miRTarBase - #MIRT479618


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pre-miRNA Information
pre-miRNA hsa-mir-4524a   
Genomic Coordinates chr17: 69099564 - 69099632
Description Homo sapiens miR-4524a stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4524a-5p
Sequence 6| AUAGCAGCAUGAACCUGUCUCA |27
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1322445998 8 dbSNP
rs1350790266 13 dbSNP
rs1263495678 21 dbSNP
Putative Targets

Gene Information
Gene Symbol CDC25A   
Synonyms CDC25A2
Description cell division cycle 25A
Transcript NM_001789   
Other Transcripts NM_201567   
Expression
Putative miRNA Targets on CDC25A
3'UTR of CDC25A
(miRNA target sites are highlighted)		 
>CDC25A|NM_001789|3'UTR
   1 GGGCGGCAGGACCAGCCAGCAGCAGCCCAAGCTTCCCTCCATCCCCCTTTACCCTCTTTGCTGCAGAGAAACTTAAGCAA
  81 AGGGGACAGCTGTGTGACATTTGGAGAGGGGGCCTGGGACTTCCATGCCTTAAACCTACCTCCCACACTCCCAAGGTTGG
 161 AGCCCAGGGCATCTTGCTGGCTACGCCTCTTCTGTCCCTGTTAGACGTCCTCCGTCCATATCAGAACTGTGCCACAATGC
 241 AGTTCTGAGCACCGTGTCAAGCTGCTCTGAGCCACAGTGGGATGAACCAGCCGGGGCCTTATCGGGCTCCAGCCATCTCA
 321 TGAGGGGAGAGGAGACGGAGGGGAGTAGAGAAGTTACACAGAAATGCTGCTGGCCAAATAGCAAAGACAACCTGGGAAGG
 401 AAAGGTCTTTGTGGGATAATCCATATGTTTAATTTATTCAACTTCATCAATCACTTTATTTTATTTTTTTTTCTAACTCC
 481 TGGAGACTTATTTTACTGCTTCATTAGGTTGAAATACTGCCATTCTAGGTAGGGTTTTATTATCCCAGGGACTACCTCGG
 561 CTTTTAATTTAAAAAAAAAAAAGAAGTGGGTAAGAAAATGCAAACCTGTTATAAGTTATCGGACAGAAAGCTAGGTGCTC
 641 TGTCACCCCCAGGAGGCGCTGTGGTACTGGGGCTGCTGCTATTTAAGCCAAGAACTGAGGTCCTGGTGAGAGCGTTGGAC
 721 CCAGGCTTGGCTGCCTGACATAAGCTAAATCTCCCAGACCCACCACTGGCTACCGATATCTATTTGGTGGGAGGTGTGGC
 801 CCTGTTCTTCCTCACCCCAGTTCCATGACATTGGCTGGTATAGGAGCCACAGTCAGGAAAGCACTTGAGGCAGCATCTGT
 881 TGGGCCACCCCCGGCTCAGTGCTGGAATGTTGCAGTGTAGGTTTCCCAGGGAAGGGGGGTGGGGGTAGGTGGGCTCCACA
 961 GGATGGGGGAGGAGCATGTCCACTGAGTATCTTCCTTATGTTGCTGTGATATTGATAGCTTTTATTTTCTAATTTTTAAA
1041 AAATGGTCATATTATGAGTCAAAGAGTATCAAATCAGTGTTGGATGGACCACCCAAGGGTGAGGAGAGGGGCTGGAAGCC
1121 CTGGGCATTAGGAGAAGGGAGTGGGTGCTGGCATGGACATGACTGGATAGAATTTTCTCAGGAGGGAGCTTGGTGGATTT
1201 TGAAGGTAAAACTTTCTGGGTTTATCATGTTTTAATTTTAGAGACAGGGAGTGATGAATCATCACCGGTTGTCCCCTTAT
1281 CTAACTCCATAAAAGTGGGAATTTCAAAAGAACACCTCATCCAAGGAGCTGGGGCAGACTTCATTGATTCTAGAGAGACC
1361 TGTTTCAGTGCCTACTCATCCCTGCCCTCTGGTGCCAGCCTCCTTACCATCACGGCTTCACTGAGGTGTAGGTGGGTTTT
1441 TCTTAAACAGGAGACAGTCTCTCCCCTCTTACCTCAACTTCTTGGGGTGGGAATCAGTGATACTGGAGATGGCTAGTTGC
1521 TGTGTTACGGGTTTGAGTTACATTTGGCTATAAAACAATCTTGTTGGGAAAAATGTGGGGGAGAGGACTTCTTCCTACAC
1601 GCGCATTGAGACAGATTCCAACTGGTTAATGATATTGTTTGTAAGAAAGAGATTCTGTTGGTTGACTGCCTAAAGAGAAA
1681 GGTGGGATGGCCTTCAGATTATACCAGCTTAGCTAGCATTACTAACCAACTGTTGGAAGCTCTGAAAATAAAAGATCTTG
1761 AACCCATAAAAAAAAAAA
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' acucUGUCCAAGUACGACGAUa 5'
              || ||  | |||||||| 
Target 5' tggtACTGGGGC-TGCTGCTAt 3'
 662 - 682 153.00 -18.20
2 
miRNA  3' acUCUGUCCAA---G----UACGACGAUa 5'
            ||| | |||   |    ||||||||: 
Target 5' gtAGAGAAGTTACACAGAAATGCTGCTGg 3'
 345 - 373 142.00 -16.01
3 
miRNA  3' acUC-UGUCCAAGUACGACGAua 5'
            || || |  ||| ||||||  
