pre-miRNA Information
pre-miRNA hsa-mir-4747   
Genomic Coordinates chr19: 4932687 - 4932740
Description Homo sapiens miR-4747 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4747-5p
Sequence 1| AGGGAAGGAGGCUUGGUCUUAG |22
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs560927363 4 dbSNP
rs1471226927 10 dbSNP
rs763137545 12 dbSNP
rs767337154 15 dbSNP
rs775298039 16 dbSNP
rs760472311 19 dbSNP
rs1207950315 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TGIF1   
Synonyms HPE4, TGIF
Description TGFB induced factor homeobox 1
Transcript NM_003244   
Other Transcripts NM_170695 , NM_173207 , NM_173208 , NM_173209 , NM_173210 , NM_173211 , NM_174886   
Expression
Putative miRNA Targets on TGIF1
3'UTR of TGIF1
(miRNA target sites are highlighted)
>TGIF1|NM_003244|3'UTR
   1 CCCATTTTCAAGCAAAACAGTTCTCAGAAATGTCATGATTGCCGGGGTGAAGGCAAGAGATGAATTGCATTATTTTATAT
  81 ATTTTTTATTAATATTTGCACATGGGATTGCTAAAACAGCTTCCTGTTACTGAGATGTCTTCAATGGAATACAGTCATTC
 161 CAAGAACTATAAACTTAAAGCTACTGTAGAAACAAAGGGTTTTCTTTTTTAAATGTTTCTTGGTAGATTATTCATAATGT
 241 GAGATGGTTCCCAATATCATGTGATTTTTTTTTTCCTCCCCTTCCCTTTTTTTGTTATTTTTTCAGACTGTGCAATACTT
 321 AGAGAACCTATAGCATCTTCTCATTCCCATGTGGAACAGGATGCCCACATACTGTCTAATTAATAAATTTTCCATTTTTT
 401 TTCAAACAAGTATGAATCTAGTTGGTTGATGCCTTTTTTTTCATGACATAATAAAGTATTTTCTTTAAAAAAAAAAAAAA
 481 AAA
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' gauucugguucGGA--GGAAGGGa 5'
                     |||  ||||||| 
Target 5' attttttttttCCTCCCCTTCCCt 3'
264 - 287 145.00 -17.30
2
miRNA  3' gaUUCU--GGU-UCG-----GAGGAAGGGa 5'
            :|||  |:| |||     ||| ||||| 
Target 5' taGAGAACCTATAGCATCTTCTCATTCCCa 3'
320 - 349 126.00 -14.00
3
miRNA  3' gauucUGGUUCGGAGGAAGGGa 5'
               :|:||  |  |||||: 
Target 5' ggattGCTAAAACAGCTTCCTg 3'
105 - 126 105.00 -12.12
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
326711 20 ClinVar
326712 134 ClinVar
326713 265 ClinVar
326714 337 ClinVar
326715 408 ClinVar
326716 434 ClinVar
COSN31599516 9 COSMIC
COSN30705872 28 COSMIC
COSN31555417 28 COSMIC
COSN32052967 28 COSMIC
COSN22859456 38 COSMIC
COSN31599713 43 COSMIC
COSN30180586 46 COSMIC
COSN30499844 61 COSMIC
COSN30160187 63 COSMIC
COSN31581054 85 COSMIC
COSN31598398 108 COSMIC
COSN28040711 193 COSMIC
COSN26642246 211 COSMIC
COSN20114634 275 COSMIC
COSN31486181 293 COSMIC
COSN26647791 298 COSMIC
COSN26648860 305 COSMIC
COSN31566910 325 COSMIC
COSN8604526 336 COSMIC
COSN30118550 365 COSMIC
COSN30162987 400 COSMIC
COSN8604527 413 COSMIC
COSN31593909 420 COSMIC
COSN6120776 653 COSMIC
COSN58516 746 COSMIC
COSN25035620 760 COSMIC
COSN25490078 775 COSMIC
COSN22278487 798 COSMIC
COSN5425178 854 COSMIC
COSN6120779 1031 COSMIC
COSN22623880 1084 COSMIC
COSN1739258 1124 COSMIC
COSN6120781 1250 COSMIC
COSN22308598 1304 COSMIC
COSN27408669 1585 COSMIC
COSN27893083 1631 COSMIC
COSN1739259 1661 COSMIC
COSN9332280 1742 COSMIC
COSN8678309 1777 COSMIC
COSN22887885 1797 COSMIC
