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 PHYHIP   
Synonyms DYRK1AP3, PAHX-AP, PAHXAP1
Description phytanoyl-CoA 2-hydroxylase interacting protein
Transcript NM_001099335   
Other Transcripts NM_014759   
Expression
Putative miRNA Targets on PHYHIP
3'UTR of PHYHIP
(miRNA target sites are highlighted)
>PHYHIP|NM_001099335|3'UTR
   1 GGACTCCTGGGGAGCTGGGGGGCGAGGGAGAGATGAGCGGAAGGTGGAGGTGGGTAGCCCAGGTTCAGGGAGCTGGCTTT
  81 CTCTCTCCTGCCCCCCTGCTCCCTCCACTCTGCCCAGCTGCCCTCCCCTCGCCCCTTGGCATTGGAGGCAACAGACGGTG
 161 GTCCTCTTGGTAAGTGTGGCCCACACCCAGCCTGGTGGACATGGAAAGGCTTCTCAGCCTCTGTAGTTGGCAGCTGGGCT
 241 GGACTTCTGGAGAACTTCCCCTTTCCTCTGGTTTCCTTGTCCTACTGTTCTTTGCCTCGTCCAGGTCTCTATCTCCCAAA
 321 GACCTGCCCACCTCCTGGGCTCTCCCAGGGAAGCCCCTCTGGGCCAAAGCCCATGGGTAGCTTGGCTGCCTCCAGAAGAG
 401 ATGCAGAGAGCTGTGGGGCGATCTTTCTTAGTCCCACTCACCCCACTCAGGGCCAACCACAGAATGCCCCCTCCCTGCTG
 481 AGCTGGGTCTCTGGGGCTTCCCACTCCAGGCCTGGATCCCTTCCTTCTATAAATAGTCTCCTGCACCACCGTGACTCCCT
 561 GGCTGCTCCTTGCCCCAAAGAACCCTCTTCCTGCATGGGAGAGCTGTCCCTCCTTCTCCACCTGCCCACCGGGACACTCC
 641 CCCTGCTCTCTAGAAAGGAACTCTCTTTCTTCTCTTGGCACTGGGGGCGTCAGGCTGTCGGATGTTCCTTCCTTCCATAC
 721 CCCAGCATACCTTCTCCTTGCTTAGAGTGCAGGGGTCTGAGACAGCAGCCACTGGGGTTGAGGAGGGGGAGGAGACCCCT
 801 GAGACCCAGAGGTGCCCCTTCCTCAGCTGGGAGTGGGCCGCCTCATGCTCTGCTGGGGCCTGGCATGGAACGTGAGACCT
 881 GTAAGCTGTCCCGCGGGCCCCGGCACCCCGCCCAGCTGTGCACTTTGCTCACTCGCTCTGCCATGGTGCCATGACTGTAC
 961 TGTGCCCATGCGTGACCTGGACTGTGGACCCTCTGCTGCTCCGCCTCTCCCCTCCCCACTGGCTCTGTCTGCTCTCCTGC
1041 CACCCTGCTGGCCGGGAGCCCCTCCCCGGGGAGTTCTTGGTGAAGTCCTTCCCGGGCCTCCTTGTGTTTTTGCCTCATTC
1121 CTACTGTCACACAGGTCACGAGGGTGGACTCCCTACAATCAACAAAGCAAACAGAGAGCCTGTGGGAGGGGCTGACAGCA
1201 GCAGCCGGCTGTTTGGGGGATGATGGAGGTGACATCAGGCAGAGGAGAGTGCAGCCTCACAGTGACTTTCTCAGAGGTGA
1281 CAGAGATGATGGATGAGCAGCTGGATTTTCGTGATGAAGGACGGAAGCAGCAGCGGGCCGGCAAGGCCATACCTCGGTGA
1361 GGGACAGGTGGACAACGGTCACCTATCTGTAGCCAGGGGCAGTTGTGTGGCCAGCTGTCTCTCTGGGATGAGTCAGGAGG
1441 CCTGGAGGCTTGGGGAGAGGTGTGGAGAAGGAGAGAACATGGCCCAGGCCCTTTCCTTCCCCCTGTGCTGACAGCATTGC
1521 TGTGGGGGTGGCCCACTGCCCTCCCCTGGCCCTCATGTCCCCCCGGGGCTGGGGTCCGCCTGCCTGTGCTGTGCTTGCGA
1601 CGTGCATCAATAAACCACCATGGCCTGAGGGCCCTGCTCGTCTCAGTCCAAAAAAAAAAAAAAAAAA
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' ggguGGUCGAC--GA-GGGACCGGGu 5'
              ||| |||  || ||||||||| 
Target 5' tggcCCA-CTGCCCTCCCCTGGCCCt 3'
1529 - 1553 164.00 -32.30
2
miRNA  3' ggGUGGUCG-AC-GAGGGACCGGgu 5'
            ||||| | || |||||||||:  
Target 5' tgCACCACCGTGACTCCCTGGCTgc 3'
542 - 566 145.00 -30.30
3
miRNA  3' ggguGGUCGAC--GA-GGGACCGGGu 5'
              |||||||  || |||| |||| 
Target 5' ctgcCCAGCTGCCCTCCCCTCGCCCc 3'