Target 5' tgAGCACCGTGTCAAGCTGCTct 3'
 246 - 268 140.00 -13.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26969964 43 COSMIC
COSN26969962 73 COSMIC
COSN30472403 83 COSMIC
COSN31531242 167 COSMIC
COSN31589040 184 COSMIC
COSN28676872 266 COSMIC
COSN31547405 353 COSMIC
COSN23991287 359 COSMIC
COSN31543954 463 COSMIC
COSN20937139 570 COSMIC
COSN26642908 634 COSMIC
COSN26645174 652 COSMIC
COSN31543968 721 COSMIC
COSN31589037 770 COSMIC
COSN30176998 877 COSMIC
COSN31540639 893 COSMIC
COSN7699618 969 COSMIC
COSN26678754 1126 COSMIC
COSN31584989 1237 COSMIC
COSN31551573 1267 COSMIC
COSN22754222 1287 COSMIC
COSN31530793 1398 COSMIC
COSN24826517 1600 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs746219615 3 dbSNP
rs372516294 4 dbSNP
rs762990006 5 dbSNP
rs1203504897 8 dbSNP
rs960616694 9 dbSNP
rs1368874758 10 dbSNP
rs749830055 11 dbSNP
rs1433327647 17 dbSNP
rs559315178 23 dbSNP
rs777662596 29 dbSNP
rs756196630 35 dbSNP
rs1375954845 36 dbSNP
rs1175421823 37 dbSNP
rs1399725379 38 dbSNP
rs369158657 43 dbSNP
rs767717332 46 dbSNP
rs1364744714 47 dbSNP
rs774254706 48 dbSNP
rs755244465 50 dbSNP
rs1042487 60 dbSNP
rs1014727122 65 dbSNP
rs1005161725 68 dbSNP
rs1361884929 69 dbSNP
rs1246263035 87 dbSNP
rs1310769900 110 dbSNP
rs887847951 112 dbSNP
rs1293443975 113 dbSNP
rs1351264693 118 dbSNP
rs1227952399 120 dbSNP
rs1049639131 129 dbSNP
rs773473242 135 dbSNP
rs1180036837 142 dbSNP
rs939906056 148 dbSNP
rs1407960979 152 dbSNP
rs912491066 153 dbSNP
rs541295691 154 dbSNP
rs1378748710 157 dbSNP
rs1419292077 160 dbSNP
rs1160371282 161 dbSNP
rs1303253699 162 dbSNP
rs1425942371 167 dbSNP
rs777751002 170 dbSNP
rs1347303306 177 dbSNP
rs1366355371 184 dbSNP
rs933325273 187 dbSNP
rs1040401085 199 dbSNP
rs1409228505 202 dbSNP
rs921962958 206 dbSNP
rs3731560 207 dbSNP
rs558137527 210 dbSNP
rs1223333103 213 dbSNP
rs1238973754 214 dbSNP
rs758609584 214 dbSNP
rs546227352 217 dbSNP
rs913519771 218 dbSNP
rs1207946262 229 dbSNP
rs1255304312 232 dbSNP
rs1461691956 237 dbSNP
rs1205690253 250 dbSNP
rs750909187 251 dbSNP
rs1053288911 252 dbSNP
rs936190962 253 dbSNP
rs186188935 254 dbSNP
rs979563153 255 dbSNP
rs557425772 260 dbSNP
rs1410626173 262 dbSNP
rs17464 266 dbSNP
rs1176004602 276 dbSNP
rs1226292975 280 dbSNP
rs978269303 288 dbSNP
rs966928571 292 dbSNP
rs762218762 293 dbSNP
rs1441046081 297 dbSNP
rs1025205252 298 dbSNP
rs1349808853 300 dbSNP
rs1014281345 303 dbSNP
rs1406685267 304 dbSNP
rs1282360306 314 dbSNP
rs991796050 315 dbSNP
rs1205466574 324 dbSNP
rs960605306 327 dbSNP
rs1292407399 331 dbSNP
rs183704983 332 dbSNP
rs1205527945 335 dbSNP
rs553307582 336 dbSNP
rs898255797 337 dbSNP
rs1036794665 343 dbSNP
rs1430424911 349 dbSNP
rs1481740238 351 dbSNP
rs879943370 352 dbSNP
rs1420845998 357 dbSNP
rs534961535 361 dbSNP
rs951941275 364 dbSNP
rs1027508088 367 dbSNP
rs867904545 370 dbSNP
rs747577309 371 dbSNP
rs1433844546 372 dbSNP
rs1302371723 373 dbSNP
rs900595784 395 dbSNP
rs1345844027 397 dbSNP
rs1225273937 399 dbSNP
rs890988680 401 dbSNP
rs1338849906 405 dbSNP
rs1275169121 411 dbSNP
rs1411689547 411 dbSNP