COSN1205414 1998 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1247279748 1 dbSNP
rs1231971234 5 dbSNP
rs1308225202 14 dbSNP
rs1374452107 15 dbSNP
rs1241852013 16 dbSNP
rs145621092 20 dbSNP
rs1355216701 21 dbSNP
rs1221785461 24 dbSNP
rs370491897 26 dbSNP
rs1300086123 28 dbSNP
rs756742227 29 dbSNP
rs1453791263 34 dbSNP
rs1390743487 35 dbSNP
rs75078688 37 dbSNP
rs781153445 41 dbSNP
rs900139143 43 dbSNP
rs745773389 44 dbSNP
rs563701713 45 dbSNP
rs775304618 50 dbSNP
rs1439258052 55 dbSNP
rs1348596934 61 dbSNP
rs1051495561 63 dbSNP
rs954279745 66 dbSNP
rs1166317308 68 dbSNP
rs1391494896 77 dbSNP
rs986932552 80 dbSNP
rs1192672324 86 dbSNP
rs890190970 87 dbSNP
rs912746852 90 dbSNP
rs1327015985 91 dbSNP
rs1225201155 92 dbSNP
rs1008420080 94 dbSNP
rs955748503 102 dbSNP
rs1032232953 103 dbSNP
rs1276786624 104 dbSNP
rs892060141 105 dbSNP
rs1307094723 111 dbSNP
rs529315164 114 dbSNP
rs1221273162 120 dbSNP
rs549486635 130 dbSNP
rs886053783 134 dbSNP
rs970083619 136 dbSNP
rs1044071985 138 dbSNP
rs980089529 141 dbSNP
rs1035802830 143 dbSNP
rs566210101 145 dbSNP
rs1248423071 146 dbSNP
rs1481742862 147 dbSNP
rs752943244 148 dbSNP
rs1200764848 153 dbSNP
rs1428579350 161 dbSNP
rs527462805 163 dbSNP
rs1473492597 165 dbSNP
rs983319248 169 dbSNP
rs907668404 185 dbSNP
rs1175505633 192 dbSNP
rs1056870215 193 dbSNP
rs1238239036 194 dbSNP
rs1212763873 199 dbSNP
rs111818038 206 dbSNP
rs1262848247 210 dbSNP
rs1229556071 215 dbSNP
rs1331788615 223 dbSNP
rs11571513 224 dbSNP
rs1390293418 227 dbSNP
rs1379499517 231 dbSNP
rs1304225890 232 dbSNP
rs1037555510 238 dbSNP
rs539732863 245 dbSNP
rs1208350262 248 dbSNP
rs1405083576 265 dbSNP
rs1491005622 265 dbSNP
rs199685547 265 dbSNP
rs34622075 265 dbSNP
rs565605009 265 dbSNP
rs71366664 265 dbSNP
rs78848135 265 dbSNP
rs886053784 265 dbSNP
rs77372929 266 dbSNP
rs1418571146 268 dbSNP
rs1414872313 270 dbSNP
rs921845212 271 dbSNP
rs1355942520 275 dbSNP
rs1462129889 279 dbSNP
rs1297112591 280 dbSNP
rs1348087150 282 dbSNP
rs1406761576 287 dbSNP
rs1466678731 292 dbSNP
rs1283811554 295 dbSNP
rs1344750218 298 dbSNP
rs76499577 300 dbSNP
rs1314154217 311 dbSNP
rs1243354943 313 dbSNP
rs11571514 323 dbSNP
rs1274782911 331 dbSNP
rs886053785 337 dbSNP
rs1051360288 358 dbSNP
rs1308303366 362 dbSNP
rs1321032411 367 dbSNP
rs1436965878 372 dbSNP
rs569631047 386 dbSNP
rs1382783748 389 dbSNP
rs535121145 392 dbSNP
rs1288202930 394 dbSNP
rs1350545552 395 dbSNP
rs1458295843 395 dbSNP
rs1165506635 397 dbSNP
rs935045766 398 dbSNP
rs995873867 401 dbSNP
rs1249749265 403 dbSNP
rs1189660808 407 dbSNP
rs115682894 408 dbSNP
rs1260337749 419 dbSNP
rs1223937701 422 dbSNP
rs1205060697 424 dbSNP
rs1192271300 434 dbSNP
rs1489067849 434 dbSNP
rs397858239 434 dbSNP
rs1268841837 441 dbSNP
rs188912525 442 dbSNP
rs1358334747 448 dbSNP
rs1479715678 449 dbSNP
rs1188677622 450 dbSNP
rs192439935 452 dbSNP
rs1420587546 457 dbSNP
rs1428821515 461 dbSNP
rs1169299785 462 dbSNP
