miRTarBase - #MIRT445477


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pre-miRNA Information
pre-miRNA hsa-mir-3679   
Genomic Coordinates chr2: 134127125 - 134127192
Description Homo sapiens miR-3679 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3679-5p
Sequence 6| UGAGGAUAUGGCAGGGAAGGGGA |28
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 17 2 + 134127146 26487287 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN28578769 23 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1490236859 15 dbSNP
rs982355045 16 dbSNP
rs1053094244 17 dbSNP
rs893220051 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol KDM6A   
Synonyms KABUK2, UTX, bA386N14.2
Description lysine demethylase 6A
Transcript NM_021140   
Expression
Putative miRNA Targets on KDM6A
3'UTR of KDM6A
(miRNA target sites are highlighted)		 
>KDM6A|NM_021140|3'UTR
   1 TATTGTTCCATGGACATTAAATGAGACCTTTTCTGCTATTCAGGAAATAACCCAGTTCTGCACCACTGGTTTTTGTAGCT
  81 ATCTCGTAAGGCTGCTGGCTGAAAACTGTGTCTATGCAACCTTCCAAGTGCGGAGTGTCAACCAACTGGACGGGAGAGAG
 161 TACTGCTCCTACTCCAGGACTCTCACAAAGCTGATGAGCTGTACTTCAGAAAAAAATAATAATTTCCATGTTTTGTATAT
 241 ATCTGACAAAACTGGCAACATCTTACAGACTACTGACTTGAAGACAACCTCTTTTATATTTCTCTATTTCTGGGCTGATG
 321 AATTTGTTTTCATCTGTCTTTTCCCCCTTCAGAATTTTCCTTGGAAAAAAAATACTAGCCTAGCTGGTCATTTCTTTGTA
 401 AGGTAGTTAGCAATTTTAAGTCTTTCTTTGGTCAACTTTTTTTTAATGTGAAAAGTTAGGTAAGACACTTTTTTACTGCT
 481 TTTATGTTTTTCTGTCTTGTTTTGAGACCATGATGGTTACACTTTTGGTTCCTAAATAAAATTTAAAAAATTAACAGCCA
 561 AGTCACAAAGGTAATGGATTGCACATAGACTAAGGAATAAACTTCAGATTTGTGATTTTTGTTTCTAATCTTGATGTAAA
 641 TTTACACTATTTATAAATACATATTTATTGCTTGAAAATATTTGTGAATGGAATGCTGTTATTTTTTCCAGATTTACCTG
 721 CCATTGAAATTTTAAGGAGTTCTGTAATTTCAAACACTACTCCTATTACATTTTCTATGTGTAAATAAAACTGCTTAGCA
 801 TTGTACAGAAACTTTTATTAAAATTGTTTAATGTTTAAAGAGTTTTCTATTGTTTGAGTTTTAAAAAAGACTTTATGTAC
 881 AGTGCCCAGTTTTTGTTCATTTTTGAAATCTGATTATATATATTTTATATATACTTATGTATGTATATATAATATATATA
 961 GAAATCTGGATATATATGTATAAATCTTTAGAACTTAAATTTTTCTCGTTTTAAGTTTCACATCTATGGTAGATTTTTGA
1041 GGTGTCTACTGTAAAGTATTGCTTACAAAAAGTATGATTATTTTTAAAGAAATATATATGGTATGTATCCTCAAGACCTA
1121 AAATGTCAGACTGGTTTATTGTTAAGTTGCAATTACTGCAATGACAGACCAATAAACAATTGCTGCCAAAATGTAGTATA
1201 AA
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' aggggaagggACGGU--AUAGGAGu 5'
                    || :|  ||||||| 
Target 5' gaaatatataTGGTATGTATCCTCa 3'
 1089 - 1113 143.00 -11.00
2 
miRNA  3' aggGGAAGGGACGGUAUAGGagu 5'
             ||||::||||  |||:|   
Target 5' agaCCTTTTCTGC--TATTCagg 3'
 24 - 44 116.00 -17.44
3 
miRNA  3' aggggaaGGGACGGUAU-AGGAGu 5'
                 |:|| ::||| |:||| 