110 - 135 145.00 -26.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30480437 7 COSMIC
COSN30166952 16 COSMIC
COSN30452303 27 COSMIC
COSN30486681 81 COSMIC
COSN26576120 89 COSMIC
COSN9459199 117 COSMIC
COSN30125712 128 COSMIC
COSN4878819 395 COSMIC
COSN27745643 419 COSMIC
COSN28480939 420 COSMIC
COSN31591329 551 COSMIC
COSN23372029 975 COSMIC
COSN8077347 1003 COSMIC
COSN18815904 1371 COSMIC
COSN31579268 1483 COSMIC
COSN31584013 1536 COSMIC
COSN30545413 1549 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs771305403 2 dbSNP
rs749484824 3 dbSNP
rs1354117841 6 dbSNP
rs1297548146 7 dbSNP
rs1424681199 9 dbSNP
rs1366875886 10 dbSNP
rs1161201073 12 dbSNP
rs770574682 13 dbSNP
rs777718895 15 dbSNP
rs755883061 17 dbSNP
rs752632439 18 dbSNP
rs781182155 20 dbSNP
rs746825184 21 dbSNP
rs754483391 21 dbSNP
rs200690637 23 dbSNP
rs1490676035 24 dbSNP
rs760531230 27 dbSNP
rs1271105792 31 dbSNP
rs180801147 32 dbSNP
rs762623720 33 dbSNP
rs750009937 34 dbSNP
rs764377851 35 dbSNP
rs1314928256 37 dbSNP
rs376097571 38 dbSNP
rs1405475166 39 dbSNP
rs1347361625 42 dbSNP
rs1362805007 44 dbSNP
rs1162089467 45 dbSNP
rs768047658 47 dbSNP
rs1403819709 50 dbSNP
rs1369556810 51 dbSNP
rs1008574136 57 dbSNP
rs1156500541 58 dbSNP
rs886078665 59 dbSNP
rs1300853887 60 dbSNP
rs1047642521 70 dbSNP
rs1347203827 75 dbSNP
rs1408250624 87 dbSNP
rs930528472 89 dbSNP
rs775269522 91 dbSNP
rs1359775661 92 dbSNP
rs1051343791 93 dbSNP
rs1200724784 95 dbSNP
rs1490861233 97 dbSNP
rs546457354 101 dbSNP
rs928951905 112 dbSNP
rs1220591134 114 dbSNP
rs565074652 118 dbSNP
rs973556686 121 dbSNP
rs937829084 122 dbSNP
rs868298414 126 dbSNP
rs1286569418 128 dbSNP
rs553317607 130 dbSNP
rs981904102 131 dbSNP
rs535196258 132 dbSNP
rs1321088265 133 dbSNP
rs913186949 149 dbSNP
rs960252168 156 dbSNP
rs567770599 157 dbSNP
rs957644798 158 dbSNP
rs1367032166 161 dbSNP
rs1033261987 164 dbSNP
rs1405803375 165 dbSNP
rs1282594935 166 dbSNP
rs1317380035 168 dbSNP
rs1343156397 174 dbSNP
rs1405411044 186 dbSNP
rs974934905 187 dbSNP
rs1298192356 190 dbSNP
rs1382192429 191 dbSNP
rs1243858208 196 dbSNP
rs771842585 200 dbSNP
rs1357327719 213 dbSNP
rs1204718540 220 dbSNP
rs965211132 221 dbSNP
rs1449061727 224 dbSNP
rs967780730 229 dbSNP
rs1429410950 230 dbSNP
rs1443539003 241 dbSNP
rs1018712354 256 dbSNP
rs1181205918 258 dbSNP
rs1009021611 263 dbSNP
rs1369622673 266 dbSNP
rs1345463213 277 dbSNP
rs138718567 284 dbSNP
rs1405556728 285 dbSNP
rs1025970022 286 dbSNP
rs1468593610 287 dbSNP
rs1012042259 291 dbSNP
rs994458270 296 dbSNP
rs146023136 298 dbSNP
rs188440953 299 dbSNP