rs1051015451 422 dbSNP
rs932601628 423 dbSNP
rs1200847144 427 dbSNP
rs1481690374 443 dbSNP
rs544918825 450 dbSNP
rs570815730 452 dbSNP
rs551716955 457 dbSNP
rs1263045094 458 dbSNP
rs1476017179 464 dbSNP
rs1053809050 468 dbSNP
rs1168053190 468 dbSNP
rs1403251177 470 dbSNP
rs1162473417 472 dbSNP
rs925378399 473 dbSNP
rs978193982 473 dbSNP
rs1296083631 483 dbSNP
rs1325833636 495 dbSNP
rs112950564 498 dbSNP
rs1431371396 515 dbSNP
rs1209270089 521 dbSNP
rs966854622 525 dbSNP
rs1245532639 526 dbSNP
rs1292709338 531 dbSNP
rs1362076575 532 dbSNP
rs775824485 542 dbSNP
rs1025598018 544 dbSNP
rs1283994601 547 dbSNP
rs1206596065 554 dbSNP
rs3731562 558 dbSNP
rs959891016 559 dbSNP
rs1033315471 566 dbSNP
rs1263504715 568 dbSNP
rs1225316629 569 dbSNP
rs569576821 570 dbSNP
rs1195674032 571 dbSNP
rs754285459 580 dbSNP
rs113563213 583 dbSNP
rs1182633589 583 dbSNP
rs1385521870 583 dbSNP
rs936280007 583 dbSNP
rs995145614 586 dbSNP
rs1300020347 587 dbSNP
rs1320137044 587 dbSNP
rs1338795603 590 dbSNP
rs1382244376 595 dbSNP
rs1315779019 606 dbSNP
rs1363646923 608 dbSNP
rs962411709 609 dbSNP
rs1238245939 611 dbSNP
rs761004703 612 dbSNP
rs1279345276 614 dbSNP
rs1015285726 615 dbSNP
rs548250731 619 dbSNP
rs1318215252 620 dbSNP
rs890961796 620 dbSNP
rs529764899 621 dbSNP
rs1202540263 624 dbSNP
rs745354537 625 dbSNP
rs1044574962 634 dbSNP
rs947774560 638 dbSNP
rs1210951892 641 dbSNP
rs1179142393 642 dbSNP
rs916367253 642 dbSNP
rs559469193 644 dbSNP
rs996742392 646 dbSNP
rs541229377 650 dbSNP
rs1469205308 651 dbSNP
rs750636695 657 dbSNP
rs1408309985 658 dbSNP
rs1444862851 668 dbSNP
rs1039011918 671 dbSNP
rs532407675 672 dbSNP
rs936639006 673 dbSNP
rs1273421557 679 dbSNP
rs925301372 680 dbSNP
rs369438569 681 dbSNP
rs878952722 690 dbSNP
rs778772639 706 dbSNP
rs574374517 711 dbSNP
rs756972101 713 dbSNP
rs1249331492 714 dbSNP
rs959619837 720 dbSNP
rs926885500 721 dbSNP
rs1426941745 725 dbSNP
rs1480074161 730 dbSNP
rs1177002953 734 dbSNP
rs3731563 740 dbSNP
rs1186971938 743 dbSNP
rs1464588647 747 dbSNP
rs1263565707 751 dbSNP
rs1297652177 753 dbSNP
rs3731564 754 dbSNP
rs1393348779 762 dbSNP
rs974607680 765 dbSNP
rs964786144 769 dbSNP
rs1322063318 770 dbSNP
rs559117113 774 dbSNP
rs759213609 775 dbSNP
rs557110736 776 dbSNP
rs1285690475 777 dbSNP
rs891763157 778 dbSNP
rs370933921 779 dbSNP
rs1000818330 782 dbSNP
rs997103478 787 dbSNP
rs540864965 791 dbSNP
rs1054359833 795 dbSNP
rs1044537133 799 dbSNP
rs948930704 803 dbSNP
rs894884589 811 dbSNP
rs1200103926 815 dbSNP
rs1271014293 816 dbSNP
rs1426641343 817 dbSNP
rs1433950537 818 dbSNP
rs1383012396 825 dbSNP
rs1373713430 827 dbSNP
rs1463725373 829 dbSNP
rs1337824997 831 dbSNP
rs1365365511 834 dbSNP
rs1056110197 837 dbSNP
rs1302069098 839 dbSNP
rs553106895 848 dbSNP
rs143237021 849 dbSNP
rs1382139691 856 dbSNP
rs907490230 862 dbSNP
rs1326447315 864 dbSNP
rs1229187557 865 dbSNP
rs983145865 870 dbSNP
rs1289093022 873 dbSNP
rs1358247695 886 dbSNP
rs1223013967 887 dbSNP
rs930547157 888 dbSNP
rs1400696291 890 dbSNP
rs573241617 892 dbSNP
rs1262533659 893 dbSNP
rs1462932931 893 dbSNP