Target 5' agacaacCTCTTTTATATTTCTCt 3'
 282 - 305 112.00 -12.80
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1175477681 2 dbSNP
rs772219795 4 dbSNP
rs1468032373 8 dbSNP
rs868775566 10 dbSNP
rs1173519526 13 dbSNP
rs775265110 16 dbSNP
rs1464862327 19 dbSNP
rs1243165696 23 dbSNP
rs368788471 24 dbSNP
rs768322350 29 dbSNP
rs1310503246 30 dbSNP
rs1350761254 35 dbSNP
rs12009027 36 dbSNP
rs1298576667 43 dbSNP
rs1313819504 47 dbSNP
rs761623482 49 dbSNP
rs1256487428 51 dbSNP
rs1250541292 52 dbSNP
rs192800843 56 dbSNP
rs747617025 70 dbSNP
rs1350251327 82 dbSNP
rs375262951 86 dbSNP
rs957312603 87 dbSNP
rs986649578 102 dbSNP
rs775611554 107 dbSNP
rs1249411905 115 dbSNP
rs1356928766 117 dbSNP
rs1174671593 132 dbSNP
rs185546488 133 dbSNP
rs113611077 137 dbSNP
rs1396465569 143 dbSNP
rs189581367 152 dbSNP
rs181547731 153 dbSNP
rs919885618 160 dbSNP
rs931559332 172 dbSNP
rs760461581 173 dbSNP
rs1482523276 186 dbSNP
rs1236990210 195 dbSNP
rs948560938 199 dbSNP
rs1486794983 205 dbSNP
rs981271676 208 dbSNP
rs1272715795 228 dbSNP
rs1225966825 229 dbSNP
rs928070003 230 dbSNP
rs563385889 238 dbSNP
rs1296296937 244 dbSNP
rs916835108 245 dbSNP
rs184403853 248 dbSNP
rs939421836 256 dbSNP
rs1311776806 259 dbSNP
rs1036361934 266 dbSNP
rs1376948635 298 dbSNP
rs753755566 305 dbSNP
rs759088073 307 dbSNP
rs930612101 313 dbSNP
rs1373997610 315 dbSNP
rs1172915012 326 dbSNP
rs906961328 333 dbSNP
rs1413657202 334 dbSNP
rs748999465 342 dbSNP
rs1383694592 347 dbSNP
rs1170161098 348 dbSNP
rs1049304623 351 dbSNP
rs764835502 361 dbSNP
rs189082691 362 dbSNP
rs758082394 365 dbSNP
rs1206298478 366 dbSNP
rs1319894746 371 dbSNP
rs1389723646 373 dbSNP
rs1292570151 381 dbSNP
rs1233427246 383 dbSNP
rs1019098154 391 dbSNP
rs901612262 397 dbSNP
rs1285832580 404 dbSNP
rs770821116 407 dbSNP
rs1390474692 417 dbSNP
rs1338852046 420 dbSNP
rs1300298480 421 dbSNP
rs1456686530 425 dbSNP
rs998602036 432 dbSNP
rs1383437804 437 dbSNP
rs1463143093 437 dbSNP
rs763585850 437 dbSNP
rs1409858215 445 dbSNP
rs1031374825 462 dbSNP
rs774321921 464 dbSNP
rs989774118 467 dbSNP
rs1252886595 483 dbSNP
rs1023320362 489 dbSNP
rs1312849038 507 dbSNP
rs11550306 512 dbSNP
rs1343979708 515 dbSNP
rs11550307 516 dbSNP
rs889692575 517 dbSNP
rs530623282 522 dbSNP
rs1336782807 523 dbSNP
rs1265722191 526 dbSNP
rs1237655125 528 dbSNP
rs1336026154 532 dbSNP
rs1008491216 543 dbSNP
rs969989810 544 dbSNP
rs1385512959 552 dbSNP
rs1227927824 553 dbSNP
rs1250383240 570 dbSNP
rs1019419892 580 dbSNP
rs752035232 587 dbSNP
rs1326921372 613 dbSNP
rs1463488873 641 dbSNP