rs937872588 305 dbSNP
rs1341095626 317 dbSNP
rs1007443762 323 dbSNP
rs552216117 328 dbSNP
rs527565264 329 dbSNP
rs1051612795 334 dbSNP
rs761651524 341 dbSNP
rs774463765 342 dbSNP
rs950147367 345 dbSNP
rs1186043251 348 dbSNP
rs1486221870 350 dbSNP
rs913310061 356 dbSNP
rs1244079215 357 dbSNP
rs1361694449 358 dbSNP
rs1473490144 361 dbSNP
rs1159636047 362 dbSNP
rs1468191621 363 dbSNP
rs566091538 373 dbSNP
rs1174213911 375 dbSNP
rs1201963945 385 dbSNP
rs1390872246 387 dbSNP
rs1327168806 391 dbSNP
rs369567753 399 dbSNP
rs988852313 402 dbSNP
rs1223883830 408 dbSNP
rs897474059 419 dbSNP
rs935972391 420 dbSNP
rs1257066811 423 dbSNP
rs1293317487 431 dbSNP
rs926205005 435 dbSNP
rs1213533067 443 dbSNP
rs547781961 445 dbSNP
rs1037462156 467 dbSNP
rs941735039 468 dbSNP
rs529407620 474 dbSNP
rs1290301862 477 dbSNP
rs1267962080 480 dbSNP
rs1479317202 487 dbSNP
rs1449935670 494 dbSNP
rs964908185 503 dbSNP
rs1337876422 505 dbSNP
rs562083666 519 dbSNP
rs928913242 523 dbSNP
rs987648772 529 dbSNP
rs1166230446 537 dbSNP
rs1170298972 540 dbSNP
rs1430669153 544 dbSNP
rs950559901 546 dbSNP
rs1429230175 547 dbSNP
rs1302737830 550 dbSNP
rs550246524 552 dbSNP
rs531841696 553 dbSNP
rs967413713 554 dbSNP
rs1326365740 556 dbSNP
rs1022006052 558 dbSNP
rs1444302416 560 dbSNP
rs1205479725 561 dbSNP
rs994492376 566 dbSNP
rs962987464 574 dbSNP
rs1192699817 579 dbSNP
rs1267702918 580 dbSNP
rs564689992 587 dbSNP
rs546104655 591 dbSNP
rs572376766 594 dbSNP
rs1190875574 606 dbSNP
rs543905462 613 dbSNP
rs1450131850 627 dbSNP
rs1203688646 630 dbSNP
rs1002492257 631 dbSNP
rs770392636 633 dbSNP
rs748788688 634 dbSNP
rs1459578823 641 dbSNP
rs541385836 643 dbSNP
rs1009402478 654 dbSNP
rs1299243628 661 dbSNP
rs1381056784 663 dbSNP
rs1300408455 667 dbSNP
rs891910538 674 dbSNP
rs574363146 682 dbSNP
rs142149837 687 dbSNP
rs1356824911 688 dbSNP
rs1223234902 689 dbSNP
rs1265831869 700 dbSNP
rs769563876 708 dbSNP
rs1485398081 710 dbSNP
rs1381636485 715 dbSNP
rs1249792199 716 dbSNP
rs1465445700 722 dbSNP
rs1183069525 730 dbSNP
rs890284320 731 dbSNP
rs1398176683 734 dbSNP
rs1394731513 742 dbSNP
rs1363630045 746 dbSNP
rs1452053806 748 dbSNP
rs1298107862 749 dbSNP
rs936003657 751 dbSNP
rs993785841 753 dbSNP
rs1452459298 754 dbSNP
rs1335506881 755 dbSNP
rs1356774472 765 dbSNP
rs1376280017 767 dbSNP
rs1161823389 768 dbSNP
rs1229707775 774 dbSNP
rs925903066 775 dbSNP
rs763028618 777 dbSNP
rs1039309476 785 dbSNP
rs1424065349 786 dbSNP
rs537923653 787 dbSNP
rs1185606047 790 dbSNP
rs1202908799 793 dbSNP
rs528736197 796 dbSNP
rs894255931 810 dbSNP
rs558682309 818 dbSNP
rs1250070889 821 dbSNP
