miRTarBase - #MIRT461285


—
pre-miRNA Information
pre-miRNA hsa-mir-4640   
Genomic Coordinates chr6: 30890883 - 30890972
Description Homo sapiens miR-4640 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4640-5p
Sequence 9| UGGGCCAGGGAGCAGCUGGUGGG |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1392105945 7 dbSNP
rs939712790 9 dbSNP
rs762825841 15 dbSNP
rs71552023 20 dbSNP
rs1305909531 21 dbSNP
rs750017220 21 dbSNP
rs1375436057 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B32FZJ miR-4640 Safety Biomarker (SAF) Clinical/Experimental Data Expression lower Urine Quantitative polymerase chain reaction
Gene Information
Gene Symbol COX10   
Synonyms -
Description COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor
Transcript NM_001303   
Expression
Putative miRNA Targets on COX10
3'UTR of COX10
(miRNA target sites are highlighted)		 
>COX10|NM_001303|3'UTR
   1 GAGCACTGGGACGCCCACCGCCCCTTTCCCTCCGCTGCCAGGCGAGCATGTTGTGGTAATTCTGGAACACAAGAAGAGAA
  81 ATTGCTGGGTTTAGAACAAGATTATAAACGAATTCGGTGCTCAGTGATCACTTGACAGTTTTTTTTTTTTTTAAATATTA
 161 CCCAAAATGCTCCCCAAATAAGAAATGCATCAGCTCAGTCAGTGAATACAAAAAAGGAATTATTTTTCCCTTTGAGGGTC
 241 TTTATACATCTCTCCTCCAACCCCACCCTCTATTCTGTTTCTTCCTCCTCACATGGGGGTACACATACACAGCTTCCTCT
 321 TTTGGTTCCATCCTTACCACCACACCACACGCACACTCCACATGCCCAGCAGAGTGGCACTTGGTGGCCAGAAAGTGTGA
 401 GCCTCATGATCTGCTGTCTGTAGTTCTGTGAGCTCAGGTCCCTCAAAGGCCTCGGAGCACCCCCTTCCTGGTGACTGAGC
 481 CAGGGCCTGCATTTTTGGTTTTCCCCACCCCACACATTCTCAACCATAGTCCTTCTAACAATACCAATAGCTAGGACCCG
 561 GCTGCTGTGCACTGGGACTGGGGATTCCACATGTTTGCCTTGGGAGTCTCAAGCTGGACTGCCAGCCCCTGTCCTCCCTT
 641 CACCCCCATTGCGTATGAGCATTTCAGAACTCCAAGGAGTCACAGGCATCTTTATAGTTCACGTTAACATATAGACACTG
 721 TTGGAAGCAGTTCCTTCTAAAAGGGTAGCCCTGGACTTAATACCAGCCGGATACCTCTGGCCCCCACCCCATTACTGTAC
 801 CTCTGGAGTCACTACTGTGGGTCGCCACTCCTCTGCTACACAGCACGGCTTTTTCAAGGCTGTATTGAGAAGGGAAGTTA
 881 GGAAGAAGGGTGTGCTGGGCTAACCAGCCCACAGAGCTCACATTCCTGTCCCTTGGGTGAAAAATACATGTCCATCCTGA
 961 TATCTCCTGAATTCAGAAATTAGCCTCCACATGTGCAATGGCTTTAAGAGCCAGAAGCAGGGTTCTGGGAATTTTGCAAG
1041 TTATCCTGTGGCCAGGTGTGGTCTCGGTTACCAAATACGGTTACCTGCAGCTTTTTAGTCCTTTGTGCTCCCACGGGTCT
1121 GCAGAGTCCCATCTGCCCAAAGGTCTTGAAGCTTGACAGGATGTTTTCATTACTCAGTCTCCCAGGGCACTGCTGGTCCG
1201 TAGGGATTCATTGGTCGGGGTGGGAGAGTTAAACAACATTTAAACAGAGTTCTCTCAAAAATGTCTAAAGGGATTGTAGG
1281 TAGATAACATCCAATCACTGTTTGCACTTATCTGAAATCTTCCCTCTTGGCTGCCCCCAGGTATTTACTGTGGAGAACAT
1361 TGCATAGGAATGTCTGGAAAAAGCCTCTACAACTTGTTACAGCCTTCACATTTGTACAATTCATTGATTCTCTTTTCCTT
1441 CCACAATAAAATGGTATACAAGAACAAAAAAAAAAAAAAA
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' ggGUGGUC-GACGA--GGGACCGGGu 5'
            :||||| | | |  |:||||||| 
Target 5' aaTACCAGCCGGATACCTCTGGCCCc 3'
 759 - 784 163.00 -27.00
2 
miRNA  3' ggguGGUCGACGAGG-GACCGGGu 5'
              ||||  || |: ||||:|| 
Target 5' tctcCCAG-GGCACTGCTGGTCCg 3'
 1178 - 1200 138.00 -24.80
3 
miRNA  3' ggGUG-GUCGA-CG-AGGGACCGGGu 5'
            |||  ||||  | |:|||| ||| 
Target 5' ccCACAGAGCTCACATTCCTGTCCCt 3'
 908 - 933 129.00 -25.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