rs1182010923 898 dbSNP
rs1384887083 900 dbSNP
rs974556912 904 dbSNP
rs1425509860 905 dbSNP
rs1165923315 909 dbSNP
rs1453695343 915 dbSNP
rs570752950 917 dbSNP
rs1289917058 921 dbSNP
rs1392147098 928 dbSNP
rs964569044 931 dbSNP
rs1449117802 933 dbSNP
rs371942651 934 dbSNP
rs1018803185 935 dbSNP
rs1246253114 936 dbSNP
rs1314851712 940 dbSNP
rs1316897547 940 dbSNP
rs1189372094 943 dbSNP
rs1215006539 944 dbSNP
rs945406842 945 dbSNP
rs1486787271 946 dbSNP
rs918005807 946 dbSNP
rs1242591561 955 dbSNP
rs1255205989 956 dbSNP
rs1196365230 959 dbSNP
rs1056611693 965 dbSNP
rs938158832 970 dbSNP
rs1418824724 971 dbSNP
rs368191551 973 dbSNP
rs1366108226 974 dbSNP
rs1468688995 980 dbSNP
rs1217255064 982 dbSNP
rs865861450 983 dbSNP
rs558800977 994 dbSNP
rs1271894413 996 dbSNP
rs1304171821 998 dbSNP
rs375481614 998 dbSNP
rs987530414 999 dbSNP
rs926846164 1012 dbSNP
rs1242153569 1018 dbSNP
rs569596896 1038 dbSNP
rs1339137281 1043 dbSNP
rs773155436 1055 dbSNP
rs1333897848 1056 dbSNP
rs962935770 1063 dbSNP
rs1032058239 1065 dbSNP
rs185872086 1069 dbSNP
rs767421001 1079 dbSNP
rs1178198483 1090 dbSNP
rs1306277931 1098 dbSNP
rs982428746 1102 dbSNP
rs904771574 1103 dbSNP
rs1176265990 1109 dbSNP
rs758533060 1114 dbSNP
rs955129662 1118 dbSNP
rs1469829113 1119 dbSNP
rs1029809439 1120 dbSNP
rs527790569 1135 dbSNP
rs1352447656 1141 dbSNP
rs3731565 1145 dbSNP
rs765237683 1148 dbSNP
rs1298598454 1153 dbSNP
rs1352025235 1156 dbSNP
rs1403054890 1159 dbSNP
rs1282520801 1167 dbSNP
rs1324148182 1170 dbSNP
rs1221066816 1206 dbSNP
rs1013133748 1208 dbSNP
rs1471923062 1213 dbSNP
rs895963015 1215 dbSNP
rs1057230148 1216 dbSNP
rs1000072837 1234 dbSNP
rs903107201 1237 dbSNP
rs1003669411 1249 dbSNP
rs886223356 1250 dbSNP
rs1047846409 1251 dbSNP
rs1192481223 1255 dbSNP
rs1416764074 1255 dbSNP
rs1182205228 1256 dbSNP
rs1484006417 1257 dbSNP
rs116119378 1260 dbSNP
rs1170633810 1261 dbSNP
rs1372216828 1261 dbSNP
rs1203815046 1262 dbSNP
rs1422564326 1263 dbSNP
rs769202800 1266 dbSNP
rs181081390 1267 dbSNP
rs1438520723 1275 dbSNP
rs1268500234 1279 dbSNP
rs943285468 1280 dbSNP
rs1056936819 1287 dbSNP
rs911688627 1301 dbSNP
rs938149540 1305 dbSNP
rs987312938 1313 dbSNP
rs1357511569 1319 dbSNP
rs532342450 1320 dbSNP
rs1240136264 1322 dbSNP
rs905330670 1324 dbSNP
rs1491001784 1328 dbSNP
rs565105638 1329 dbSNP
rs1239872108 1334 dbSNP
rs1287080964 1336 dbSNP
rs1038511488 1339 dbSNP
rs753961712 1343 dbSNP
rs1442383723 1349 dbSNP
rs561460755 1352 dbSNP
rs754204789 1355 dbSNP
rs1407030866 1358 dbSNP
rs1316076936 1360 dbSNP
rs1325577891 1374 dbSNP
rs1431624900 1380 dbSNP
rs763308934 1383 dbSNP
rs764555189 1383 dbSNP
rs1403840189 1385 dbSNP
rs1380926810 1386 dbSNP
rs372188111 1398 dbSNP
rs1022938404 1402 dbSNP
rs983020636 1405 dbSNP
rs1358837556 1406 dbSNP
rs1158942085 1407 dbSNP
rs1473410820 1409 dbSNP
rs1284231183 1413 dbSNP
rs1013080400 1414 dbSNP
rs1181436887 1428 dbSNP
rs531524136 1431 dbSNP
rs563673171 1436 dbSNP
rs541864650 1447 dbSNP
rs1459705440 1454 dbSNP
rs574838246 1456 dbSNP
rs1196070528 1464 dbSNP
rs1385661457 1472 dbSNP