rs1368205734 467 dbSNP
rs891918279 480 dbSNP
rs1294502984 484 dbSNP
rs1303176743 484 dbSNP
rs1387313361 485 dbSNP
rs1392734413 488 dbSNP
rs1011742518 491 dbSNP
rs1364896617 493 dbSNP
rs1422791670 496 dbSNP
rs1365262640 501 dbSNP
rs1021916795 502 dbSNP
rs1434125520 505 dbSNP
rs1463657133 507 dbSNP
rs111809301 512 dbSNP
rs906098807 515 dbSNP
rs1371728729 518 dbSNP
rs1001556763 519 dbSNP
rs79394299 526 dbSNP
rs1434299598 532 dbSNP
rs960160932 537 dbSNP
rs1490039637 538 dbSNP
rs113796695 539 dbSNP
rs1015007948 542 dbSNP
rs963578417 544 dbSNP
rs1250572158 546 dbSNP
rs1361809126 547 dbSNP
rs973198007 549 dbSNP
rs1281297333 555 dbSNP
rs1332802755 555 dbSNP
rs921876710 556 dbSNP
rs73939394 557 dbSNP
rs987110539 558 dbSNP
rs911512212 559 dbSNP
rs1394573129 560 dbSNP
rs563864981 561 dbSNP
rs1466869477 562 dbSNP
rs1432155143 564 dbSNP
rs1174924742 565 dbSNP
rs1251948065 571 dbSNP
rs529270236 572 dbSNP
rs1021755906 576 dbSNP
rs968507854 578 dbSNP
rs1435770814 579 dbSNP
rs980149227 581 dbSNP
rs379584 589 dbSNP
rs938583046 597 dbSNP
rs750011225 603 dbSNP
rs559858429 604 dbSNP
rs1222854314 614 dbSNP
rs528614995 617 dbSNP
rs1329718042 624 dbSNP
rs1289116479 627 dbSNP
rs1444425463 632 dbSNP
rs907706892 635 dbSNP
rs757977031 646 dbSNP
rs1185097343 652 dbSNP
rs1396762692 653 dbSNP
rs547577192 664 dbSNP
rs898539667 666 dbSNP
rs1469760008 669 dbSNP
rs1043227193 671 dbSNP
rs1163668749 673 dbSNP
rs906129534 674 dbSNP
rs1413317922 677 dbSNP
rs1159838950 684 dbSNP
rs1468154408 685 dbSNP
rs1362925330 686 dbSNP
rs1187836415 687 dbSNP
rs1384068550 689 dbSNP
rs1049732346 695 dbSNP
rs1202769391 705 dbSNP
rs1465318958 706 dbSNP
rs1286254378 713 dbSNP
rs889812359 718 dbSNP
rs570632488 727 dbSNP
rs1057158523 729 dbSNP
rs895846496 731 dbSNP
rs1385201922 734 dbSNP
rs533026179 736 dbSNP
rs1345610716 744 dbSNP
rs757972978 745 dbSNP
rs419499 749 dbSNP
rs1452337534 754 dbSNP
rs1318243174 759 dbSNP
rs1015453288 761 dbSNP
rs1021809854 763 dbSNP
rs968852593 764 dbSNP
rs963477530 773 dbSNP
rs979846174 776 dbSNP
rs1383629693 778 dbSNP
rs994648378 780 dbSNP
rs569886691 782 dbSNP
rs1446129564 799 dbSNP
rs953303909 810 dbSNP
rs535063283 811 dbSNP
rs1449830369 812 dbSNP
rs1243571749 819 dbSNP
rs911808704 819 dbSNP
rs1213563933 820 dbSNP
rs1033964311 825 dbSNP
rs1385281374 826 dbSNP
rs1283679861 827 dbSNP
rs7237593 833 dbSNP
rs573784202 835 dbSNP
rs987809073 837 dbSNP
rs1245778008 841 dbSNP
rs992700861 841 dbSNP
rs754636855 842 dbSNP
rs1272229484 845 dbSNP
rs61506158 851 dbSNP
rs780922074 857 dbSNP
rs1429259438 858 dbSNP
rs11877289 869 dbSNP
rs151283676 875 dbSNP
rs1316789792 877 dbSNP
rs1207232065 880 dbSNP
rs557614872 886 dbSNP
rs1363405715 889 dbSNP
rs1162544600 891 dbSNP
rs927407331 895 dbSNP
rs1462427491 911 dbSNP
rs931368314 913 dbSNP
rs1475065965 918 dbSNP
rs1049866331 923 dbSNP
rs1183805502 929 dbSNP
rs182360931 931 dbSNP
rs1289596082 935 dbSNP
rs773136450 945 dbSNP
rs1222037794 946 dbSNP