321818 14 ClinVar
321819 139 ClinVar
321820 139 ClinVar
890315 145 ClinVar
321821 153 ClinVar
321822 298 ClinVar
890316 306 ClinVar
321823 323 ClinVar
321824 372 ClinVar
321825 409 ClinVar
321826 439 ClinVar
892116 486 ClinVar
321827 536 ClinVar
892117 540 ClinVar
321828 564 ClinVar
321829 591 ClinVar
321830 629 ClinVar
888669 629 ClinVar
321831 647 ClinVar
321832 647 ClinVar
888670 654 ClinVar
890373 721 ClinVar
321833 740 ClinVar
321834 758 ClinVar
321835 824 ClinVar
321836 831 ClinVar
890933 860 ClinVar
890934 895 ClinVar
890935 905 ClinVar
321837 975 ClinVar
892165 1003 ClinVar
892166 1033 ClinVar
321838 1077 ClinVar
321839 1079 ClinVar
888723 1080 ClinVar
321840 1102 ClinVar
888724 1149 ClinVar
888725 1268 ClinVar
321841 1325 ClinVar
321842 1368 ClinVar
890428 1384 ClinVar
321843 1386 ClinVar
321844 1459 ClinVar
COSN30522231 7 COSMIC
COSN6099339 18 COSMIC
COSN26971634 20 COSMIC
COSN18740699 36 COSMIC
COSN30699786 45 COSMIC
COSN20113579 152 COSMIC
COSN6414828 152 COSMIC
COSN20113577 153 COSMIC
COSN20113578 153 COSMIC
COSN6414829 153 COSMIC
COSN20079090 154 COSMIC
COSN9655908 279 COSMIC
COSN9655909 343 COSMIC
COSN32058036 372 COSMIC
COSN31644993 571 COSMIC
COSN25043377 744 COSMIC
COSN32058037 758 COSMIC
COSN20113580 834 COSMIC
COSN513234 900 COSMIC
COSN23577342 940 COSMIC
COSN30019483 1300 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1292225268 1 dbSNP
rs766853368 3 dbSNP
rs751928758 6 dbSNP
rs760139431 7 dbSNP
rs1338818407 8 dbSNP
rs1391526058 12 dbSNP
rs753213748 13 dbSNP
rs371047487 14 dbSNP
rs1401740459 17 dbSNP
rs777899213 20 dbSNP
rs375602415 21 dbSNP
rs1157495493 26 dbSNP
rs971466945 30 dbSNP
rs887469940 34 dbSNP
rs757407927 35 dbSNP
rs1332474236 37 dbSNP
rs1322588618 40 dbSNP
rs1408904779 43 dbSNP
rs778711767 44 dbSNP
rs373074821 45 dbSNP
rs1313708937 48 dbSNP
rs1199167306 49 dbSNP
rs1030813575 50 dbSNP
rs1265153023 51 dbSNP
rs113030493 54 dbSNP
rs565856283 56 dbSNP
rs991886958 72 dbSNP
rs1307038402 73 dbSNP
rs1270998460 93 dbSNP
rs956616845 99 dbSNP
rs1351143025 110 dbSNP
rs1021249227 111 dbSNP
rs534881287 116 dbSNP
rs915166969 117 dbSNP
rs979348798 124 dbSNP
rs964028641 131 dbSNP
rs1441055000 139 dbSNP
rs1465639470 139 dbSNP
rs200239586 139 dbSNP
rs201518254 139 dbSNP
rs555034592 139 dbSNP
rs878954736 139 dbSNP
rs886052600 139 dbSNP
rs886052601 139 dbSNP
rs762095727 141 dbSNP
rs1425049474 142 dbSNP
rs74342589 152 dbSNP
rs1386342086 153 dbSNP
rs886052602 153 dbSNP
rs879003213 154 dbSNP
rs1320943035 155 dbSNP
rs1366258746 156 dbSNP
rs1227982889 158 dbSNP
rs1236513087 163 dbSNP
rs953942489 170 dbSNP
rs1458258725 181 dbSNP
rs1262477519 185 dbSNP
rs1207909865 187 dbSNP
rs985440503 193 dbSNP
rs1301760730 195 dbSNP
rs1222932781 207 dbSNP
rs1370747320 210 dbSNP
rs1323587659 217 dbSNP
rs975120964 230 dbSNP
rs912531291 231 dbSNP
rs922335150 235 dbSNP
rs944123418 245 dbSNP
rs1336699547 249 dbSNP
rs1463933654 251 dbSNP
rs1465000448 257 dbSNP
rs1221579890 265 dbSNP
rs1361365353 273 dbSNP
rs567457401 274 dbSNP
rs1418802352 276 dbSNP