rs867885902 1485 dbSNP
rs1473634081 1491 dbSNP
rs1035812127 1493 dbSNP
rs1156560662 1496 dbSNP
rs75864198 1497 dbSNP
rs1407226704 1498 dbSNP
rs1401203630 1500 dbSNP
rs150274172 1503 dbSNP
rs1452204803 1508 dbSNP
rs1337577614 1510 dbSNP
rs886168669 1513 dbSNP
rs554310421 1521 dbSNP
rs879786465 1528 dbSNP
rs1279326926 1529 dbSNP
rs140929323 1529 dbSNP
rs898808826 1531 dbSNP
rs1230706863 1541 dbSNP
rs1269493222 1541 dbSNP
rs975563970 1546 dbSNP
rs1202675551 1556 dbSNP
rs1256467938 1558 dbSNP
rs1443764638 1560 dbSNP
rs963829464 1564 dbSNP
rs1032809325 1567 dbSNP
rs978604601 1568 dbSNP
rs1266606448 1569 dbSNP
rs1161206948 1571 dbSNP
rs967263433 1573 dbSNP
rs577005004 1575 dbSNP
rs1014199516 1576 dbSNP
rs775855724 1577 dbSNP
rs943236066 1580 dbSNP
rs1389890477 1582 dbSNP
rs776193357 1583 dbSNP
rs911848818 1585 dbSNP
rs1412249172 1586 dbSNP
rs575609624 1592 dbSNP
rs934537558 1600 dbSNP
rs1222421663 1601 dbSNP
rs558740232 1602 dbSNP
rs537719084 1603 dbSNP
rs1346767378 1607 dbSNP
rs576665303 1612 dbSNP
rs1272035011 1621 dbSNP
rs1483231055 1633 dbSNP
rs772699840 1634 dbSNP
rs770103969 1635 dbSNP
rs1266749489 1638 dbSNP
rs1199761387 1640 dbSNP
rs1459007064 1640 dbSNP
rs1379379223 1643 dbSNP
rs915876511 1647 dbSNP
rs1167506793 1649 dbSNP
rs1386245025 1651 dbSNP
rs1397698281 1651 dbSNP
rs1038481606 1653 dbSNP
rs1301652812 1657 dbSNP
rs1345499792 1662 dbSNP
rs1470275347 1666 dbSNP
rs1427109582 1672 dbSNP
rs756639208 1676 dbSNP
rs941516679 1683 dbSNP
rs991484149 1690 dbSNP
rs1224811667 1694 dbSNP
rs1269184370 1704 dbSNP
rs960277772 1705 dbSNP
rs1035926161 1708 dbSNP
rs1207109654 1713 dbSNP
rs537847911 1716 dbSNP
rs1490168670 1718 dbSNP
rs535862051 1729 dbSNP
rs951550511 1740 dbSNP
rs1242182420 1761 dbSNP
rs1190169299 1765 dbSNP
rs1463248063 1767 dbSNP
rs1426771704 1771 dbSNP
rs565724637 1777 dbSNP
rs1246612070 1790 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' acucUGUCCAAGUACGACGAUa 5'
              || ||  | |||||||| 
Target 5' ugguACUGGGGC-UGCUGCUAu 3'
 		6 - 26
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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000302506.3 | 3UTR | CGCUGUGGUACUGGGGCUGCUGCUAUUUAAGCCAAG
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
180 hsa-miR-4524a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055251 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT055826 PLEKHA1 pleckstrin homology domain containing A1 2 2
MIRT060573 CCND1 cyclin D1 2 2
MIRT061013 C1ORF21 chromosome 1 open reading frame 21 2 6
MIRT064694 CCND2 cyclin D2 2 4
MIRT075268 SNTB2 syntrophin beta 2 2 4
MIRT079668 NAPG NSF attachment protein gamma 2 12
MIRT081651 CCNE1 cyclin E1 2 4
MIRT082996 PNPLA6 patatin like phospholipase domain containing 6 2 2
MIRT083463 RALGAPB Ral GTPase activating protein non-catalytic beta subunit 2 4
MIRT085755 RIF1 replication timing regulatory factor 1 2 2
MIRT086022 UBR3 ubiquitin protein ligase E3 component n-recognin 3 (putative) 2 2
MIRT087431 ZNRF3 zinc and ring finger 3 2 2
MIRT088786 SOCS5 suppressor of cytokine signaling 5 2 2