rs889782687 957 dbSNP
rs943982292 964 dbSNP
rs1159753455 966 dbSNP
rs937491216 971 dbSNP
rs1339377849 973 dbSNP
rs1284481128 975 dbSNP
rs1407226045 977 dbSNP
rs1343112909 978 dbSNP
rs1301938547 982 dbSNP
rs1410088536 985 dbSNP
rs1057513384 989 dbSNP
rs1355889250 994 dbSNP
rs1408658985 1000 dbSNP
rs896057609 1001 dbSNP
rs447982 1002 dbSNP
rs1425866344 1007 dbSNP
rs768591600 1014 dbSNP
rs56385005 1015 dbSNP
rs1266887555 1017 dbSNP
rs892016340 1017 dbSNP
rs1198730506 1018 dbSNP
rs1408028441 1027 dbSNP
rs1022192641 1040 dbSNP
rs1453730506 1040 dbSNP
rs1437618274 1041 dbSNP
rs1264083498 1043 dbSNP
rs1225911714 1048 dbSNP
rs904718447 1054 dbSNP
rs1001232479 1055 dbSNP
rs1223831019 1057 dbSNP
rs1034103207 1059 dbSNP
rs387462 1060 dbSNP
rs777674417 1065 dbSNP
rs1440934170 1081 dbSNP
rs1338396737 1088 dbSNP
rs1468192703 1095 dbSNP
rs899268634 1101 dbSNP
rs1175871012 1105 dbSNP
rs1419745753 1109 dbSNP
rs555341726 1110 dbSNP
rs1175716290 1111 dbSNP
rs1373250244 1115 dbSNP
rs866674874 1115 dbSNP
rs1028784771 1116 dbSNP
rs1205935966 1134 dbSNP
rs1460409041 1137 dbSNP
rs543010815 1142 dbSNP
rs1263046836 1162 dbSNP
rs559795406 1168 dbSNP
rs528547920 1169 dbSNP
rs1019306728 1170 dbSNP
rs1324689176 1173 dbSNP
rs956628818 1177 dbSNP
rs1316943797 1180 dbSNP
rs1450173399 1183 dbSNP
rs988228444 1185 dbSNP
rs867378667 1186 dbSNP
rs1405351338 1191 dbSNP
rs1203949386 1194 dbSNP
rs973364901 1195 dbSNP
rs1347062674 1197 dbSNP
rs186653381 1201 dbSNP
rs1418763357 1203 dbSNP
rs980557238 1221 dbSNP
rs1440292107 1224 dbSNP
rs1183374939 1225 dbSNP
rs74692024 1226 dbSNP
rs985537640 1235 dbSNP
rs911276306 1239 dbSNP
rs1472263911 1243 dbSNP
rs1487106844 1244 dbSNP
rs1258464222 1245 dbSNP
rs944119546 1246 dbSNP
rs191807591 1248 dbSNP
rs937522270 1250 dbSNP
rs377760755 1259 dbSNP
rs1295970179 1273 dbSNP
rs1383885761 1282 dbSNP
rs946278650 1283 dbSNP
rs1431230129 1284 dbSNP
rs920451556 1284 dbSNP
rs142659618 1285 dbSNP
rs917508077 1286 dbSNP
rs1165705537 1292 dbSNP
rs527358457 1295 dbSNP
rs940924325 1307 dbSNP
rs904688033 1312 dbSNP
rs1194293434 1313 dbSNP
rs1001618049 1321 dbSNP
rs1055895462 1327 dbSNP
rs895540385 1330 dbSNP
rs1036779030 1333 dbSNP
rs1329696556 1339 dbSNP
rs1335231220 1349 dbSNP
rs563563268 1350 dbSNP
rs1270345032 1359 dbSNP
rs1408588067 1361 dbSNP
rs1285713065 1363 dbSNP
rs1014983712 1377 dbSNP
rs1346650414 1398 dbSNP
rs899132819 1403 dbSNP
rs961763703 1406 dbSNP
rs878991153 1408 dbSNP
rs115310714 1409 dbSNP
rs1342443188 1413 dbSNP
rs371274241 1420 dbSNP
rs1197180200 1423 dbSNP
rs1390244849 1423 dbSNP
rs953284628 1430 dbSNP
rs183989261 1434 dbSNP
rs985935023 1435 dbSNP
rs1481023822 1436 dbSNP
rs1009168534 1438 dbSNP
rs7229123 1441 dbSNP
rs1202991027 1443 dbSNP
rs892387690 1446 dbSNP
rs1480687119 1452 dbSNP
rs1197906894 1453 dbSNP
rs1250780456 1453 dbSNP
rs534356712 1470 dbSNP
rs1479538475 1474 dbSNP
rs1250491303 1480 dbSNP
rs1224070523 1483 dbSNP