rs1378761177 284 dbSNP
rs1180712179 293 dbSNP
rs750646095 295 dbSNP
rs8076247 298 dbSNP
rs183903455 299 dbSNP
rs941546985 300 dbSNP
rs557163590 302 dbSNP
rs1484199591 304 dbSNP
rs143758001 306 dbSNP
rs1214882970 308 dbSNP
rs573026653 318 dbSNP
rs368791319 320 dbSNP
rs11078233 323 dbSNP
rs1381518440 331 dbSNP
rs1312312917 335 dbSNP
rs1458727983 343 dbSNP
rs1321086195 351 dbSNP
rs1013303600 352 dbSNP
rs1045759022 356 dbSNP
rs907276647 357 dbSNP
rs1160776139 358 dbSNP
rs1013789256 365 dbSNP
rs1384773469 371 dbSNP
rs11078234 372 dbSNP
rs1425620914 373 dbSNP
rs1256864899 380 dbSNP
rs966542131 381 dbSNP
rs1000674901 382 dbSNP
rs1415547434 382 dbSNP
rs1030782217 385 dbSNP
rs1217014758 396 dbSNP
rs1358290125 397 dbSNP
rs956502633 400 dbSNP
rs886052603 409 dbSNP
rs1327767942 411 dbSNP
rs1230801261 413 dbSNP
rs1269241958 423 dbSNP
rs1010760230 424 dbSNP
rs953971887 427 dbSNP
rs1022607159 428 dbSNP
rs146848128 438 dbSNP
rs75823746 439 dbSNP
rs1339040987 442 dbSNP
rs560578836 454 dbSNP
rs751457905 455 dbSNP
rs757031938 459 dbSNP
rs955102373 461 dbSNP
rs965399188 464 dbSNP
rs1459549195 465 dbSNP
rs973257196 468 dbSNP
rs918660319 469 dbSNP
rs1476816776 476 dbSNP
rs1425599659 478 dbSNP
rs982494983 484 dbSNP
rs529638594 485 dbSNP
rs931361027 486 dbSNP
rs1483353725 488 dbSNP
rs1048606415 499 dbSNP
rs908293617 506 dbSNP
rs1249011767 510 dbSNP
rs543545046 513 dbSNP
rs1159857335 514 dbSNP
rs1424315688 524 dbSNP
rs563239177 527 dbSNP
rs886052604 536 dbSNP
rs1316610718 556 dbSNP
rs916135773 560 dbSNP
rs1057374685 561 dbSNP
rs1330857747 564 dbSNP
rs886052605 564 dbSNP
rs532204640 568 dbSNP
rs79156487 581 dbSNP
rs1321880763 591 dbSNP
rs886052606 591 dbSNP
rs1391670969 609 dbSNP
rs1330763195 618 dbSNP
rs949020072 624 dbSNP
rs896170780 626 dbSNP
rs886052607 629 dbSNP
rs907245531 633 dbSNP
rs934668785 635 dbSNP
rs552101577 644 dbSNP
rs189358985 646 dbSNP
rs7214082 647 dbSNP
rs1307585100 648 dbSNP
rs1348747550 649 dbSNP
rs1411688525 651 dbSNP
rs140898783 653 dbSNP
rs537449689 654 dbSNP
rs1367482301 662 dbSNP
rs893235842 668 dbSNP
rs1199799323 675 dbSNP
rs370121669 676 dbSNP
rs1273471040 686 dbSNP
rs1011146047 687 dbSNP
rs1331912457 699 dbSNP
rs557278632 701 dbSNP
rs1022154516 703 dbSNP
rs1000537587 704 dbSNP
rs1167594718 713 dbSNP
rs1348978006 714 dbSNP
rs1332013894 719 dbSNP
rs1413872062 719 dbSNP
rs1204006408 720 dbSNP
rs1174121283 721 dbSNP
rs1271990818 725 dbSNP
rs1466349860 730 dbSNP
rs886052608 740 dbSNP
rs1032138928 743 dbSNP
rs953879063 755 dbSNP
rs899745912 756 dbSNP
rs1802618 758 dbSNP
rs768093978 769 dbSNP
rs539889703 770 dbSNP
rs878888179 772 dbSNP
rs1428787255 776 dbSNP
rs1346144270 782 dbSNP
rs180754993 784 dbSNP
rs1238219051 785 dbSNP
rs1379345888 792 dbSNP
rs982462174 814 dbSNP
rs1168226644 815 dbSNP
rs1447315933 816 dbSNP
rs972777031 818 dbSNP
rs886052609 824 dbSNP
rs1414867581 825 dbSNP
rs1270985756 831 dbSNP
rs1359643212 831 dbSNP
rs397763766 831 dbSNP
rs201044094 834 dbSNP
rs1329621869 847 dbSNP
rs1349871479 848 dbSNP
rs962519934 857 dbSNP
rs974629254 860 dbSNP