MIRT089221 ACTR2 ARP2 actin related protein 2 homolog 2 2
MIRT093696 PI4K2B phosphatidylinositol 4-kinase type 2 beta 2 6
MIRT095090 SEC24A SEC24 homolog A, COPII coat complex component 2 4
MIRT096249 CANX calnexin 2 2
MIRT100215 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT100746 VEGFA vascular endothelial growth factor A 2 12
MIRT100904 CD2AP CD2 associated protein 2 2
MIRT102647 UBN2 ubinuclein 2 2 10
MIRT103882 FOXK1 forkhead box K1 2 2
MIRT104246 DMTF1 cyclin D binding myb like transcription factor 1 2 2
MIRT106310 ZFHX4 zinc finger homeobox 4 2 6
MIRT107696 RECK reversion inducing cysteine rich protein with kazal motifs 2 2
MIRT114943 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT117671 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT133799 SKI SKI proto-oncogene 2 2
MIRT140167 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT142279 DCTN5 dynactin subunit 5 2 8
MIRT143288 N4BP1 NEDD4 binding protein 1 2 2
MIRT165939 CREBRF CREB3 regulatory factor 2 2
MIRT175251 PSAT1 phosphoserine aminotransferase 1 2 6
MIRT186381 PNRC2 proline rich nuclear receptor coactivator 2 2 2
MIRT191470 PPM1A protein phosphatase, Mg2+/Mn2+ dependent 1A 2 2
MIRT196480 TAOK1 TAO kinase 1 2 2
MIRT201470 SNRPB2 small nuclear ribonucleoprotein polypeptide B2 2 8
MIRT204615 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 8
MIRT204646 MOB4 MOB family member 4, phocein 2 8
MIRT204749 BZW1 basic leucine zipper and W2 domains 1 2 12
MIRT206031 NUP50 nucleoporin 50 2 6
MIRT211196 FGF2 fibroblast growth factor 2 2 4
MIRT229353 ZNF449 zinc finger protein 449 2 2
MIRT247138 WEE1 WEE1 G2 checkpoint kinase 2 4
MIRT249461 ZNF691 zinc finger protein 691 2 4
MIRT256314 CDC42SE2 CDC42 small effector 2 2 2
MIRT258419 WIPI2 WD repeat domain, phosphoinositide interacting 2 2 2
MIRT265083 CHEK1 checkpoint kinase 1 2 2
MIRT270561 SETD1B SET domain containing 1B 2 2
MIRT274749 RAB3IP RAB3A interacting protein 2 2
MIRT277515 PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 2 4
MIRT289642 CBX2 chromobox 2 2 2
MIRT301001 MTMR3 myotubularin related protein 3 2 2
MIRT307149 CTDSPL CTD small phosphatase like 2 4
MIRT309021 USP53 ubiquitin specific peptidase 53 2 2
MIRT314100 PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 2 8
MIRT319338 CAPZA2 capping actin protein of muscle Z-line alpha subunit 2 2 2
MIRT320619 ZNRF2 zinc and ring finger 2 2 2
MIRT324285 LURAP1L leucine rich adaptor protein 1 like 2 2
MIRT446498 ASCC1 activating signal cointegrator 1 complex subunit 1 2 2
MIRT448437 TLL1 tolloid like 1 2 2
MIRT461537 ACTR3B ARP3 actin related protein 3 homolog B 2 2
MIRT463162 ZNF367 zinc finger protein 367 2 10
MIRT463493 ZC3H10 zinc finger CCCH-type containing 10 2 2
MIRT465154 TSC22D2 TSC22 domain family member 2 2 2
MIRT466418 TFAP2A transcription factor AP-2 alpha 2 8
MIRT468278 SFT2D2 SFT2 domain containing 2 2 2
MIRT469399 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT471941 NR6A1 nuclear receptor subfamily 6 group A member 1 2 2
MIRT473688 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT479618 CDC25A cell division cycle 25A 2 2