rs534099993 825 dbSNP
rs1161827193 826 dbSNP
rs781419430 831 dbSNP
rs1055552977 838 dbSNP
rs1469755681 839 dbSNP
rs1174849783 840 dbSNP
rs758062485 840 dbSNP
rs1480955436 844 dbSNP
rs988067976 857 dbSNP
rs755319588 859 dbSNP
rs1276647182 860 dbSNP
rs1356970219 862 dbSNP
rs950899640 865 dbSNP
rs1449552326 870 dbSNP
rs938865035 871 dbSNP
rs75233986 872 dbSNP
rs1290010664 887 dbSNP
rs147647814 890 dbSNP
rs963018067 892 dbSNP
rs1033275811 893 dbSNP
rs990584126 894 dbSNP
rs769852742 895 dbSNP
rs780576805 898 dbSNP
rs535900887 901 dbSNP
rs1301815365 902 dbSNP
rs971093550 906 dbSNP
rs1024876568 907 dbSNP
rs1404439158 908 dbSNP
rs1366231614 909 dbSNP
rs1009826428 910 dbSNP
rs1451828907 911 dbSNP
rs35756810 911 dbSNP
rs568422931 912 dbSNP
rs892278966 917 dbSNP
rs1427459099 920 dbSNP
rs868239689 922 dbSNP
rs1419426332 923 dbSNP
rs1030537821 935 dbSNP
rs1053194172 936 dbSNP
rs993446154 944 dbSNP
rs1000245474 952 dbSNP
rs1016165127 961 dbSNP
rs1005931217 965 dbSNP
rs894141496 971 dbSNP
rs1055561067 972 dbSNP
rs150364926 976 dbSNP
rs907389105 982 dbSNP
rs1478656321 984 dbSNP
rs531800501 1002 dbSNP
rs946222240 1003 dbSNP
rs1447110691 1016 dbSNP
rs111315027 1022 dbSNP
rs1370785481 1023 dbSNP
rs1423538015 1027 dbSNP
rs943364598 1028 dbSNP
rs777165552 1034 dbSNP
rs1437140701 1035 dbSNP
rs73551785 1038 dbSNP
rs911185067 1039 dbSNP
rs986846805 1040 dbSNP
rs550302406 1044 dbSNP
rs929496236 1045 dbSNP
rs919387764 1046 dbSNP
rs552306627 1048 dbSNP
rs1226774232 1051 dbSNP
rs941821383 1053 dbSNP
rs765236000 1054 dbSNP
rs796877716 1067 dbSNP
rs115919099 1068 dbSNP
rs1246717167 1071 dbSNP
rs961904122 1074 dbSNP
rs1189950675 1080 dbSNP
rs1390199329 1091 dbSNP
rs970408562 1093 dbSNP
rs1289613315 1094 dbSNP
rs1457598907 1096 dbSNP
rs754012101 1097 dbSNP
rs560455371 1098 dbSNP
rs1386352182 1122 dbSNP
rs1174201161 1123 dbSNP
rs1321315180 1124 dbSNP
rs767250796 1139 dbSNP
rs1446142404 1140 dbSNP
rs1286154911 1142 dbSNP
rs1429901549 1143 dbSNP
rs1200424404 1151 dbSNP
rs1357566866 1154 dbSNP
rs958362854 1157 dbSNP
rs62496060 1160 dbSNP
rs1209857949 1162 dbSNP
rs778711358 1164 dbSNP
rs1248135150 1165 dbSNP
rs1441300350 1168 dbSNP
rs763641856 1174 dbSNP
rs1205316216 1180 dbSNP
rs1032209308 1182 dbSNP
rs1473041254 1191 dbSNP
rs774207769 1201 dbSNP
rs574375824 1202 dbSNP
rs1466535983 1204 dbSNP
rs562489283 1206 dbSNP
rs1041448146 1207 dbSNP
rs1394353062 1208 dbSNP
rs1336475775 1209 dbSNP
rs1223272125 1215 dbSNP
rs1441677484 1221 dbSNP
rs904629715 1222 dbSNP
rs1352669107 1229 dbSNP
rs1017674844 1234 dbSNP
rs1007985756 1235 dbSNP
rs1229587041 1250 dbSNP