rs1471514204 861 dbSNP
rs1372221637 865 dbSNP
rs916118980 874 dbSNP
rs1190181991 878 dbSNP
rs1228063597 882 dbSNP
rs993513282 888 dbSNP
rs917528121 893 dbSNP
rs573080780 895 dbSNP
rs1195941102 899 dbSNP
rs75839697 905 dbSNP
rs928892059 906 dbSNP
rs762344226 910 dbSNP
rs1354304662 915 dbSNP
rs1285937376 916 dbSNP
rs1449312979 921 dbSNP
rs772348744 922 dbSNP
rs1053079453 931 dbSNP
rs555631251 936 dbSNP
rs1042063921 951 dbSNP
rs1247167805 954 dbSNP
rs1322465929 955 dbSNP
rs1403136878 957 dbSNP
rs893194386 961 dbSNP
rs1163282332 963 dbSNP
rs1475823652 968 dbSNP
rs2071245 975 dbSNP
rs1043942475 982 dbSNP
rs1388626342 986 dbSNP
rs1451546109 990 dbSNP
rs1168652564 992 dbSNP
rs543071969 994 dbSNP
rs996686074 996 dbSNP
rs1403637817 999 dbSNP
rs1450038556 1002 dbSNP
rs1326135885 1003 dbSNP
rs1292161032 1014 dbSNP
rs1228891828 1019 dbSNP
rs1276209506 1020 dbSNP
rs1317232600 1020 dbSNP
rs1395828377 1020 dbSNP
rs1220305698 1021 dbSNP
rs1006706409 1022 dbSNP
rs1019842240 1028 dbSNP
rs1351219563 1029 dbSNP
rs1029561397 1032 dbSNP
rs761021294 1037 dbSNP
rs891060099 1038 dbSNP
rs1318950589 1041 dbSNP
rs1169125692 1048 dbSNP
rs766704964 1049 dbSNP
rs901101671 1059 dbSNP
rs1366983898 1062 dbSNP
rs570342762 1067 dbSNP
rs1015291823 1076 dbSNP
rs1050216 1077 dbSNP
rs13183 1079 dbSNP
rs116445114 1080 dbSNP
rs1273785029 1081 dbSNP
rs1256123527 1091 dbSNP
rs1200429691 1097 dbSNP
rs75165393 1102 dbSNP
rs1300368496 1108 dbSNP
rs1206653886 1115 dbSNP
rs1369359178 1118 dbSNP
rs528282657 1119 dbSNP
rs1275071487 1122 dbSNP
rs1445455905 1124 dbSNP
rs751472685 1125 dbSNP
rs1373989932 1141 dbSNP
rs928879246 1142 dbSNP
rs184939367 1146 dbSNP
rs988771587 1147 dbSNP
rs151138383 1149 dbSNP
rs1355562694 1161 dbSNP
rs1194207682 1164 dbSNP
rs947383425 1166 dbSNP
rs1368065281 1170 dbSNP
rs1413104724 1175 dbSNP
rs1039079719 1176 dbSNP
rs15046 1183 dbSNP
rs189403720 1189 dbSNP
rs1439212414 1193 dbSNP
rs1165043454 1200 dbSNP
rs140067025 1201 dbSNP
rs1480921086 1212 dbSNP
rs1457162593 1215 dbSNP
rs150302052 1217 dbSNP
rs891030488 1218 dbSNP
rs1004171830 1221 dbSNP
rs1280662078 1239 dbSNP
rs1391288796 1253 dbSNP
rs923643911 1255 dbSNP
rs75844637 1268 dbSNP
rs1053491315 1285 dbSNP
rs1338308762 1293 dbSNP
rs889549673 1295 dbSNP
rs547070219 1298 dbSNP
rs1446331612 1300 dbSNP
rs1361235901 1301 dbSNP
rs898124484 1302 dbSNP
rs995581493 1312 dbSNP
rs1419361742 1316 dbSNP
rs1327803421 1321 dbSNP
rs1378629094 1323 dbSNP
rs1226502967 1324 dbSNP
rs75636595 1325 dbSNP
rs969810750 1337 dbSNP
rs143735639 1347 dbSNP
rs994135200 1350 dbSNP
rs1025557957 1352 dbSNP
rs1258006906 1356 dbSNP
rs1199642072 1359 dbSNP
rs1215543541 1363 dbSNP
rs555512140 1368 dbSNP
rs1035861407 1375 dbSNP
rs1351076366 1377 dbSNP
rs956285712 1378 dbSNP
rs145948022 1384 dbSNP
rs1050223 1386 dbSNP
rs556710307 1393 dbSNP
rs1034323463 1401 dbSNP
rs576768523 1404 dbSNP
rs1258327812 1418 dbSNP
rs1472265600 1434 dbSNP
rs975162485 1441 dbSNP
rs922026128 1442 dbSNP
rs1358942274 1449 dbSNP
rs1300242789 1454 dbSNP
rs574015313 1459 dbSNP