rs1009449985 1484 dbSNP
rs965437261 1485 dbSNP
rs570806457 1487 dbSNP
rs1330796728 1489 dbSNP
rs1329800132 1494 dbSNP
rs1393306618 1495 dbSNP
rs75802730 1496 dbSNP
rs1470612763 1505 dbSNP
rs1432055912 1515 dbSNP
rs946109384 1524 dbSNP
rs967741872 1526 dbSNP
rs1477406424 1528 dbSNP
rs1363802566 1531 dbSNP
rs1183552734 1532 dbSNP
rs1427939544 1542 dbSNP
rs768722857 1544 dbSNP
rs776918562 1548 dbSNP
rs571281600 1558 dbSNP
rs926191405 1559 dbSNP
rs937606793 1568 dbSNP
rs1055865661 1569 dbSNP
rs1202885309 1571 dbSNP
rs762214670 1571 dbSNP
rs1033454185 1573 dbSNP
rs1344421513 1574 dbSNP
rs1404807068 1594 dbSNP
rs1241489152 1595 dbSNP
rs1280164808 1595 dbSNP
rs896012144 1609 dbSNP
rs189841534 1614 dbSNP
rs993418766 1630 dbSNP
rs917390591 1631 dbSNP
rs775588547 1645 dbSNP
rs972381844 1647 dbSNP
rs1385077543 1650 dbSNP
rs920836633 1668 dbSNP
rs1159751975 1670 dbSNP
rs371106320 1671 dbSNP
rs1050366566 1688 dbSNP
rs1184030223 1689 dbSNP
rs889215403 1692 dbSNP
rs1270384555 1699 dbSNP
rs1446219570 1703 dbSNP
rs1027748068 1711 dbSNP
rs1186783085 1718 dbSNP
rs1340977955 1719 dbSNP
rs1447474370 1723 dbSNP
rs1225558813 1726 dbSNP
rs557288530 1729 dbSNP
rs374442511 1733 dbSNP
rs892339257 1735 dbSNP
rs1246903205 1736 dbSNP
rs7243976 1736 dbSNP
rs1313310360 1740 dbSNP
rs574344173 1742 dbSNP
rs185233500 1743 dbSNP
rs1389807940 1750 dbSNP
rs536950326 1754 dbSNP
rs1001888802 1761 dbSNP
rs1165553561 1765 dbSNP
rs1033318338 1773 dbSNP
rs553750148 1778 dbSNP
rs967873870 1782 dbSNP
rs960745660 1783 dbSNP
rs1487352654 1784 dbSNP
rs140487684 1785 dbSNP
rs1223528983 1787 dbSNP
rs754166400 1793 dbSNP
rs1361805651 1797 dbSNP
rs1228081358 1807 dbSNP
rs1457896854 1809 dbSNP
rs1015756013 1816 dbSNP
rs763595571 1818 dbSNP
rs374533251 1824 dbSNP
rs1292272484 1827 dbSNP
rs1363311185 1828 dbSNP
rs1387649912 1830 dbSNP
rs1322717719 1842 dbSNP
rs1410318989 1842 dbSNP
rs962270956 1843 dbSNP
rs950256387 1849 dbSNP
rs1383161469 1853 dbSNP
rs1423043834 1856 dbSNP
rs1200195514 1857 dbSNP
rs1245184730 1864 dbSNP
rs1490915851 1864 dbSNP
rs972628496 1865 dbSNP
rs765893274 1866 dbSNP
rs1317817002 1867 dbSNP
rs952273167 1873 dbSNP
rs545108904 1876 dbSNP
rs1365130013 1878 dbSNP
rs1273888730 1882 dbSNP
rs986106121 1884 dbSNP
rs1356083397 1885 dbSNP
rs1048707762 1892 dbSNP
rs910515458 1899 dbSNP
rs1406702960 1904 dbSNP
rs1177311412 1920 dbSNP
rs1481454715 1921 dbSNP
rs1423066936 1923 dbSNP
rs1190839051 1924 dbSNP
rs1007474634 1925 dbSNP
rs1235003715 1930 dbSNP
rs1018912788 1949 dbSNP
rs7229926 1957 dbSNP
rs1263642559 1958 dbSNP
rs1009369463 1960 dbSNP
rs1021219680 1965 dbSNP
rs967464535 1977 dbSNP
rs1224022654 1982 dbSNP
rs575672245 1996 dbSNP
rs1040498942 1998 dbSNP
rs1445756098 2017 dbSNP
rs1205517821 2019 dbSNP
rs913964200 2020 dbSNP
rs945253721 2026 dbSNP
rs1463766427 2034 dbSNP
rs190498550 2038 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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' gauucugguucGGA--GGAAGGGa 5'