MIRT482098 AKT3 AKT serine/threonine kinase 3 2 4
MIRT483995 ATAD5 ATPase family, AAA domain containing 5 2 12
MIRT485205 PRKAR2A protein kinase cAMP-dependent type II regulatory subunit alpha 2 8
MIRT498763 C3orf38 chromosome 3 open reading frame 38 2 8
MIRT498961 ORC4 origin recognition complex subunit 4 2 8
MIRT499440 ODF2L outer dense fiber of sperm tails 2 like 2 8
MIRT500080 L2HGDH L-2-hydroxyglutarate dehydrogenase 2 8
MIRT500305 ZNF622 zinc finger protein 622 2 8
MIRT500410 ZMAT3 zinc finger matrin-type 3 2 8
MIRT500789 TLK1 tousled like kinase 1 2 6
MIRT500930 SRPR SRP receptor alpha subunit 2 6
MIRT500943 SREK1 splicing regulatory glutamic acid and lysine rich protein 1 2 8
MIRT501068 SMAD7 SMAD family member 7 2 8
MIRT501711 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT502627 DDX3X DEAD-box helicase 3, X-linked 2 8
MIRT502910 CDCA4 cell division cycle associated 4 2 8
MIRT502935 CDC37L1 cell division cycle 37 like 1 2 8
MIRT504531 ZNF620 zinc finger protein 620 2 6
MIRT505106 YTHDC1 YTH domain containing 1 2 6
MIRT505337 TMEM245 transmembrane protein 245 2 6
MIRT505383 TMEM100 transmembrane protein 100 2 2
MIRT505678 SESTD1 SEC14 and spectrin domain containing 1 2 6
MIRT506157 PLAG1 PLAG1 zinc finger 2 8
MIRT506183 PHKA1 phosphorylase kinase regulatory subunit alpha 1 2 6
MIRT506475 MYO5A myosin VA 2 6
MIRT506826 KIF23 kinesin family member 23 2 6
MIRT507160 GAS2L3 growth arrest specific 2 like 3 2 2
MIRT507511 DYNLL2 dynein light chain LC8-type 2 2 4
MIRT507845 CCNE2 cyclin E2 2 6
MIRT510403 ZNF507 zinc finger protein 507 2 2
MIRT518078 TRIM35 tripartite motif containing 35 2 2
MIRT518982 NNT nicotinamide nucleotide transhydrogenase 2 4
MIRT521045 SLC2A3 solute carrier family 2 member 3 2 4
MIRT521190 SBNO1 strawberry notch homolog 1 2 6
MIRT522088 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 4
MIRT524846 ARPP19 cAMP regulated phosphoprotein 19 2 2
MIRT527787 TMEM44 transmembrane protein 44 2 4
MIRT537803 EFNB2 ephrin B2 2 4
MIRT540830 GNAT1 G protein subunit alpha transducin 1 2 4
MIRT541140 PISD phosphatidylserine decarboxylase 2 2
MIRT541419 CBX4 chromobox 4 2 2
MIRT543517 PRSS21 protease, serine 21 2 2
MIRT543824 GSG1 germ cell associated 1 2 2
MIRT544959 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT545179 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 2 4
MIRT545335 CCDC83 coiled-coil domain containing 83 2 2
MIRT545518 RSL24D1 ribosomal L24 domain containing 1 2 2
MIRT545670 DECR1 2,4-dienoyl-CoA reductase 1 2 2
MIRT545931 ZBTB44 zinc finger and BTB domain containing 44 2 4
MIRT546102 USP48 ubiquitin specific peptidase 48 2 4
MIRT546598 SALL1 spalt like transcription factor 1 2 4
MIRT546626 RTN4 reticulon 4 2 2
MIRT547651 KPNA3 karyopherin subunit alpha 3 2 2
MIRT547987 HCFC2 host cell factor C2 2 4
MIRT548717 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT548931 CDK17 cyclin dependent kinase 17 2 2