rs71513870 1251 dbSNP
rs1343740493 1263 dbSNP
rs187375165 1264 dbSNP
rs558785791 1292 dbSNP
rs1225357766 1293 dbSNP
rs1280041888 1294 dbSNP
rs1442655165 1295 dbSNP
rs929527317 1299 dbSNP
rs1325887953 1310 dbSNP
rs1473438417 1311 dbSNP
rs371879725 1315 dbSNP
rs1055121253 1322 dbSNP
rs1404166897 1323 dbSNP
rs898075904 1324 dbSNP
rs1376997351 1327 dbSNP
rs115208150 1334 dbSNP
rs1469073067 1335 dbSNP
rs942187928 1336 dbSNP
rs889800485 1337 dbSNP
rs748933736 1339 dbSNP
rs980521771 1340 dbSNP
rs1372843300 1343 dbSNP
rs949073313 1355 dbSNP
rs368032883 1356 dbSNP
rs1371931903 1363 dbSNP
rs972837455 1364 dbSNP
rs1276128932 1368 dbSNP
rs182138612 1370 dbSNP
rs988202206 1371 dbSNP
rs956646723 1376 dbSNP
rs1032241889 1377 dbSNP
rs1266341636 1382 dbSNP
rs979288684 1395 dbSNP
rs958583335 1407 dbSNP
rs963842235 1410 dbSNP
rs1200868091 1411 dbSNP
rs1378317416 1413 dbSNP
rs554932731 1417 dbSNP
rs1448914107 1430 dbSNP
rs1130803 1440 dbSNP
rs1167008043 1441 dbSNP
rs1203482735 1448 dbSNP
rs1034256258 1452 dbSNP
rs1372635955 1452 dbSNP
rs1007604129 1455 dbSNP
rs1293321536 1456 dbSNP
rs1388963325 1457 dbSNP
rs981126821 1477 dbSNP
rs890461120 1479 dbSNP
rs1324757546 1480 dbSNP
rs1281383651 1481 dbSNP
rs1227019563 1483 dbSNP
rs1294679566 1484 dbSNP
rs1194514041 1488 dbSNP
rs1030367382 1492 dbSNP
rs1252024373 1501 dbSNP
rs190082178 1503 dbSNP
rs898106949 1505 dbSNP
rs1037906041 1507 dbSNP
rs1267961116 1519 dbSNP
rs1006359860 1525 dbSNP
rs1464555412 1528 dbSNP
rs1186763035 1536 dbSNP
rs1392040802 1541 dbSNP
rs905318573 1551 dbSNP
rs946480184 1558 dbSNP
rs571683861 1560 dbSNP
rs1367138384 1562 dbSNP
rs914883611 1564 dbSNP
rs1164408179 1565 dbSNP
rs1388551808 1565 dbSNP
rs1433454302 1567 dbSNP
rs1314615176 1572 dbSNP
rs1451663790 1577 dbSNP
rs917654144 1578 dbSNP
rs893295569 1591 dbSNP
rs1052123419 1593 dbSNP
rs777372564 1598 dbSNP
rs988233383 1599 dbSNP
rs568380645 1601 dbSNP
rs1395652674 1602 dbSNP
rs925204480 1604 dbSNP
rs747821457 1622 dbSNP
rs1265744614 1626 dbSNP
rs550121549 1631 dbSNP
rs979319810 1632 dbSNP
rs1250015718 1634 dbSNP
rs185236469 1639 dbSNP
rs911024183 1640 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- 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' ggguggucgacgagGGACCGGGu 5'
                        |||||||| 
Target 5' --------------CCUGGCCCu 3'
1 - 9
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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000321613.3 | 3UTR | CCUGGCCCUCAUGUCCCCCCGGGGCUGGGGUCCGCCUGCCU
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)

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