rs933414698 1459 dbSNP
rs1367992585 1461 dbSNP
rs1050912877 1462 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ggGUGGUCGACGAGG-GACCgggu 5'
            ||::| |||: || ||||    
Target 5' ccCAUUA-CUGUACCUCUGGaguc 3'
 		8 - 30
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_001303 | 3UTR | GGGUAGCCCUGGACUUAAUACCAGCCGGAUACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_001303 | 3UTR | UACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_001303 | 3UTR | UAGCCCUGGACUUAAUACCAGCCGGAUACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_001303 | 3UTR | UACCAGCCGGAUACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_001303 | 3UTR | AGGGUAGCCCUGGACUUAAUACCAGCCGGAUACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_001303 | 3UTR | GGAUACCUCUGGCCCCCACCCCAUUACUGUACCUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000261643.3 | 3UTR | CCCCCACCCCAUUACUGUACCUCUGGAGUCACUACUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100106 ABT1 activator of basal transcription 1 2 8
MIRT248144 LMBR1L limb development membrane protein 1 like 2 2
MIRT327062 KLHL15 kelch like family member 15 2 2
MIRT347231 GATAD2A GATA zinc finger domain containing 2A 2 2
MIRT450221 CENPN centromere protein N 2 2
MIRT451264 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT452701 C1orf226 chromosome 1 open reading frame 226 2 2
MIRT453212 CERS1 ceramide synthase 1 2 2
MIRT454822 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT454883 RAD50 RAD50 double strand break repair protein 2 2
MIRT455783 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT455858 TMEM254 transmembrane protein 254 2 2
MIRT457615 UPK3BL uroplakin 3B like 1 2 2
MIRT457822 ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein 2 4
MIRT458344 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458376 ITM2C integral membrane protein 2C 2 2
MIRT458928 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459066 WFIKKN2 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 2 2
MIRT460138 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460818 FSTL4 follistatin like 4 2 2
MIRT461285 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT462738 EFNB1 ephrin B1 2 2
MIRT464556 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT477910 DUSP2 dual specificity phosphatase 2 2 2
MIRT479073 CNNM4 cyclin and CBS domain divalent metal cation transport mediator 4 2 4
MIRT479534 CDC5L cell division cycle 5 like 2 4
MIRT485628 EEPD1 endonuclease/exonuclease/phosphatase family domain containing 1 2 2
MIRT489896 PPIC peptidylprolyl isomerase C 2 4
MIRT490737 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491201 MLLT1 MLLT1, super elongation complex subunit 2 4
MIRT492681 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT494593 ATG7 autophagy related 7 2 2
MIRT495061 PADI3 peptidyl arginine deiminase 3 2 4
MIRT496623 TMEM67 transmembrane protein 67 2 2
MIRT497177 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT498217 TLN2 talin 2 2 2