                     |||  ||||||| 
Target 5' auuuuuuuuuuCCUCCCCUUCCCu 3'
1 - 24
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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000330513.5 | 3UTR | AUUUUUUUUUUCCUCCCCUUCCCUUUUUUUG
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
215 hsa-miR-4747-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061689 BTG2 BTG anti-proliferation factor 2 2 2
MIRT062834 BCL7A BCL tumor suppressor 7A 2 2
MIRT079371 CCDC137 coiled-coil domain containing 137 2 2
MIRT081190 MIDN midnolin 2 4
MIRT081724 ZNF507 zinc finger protein 507 2 2
MIRT110565 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT133724 SKI SKI proto-oncogene 2 4
MIRT146689 MINK1 misshapen like kinase 1 2 2
MIRT150676 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159196 NRBP1 nuclear receptor binding protein 1 2 2
MIRT180865 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT190659 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196111 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT232390 SP1 Sp1 transcription factor 2 2
MIRT331070 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT338632 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT407441 CTDSP1 CTD small phosphatase 1 2 2
MIRT444276 NKX6-1 NK6 homeobox 1 2 2
MIRT444834 PDE6D phosphodiesterase 6D 2 2
MIRT445452 EXT1 exostosin glycosyltransferase 1 2 2
MIRT445644 NPY4R neuropeptide Y receptor Y4 2 2
MIRT446157 RPL12 ribosomal protein L12 2 2
MIRT446608 HIP1 huntingtin interacting protein 1 2 2
MIRT447108 CLPX caseinolytic mitochondrial matrix peptidase chaperone subunit 2 2
MIRT449314 MRO maestro 2 2
MIRT450305 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT451245 ZNF444 zinc finger protein 444 2 2
MIRT451714 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451908 ILK integrin linked kinase 2 2
MIRT452183 KIAA1456 KIAA1456 2 2
MIRT452610 REPIN1 replication initiator 1 2 2
MIRT453422 GLG1 golgi glycoprotein 1 2 2
MIRT454006 ALKBH5 alkB homolog 5, RNA demethylase 2 2
MIRT455072 ARHGAP39 Rho GTPase activating protein 39 2 2
MIRT455319 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT455357 KDM5C lysine demethylase 5C 2 2
MIRT455589 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT455711 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT455860 TMEM254 transmembrane protein 254 2 2
MIRT455919 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT455946 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT456935 LRP10 LDL receptor related protein 10 2 2
MIRT457223 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT457431 NOL10 nucleolar protein 10 2 2
MIRT457470 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457907 ZNF212 zinc finger protein 212 2 2
MIRT458046 TSEN54 tRNA splicing endonuclease subunit 54 2 2
MIRT458073 RNLS renalase, FAD dependent amine oxidase 2 2