MIRT549067 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT549266 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT550460 OSCAR osteoclast associated, immunoglobulin-like receptor 2 4
MIRT550806 FAM229B family with sequence similarity 229 member B 2 2
MIRT552024 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT552334 ZNF704 zinc finger protein 704 2 2
MIRT552732 YRDC yrdC N6-threonylcarbamoyltransferase domain containing 2 2
MIRT553795 SZRD1 SUZ RNA binding domain containing 1 2 4
MIRT554694 RNF149 ring finger protein 149 2 2
MIRT555133 PTPRD protein tyrosine phosphatase, receptor type D 2 2
MIRT555264 PRDM4 PR/SET domain 4 2 2
MIRT556848 KANK1 KN motif and ankyrin repeat domains 1 2 4
MIRT557474 GPR27 G protein-coupled receptor 27 2 4
MIRT558018 EXT1 exostosin glycosyltransferase 1 2 2
MIRT558498 CYP26B1 cytochrome P450 family 26 subfamily B member 1 2 4
MIRT558579 CREBL2 cAMP responsive element binding protein like 2 2 4
MIRT558610 COX6B1 cytochrome c oxidase subunit 6B1 2 4
MIRT558650 CNKSR3 CNKSR family member 3 2 2
MIRT558986 CA8 carbonic anhydrase 8 2 2
MIRT559141 BTN3A3 butyrophilin subfamily 3 member A3 2 2
MIRT559327 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 2
MIRT562021 LANCL1 LanC like 1 2 2
MIRT562869 KIAA1456 KIAA1456 2 2
MIRT563074 SLC25A12 solute carrier family 25 member 12 2 2
MIRT563496 DLGAP3 DLG associated protein 3 2 2
MIRT563890 RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 2 2
MIRT564311 CCNT1 cyclin T1 2 2
MIRT564942 XKR7 XK related 7 2 2
MIRT564979 WNK3 WNK lysine deficient protein kinase 3 2 2
MIRT565423 TEF TEF, PAR bZIP transcription factor 2 2
MIRT566824 MAP3K7 mitogen-activated protein kinase kinase kinase 7 2 2
MIRT571961 KIF5B kinesin family member 5B 2 2
MIRT575877 Cask calcium/calmodulin-dependent serine protein kinase (MAGUK family) 2 3
MIRT576523 Txlna taxilin alpha 2 2
MIRT614693 TRAK1 trafficking kinesin protein 1 2 2
MIRT616065 ZC3H14 zinc finger CCCH-type containing 14 2 2
MIRT618838 ASAH2B N-acylsphingosine amidohydrolase 2B 2 2
MIRT624626 ATXN2 ataxin 2 2 2
MIRT624652 ASAH2 N-acylsphingosine amidohydrolase 2 2 2
MIRT640314 MMAB methylmalonic aciduria (cobalamin deficiency) cblB type 2 2
MIRT659248 CUL3 cullin 3 2 2
MIRT680972 DCAF17 DDB1 and CUL4 associated factor 17 2 2
MIRT682261 RS1 retinoschisin 1 2 2
MIRT682505 GLP2R glucagon like peptide 2 receptor 2 2
MIRT693904 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 2 2
MIRT699214 SLCO3A1 solute carrier organic anion transporter family member 3A1 2 2
MIRT699373 SLC30A6 solute carrier family 30 member 6 2 2
MIRT699451 SLC16A9 solute carrier family 16 member 9 2 2
MIRT701230 OCRL OCRL, inositol polyphosphate-5-phosphatase 2 2
MIRT702849 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT706163 CASK calcium/calmodulin dependent serine protein kinase 2 3
MIRT718990 UTP15 UTP15, small subunit processome component 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4524a-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4524a-5p Cetuximab resistant tissue (colorectal carcinoma)

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