MIRT498306 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT499668 NPHP3 nephrocystin 3 2 2
MIRT508080 ANKRD52 ankyrin repeat domain 52 2 2
MIRT509707 ANKRD23 ankyrin repeat domain 23 2 2
MIRT509841 FOS Fos proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT512814 ARRDC2 arrestin domain containing 2 2 2
MIRT513353 SLIT1 slit guidance ligand 1 2 2
MIRT514293 FXYD5 FXYD domain containing ion transport regulator 5 2 2
MIRT516598 FAM89A family with sequence similarity 89 member A 2 4
MIRT516616 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT518348 CCL5 C-C motif chemokine ligand 5 2 2
MIRT520130 WSB1 WD repeat and SOCS box containing 1 2 2
MIRT522072 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT526461 OSBPL5 oxysterol binding protein like 5 2 2
MIRT528278 MBL2 mannose binding lectin 2 2 2
MIRT534844 RAB15 RAB15, member RAS oncogene family 2 4
MIRT542245 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT543299 ZNF585B zinc finger protein 585B 2 2
MIRT552456 ZNF410 zinc finger protein 410 2 2
MIRT553641 TJAP1 tight junction associated protein 1 2 2
MIRT557103 HOXA3 homeobox A3 2 2
MIRT570782 FANCA Fanconi anemia complementation group A 2 2
MIRT630912 ZMAT2 zinc finger matrin-type 2 2 2
MIRT631034 ZNF878 zinc finger protein 878 2 2
MIRT639017 AAK1 AP2 associated kinase 1 2 2
MIRT648596 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT648939 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT652834 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT659347 CSRP1 cysteine and glycine rich protein 1 2 2
MIRT664163 APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F 2 2
MIRT670511 ZSCAN22 zinc finger and SCAN domain containing 22 2 2
MIRT671246 TMEM41B transmembrane protein 41B 2 2
MIRT672120 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT672313 CD3D CD3d molecule 2 2
MIRT672543 BRMS1L breast cancer metastasis-suppressor 1 like 2 2
MIRT673036 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT673814 DARS aspartyl-tRNA synthetase 2 2
MIRT674858 GINM1 glycoprotein integral membrane 1 2 2
MIRT674970 SH3BP2 SH3 domain binding protein 2 2 2
MIRT675185 KIF1C kinesin family member 1C 2 2
MIRT675219 UGDH UDP-glucose 6-dehydrogenase 2 2
MIRT675558 MED16 mediator complex subunit 16 2 2
MIRT682566 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2 2
MIRT684640 PDE4C phosphodiesterase 4C 2 2
MIRT689722 ATXN2 ataxin 2 2 2
MIRT693594 SLC39A1 solute carrier family 39 member 1 2 2
MIRT704745 CDKN2B cyclin dependent kinase inhibitor 2B 2 2
MIRT712779 ZNF154 zinc finger protein 154 2 2
MIRT718118 OTOF otoferlin 2 2
MIRT720115 SAMD4A sterile alpha motif domain containing 4A 2 2
MIRT720275 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4640 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4640-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4640-5p Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4640-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4640-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

Error report submission