rs981707695 643 dbSNP
rs961456320 654 dbSNP
rs1158104412 663 dbSNP
rs181128644 665 dbSNP
rs1337093992 700 dbSNP
rs1201660640 702 dbSNP
rs1263295255 716 dbSNP
rs1251852207 717 dbSNP
rs1365820443 720 dbSNP
rs1174212182 729 dbSNP
rs879030030 742 dbSNP
rs1460485931 745 dbSNP
rs972777757 755 dbSNP
rs1252161178 761 dbSNP
rs1193972479 795 dbSNP
rs928486956 802 dbSNP
rs1246083636 812 dbSNP
rs1204089445 831 dbSNP
rs1350750304 833 dbSNP
rs939472690 840 dbSNP
rs972131342 843 dbSNP
rs1262196274 850 dbSNP
rs781776150 863 dbSNP
rs186722498 864 dbSNP
rs990799623 868 dbSNP
rs1363703340 872 dbSNP
rs1318227509 889 dbSNP
rs1372709545 892 dbSNP
rs1460721706 893 dbSNP
rs1301104377 897 dbSNP
rs190766276 901 dbSNP
rs1395876692 911 dbSNP
rs1455404029 915 dbSNP
rs949634733 916 dbSNP
rs982708792 937 dbSNP
rs1447445184 940 dbSNP
rs1263240463 961 dbSNP
rs1198185662 970 dbSNP
rs1469375632 970 dbSNP
rs1485160786 973 dbSNP
rs1237028613 977 dbSNP
rs1334562734 977 dbSNP
rs1049028901 986 dbSNP
rs889394037 990 dbSNP
rs1269903912 1003 dbSNP
rs1228807081 1008 dbSNP
rs924096580 1009 dbSNP
rs1332307844 1016 dbSNP
rs1414211515 1021 dbSNP
rs1376345280 1022 dbSNP
rs1314990883 1034 dbSNP
rs1364042919 1047 dbSNP
rs1436428372 1047 dbSNP
rs1394078652 1070 dbSNP
rs943614891 1077 dbSNP
rs756533756 1099 dbSNP
rs1167049739 1102 dbSNP
rs902002579 1119 dbSNP
rs1382549925 1126 dbSNP
rs1374688357 1139 dbSNP
rs1185215995 1150 dbSNP
rs780200498 1153 dbSNP
rs934419149 1157 dbSNP
rs180999863 1162 dbSNP
rs1435654680 1166 dbSNP
rs1272767458 1169 dbSNP
rs1052856005 1176 dbSNP
rs768992368 1178 dbSNP
rs892865509 1180 dbSNP
rs1011277631 1198 dbSNP
rs1342135674 1202 dbSNP
rs892886243 1218 dbSNP
rs1232812735 1223 dbSNP
rs1356172880 1235 dbSNP
rs947079115 1239 dbSNP
rs779047320 1244 dbSNP
rs1322147815 1252 dbSNP
rs1408249972 1253 dbSNP
rs1201259836 1276 dbSNP
rs1022614064 1280 dbSNP
rs774426470 1286 dbSNP
rs745772497 1289 dbSNP
rs1321452730 1305 dbSNP
rs1410296292 1313 dbSNP
rs746858050 1314 dbSNP
rs142132102 1315 dbSNP
rs1035983773 1324 dbSNP
rs1460793121 1335 dbSNP
rs1417963351 1340 dbSNP
rs1189385771 1345 dbSNP
rs1261393247 1346 dbSNP
rs961198759 1347 dbSNP
rs771921570 1352 dbSNP
rs776372322 1353 dbSNP
rs1201800073 1354 dbSNP
rs1008106132 1355 dbSNP
rs775568405 1357 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions BC-1
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 GSM796038. RNA binding protein: AGO2. Condition:4-Thiouridine ...

- Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe.

Article - Gottwein E; Corcoran DL; Mukherjee N; et al.
- Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
CLIP-seq Support 1 for dataset GSM796038
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-1 / 4-Thiouridine
Location of target site ENST00000377967.4 | 3UTR | UCAAGACCUAAAAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
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
LUSC 0.993 0.04 1.000 0.5 3 Click to see details
HNSC -0.877 0.16 -1.000 0.5 3 Click to see details
THCA -0.82 0.19 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
STAD -0.588 0.3 -0.500 0.33 3 Click to see details
55 hsa-miR-3679-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT114494 PNN pinin, desmosome associated protein 2 2
MIRT169967 DNAJB9 DnaJ heat shock protein family (Hsp40) member B9 2 6
MIRT182181 POU2F1 POU class 2 homeobox 1 2 2
MIRT189380 TXLNA taxilin alpha 2 4
MIRT364735 TOR1B torsin family 1 member B 2 2
MIRT445477 KDM6A lysine demethylase 6A 2 2
MIRT446333 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 2 2
MIRT446386 SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein 2 2
MIRT446971 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT449793 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT451211 PIN1 peptidylprolyl cis/trans isomerase, NIMA-interacting 1 2 2
MIRT452098 NUCB2 nucleobindin 2 2 2
MIRT454036 DDT D-dopachrome tautomerase 2 2
MIRT461708 ZNF426 zinc finger protein 426 2 2
MIRT464957 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT465775 TMOD3 tropomodulin 3 2 2
MIRT466925 STC2 stanniocalcin 2 2 2
MIRT471388 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 2 2
MIRT473585 MAT2A methionine adenosyltransferase 2A 2 2
MIRT476070 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT477324 EPHA2 EPH receptor A2 2 2
MIRT478244 DDX3X DEAD-box helicase 3, X-linked 2 4
MIRT480449 C16orf72 chromosome 16 open reading frame 72 2 6
MIRT481866 ANKRD50 ankyrin repeat domain 50 2 2
MIRT492032 TSG101 tumor susceptibility 101 2 4
MIRT493737 GRAP2 GRB2-related adaptor protein 2 2 2
MIRT495623 PPP1R1C protein phosphatase 1 regulatory inhibitor subunit 1C 2 2
MIRT497590 SLC23A1 solute carrier family 23 member 1 2 2
MIRT504702 ZNF117 zinc finger protein 117 2 2
MIRT507794 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT510653 TMED7 transmembrane p24 trafficking protein 7 2 4
MIRT525534 FSIP2 fibrous sheath interacting protein 2 2 2
MIRT531149 CYGB cytoglobin 2 2
MIRT536003 MED13 mediator complex subunit 13 2 2
MIRT537056 GPR180 G protein-coupled receptor 180 2 2
MIRT538297 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT544755 C8orf33 chromosome 8 open reading frame 33 2 2
MIRT544927 MIS18BP1 MIS18 binding protein 1 2 2
MIRT556973 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT561714 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 2 2
MIRT563632 ZNF460 zinc finger protein 460 2 2
MIRT564705 ZNF322P1 zinc finger protein 322 pseudogene 1 2 2
MIRT572190 CALU calumenin 2 2
MIRT573900 MKI67 marker of proliferation Ki-67 2 2
MIRT576073 Poteg POTE ankyrin domain family, member G 2 2
MIRT576150 Hmox1 heme oxygenase 1 2 2
MIRT614848 PLEKHA6 pleckstrin homology domain containing A6 2 4
MIRT647592 FAM109B family with sequence similarity 109 member B 2 2
MIRT657009 KCNMB4 potassium calcium-activated channel subfamily M regulatory beta subunit 4 2 2
MIRT691268 GET4 golgi to ER traffic protein 4 2 2
MIRT695778 DENR density regulated re-initiation and release factor 2 2
MIRT698089 TPM1 tropomyosin 1 2 2
MIRT732571 IGLL5 immunoglobulin lambda like polypeptide 5 1 0
MIRT733722 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 3 0
MIRT734354 GREM1 gremlin 1, DAN family BMP antagonist 1 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-3679-5p 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3679 Doxorubicin 31703 NSC123127 approved sensitive High Hepatocellular Carcinoma cell line (HepG2)
hsa-miR-3679-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-3679-5p Doxorubicin 31703 NSC123127 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-3679-5p Curcumin 969516 NSC32982 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved resistant Low Non-Small Cell Lung Cancer tissue
hsa-miR-3679-5p Etoposide 36462 NSC141540 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Doxorubicin 31703 NSC123127 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Paclitaxel 36314 NSC125973 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Vinorelbine 44424639 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Vincristine 5978 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-3679-5p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3679-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3679-5p Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-miR-3679-5p Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-3679-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3679-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-3679-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-3679-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)

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