MIRT648347 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT649705 ZNF175 zinc finger protein 175 2 2
MIRT652554 TLX1 T-cell leukemia homeobox 1 2 2
MIRT655564 P2RX7 purinergic receptor P2X 7 2 2
MIRT659065 DEPTOR DEP domain containing MTOR interacting protein 2 2
MIRT660341 BCAT1 branched chain amino acid transaminase 1 2 2
MIRT664330 RAB8A RAB8A, member RAS oncogene family 2 2
MIRT688934 ATXN7L3B ataxin 7 like 3B 2 2
MIRT689971 ZNF185 zinc finger protein 185 with LIM domain 2 2
MIRT699514 SKIL SKI like proto-oncogene 2 2
MIRT699975 RREB1 ras responsive element binding protein 1 2 2
MIRT702676 IRS2 insulin receptor substrate 2 2 2
MIRT709357 ULK2 unc-51 like autophagy activating kinase 2 2 2
MIRT709837 PAQR7 progestin and adipoQ receptor family member 7 2 2
MIRT718716 ANKRD18A ankyrin repeat domain 18A 2 2
MIRT718879 PDIA3 protein disulfide isomerase family A member 3 2 2
MIRT724105 TMEM199 transmembrane protein 199 2 2
MIRT724763 PSG4 pregnancy specific beta-1-glycoprotein 4 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4653 Paclitaxel 36314 NSC125973 approved sensitive High Nasopharyngeal Cancer cell line (CNE-1)
hsa-mir-4653 Paclitaxel 36314 NSC125973 approved sensitive High Nasopharyngeal Cancer cell line (CNE-1)
hsa-mir-4653 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-4653-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)

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