MIRT458234 NXPH3 neurexophilin 3 2 2
MIRT458307 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458378 ITM2C integral membrane protein 2C 2 2
MIRT458967 ZNF436 zinc finger protein 436 2 2
MIRT459099 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT459446 TMEM37 transmembrane protein 37 2 2
MIRT459671 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT460727 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT460744 SRP14 signal recognition particle 14 2 2
MIRT461531 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461752 DDX11 DEAD/H-box helicase 11 2 2
MIRT461837 F2RL3 F2R like thrombin or trypsin receptor 3 2 2
MIRT462019 RIF1 replication timing regulatory factor 1 2 2
MIRT462631 PHF5A PHD finger protein 5A 2 2
MIRT462772 ZNF8 zinc finger protein 8 2 2
MIRT463032 ZNF689 zinc finger protein 689 2 2
MIRT463886 WNT7B Wnt family member 7B 2 2
MIRT463995 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464371 URM1 ubiquitin related modifier 1 2 2
MIRT465342 TPM3 tropomyosin 3 2 4
MIRT465515 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465602 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT465697 TNPO2 transportin 2 2 10
MIRT466988 SSRP1 structure specific recognition protein 1 2 4
MIRT467630 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468132 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468322 SF3B3 splicing factor 3b subunit 3 2 2
MIRT468502 SESN2 sestrin 2 2 2
MIRT468881 RREB1 ras responsive element binding protein 1 2 2
MIRT469322 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469562 RARA retinoic acid receptor alpha 2 2
MIRT469898 PTRF caveolae associated protein 1 2 2
MIRT470045 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT470068 PTGES2 prostaglandin E synthase 2 2 2
MIRT470238 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470390 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT470500 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT470689 POLR2D RNA polymerase II subunit D 2 2
MIRT470704 POGK pogo transposable element derived with KRAB domain 2 2
MIRT471083 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 2 2
MIRT472482 NACC2 NACC family member 2 2 2
MIRT473583 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474554 KLHDC3 kelch domain containing 3 2 2
MIRT474651 KLF13 Kruppel like factor 13 2 2
MIRT474843 KHSRP KH-type splicing regulatory protein 2 2
MIRT474934 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475573 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 2
MIRT476045 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476080 GRB2 growth factor receptor bound protein 2 2 2
MIRT476440 GBA2 glucosylceramidase beta 2 2 2
MIRT476764 FOSL2 FOS like 2, AP-1 transcription factor subunit 2 2
MIRT478785 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479287 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT479505 CDH6 cadherin 6 2 2
MIRT479732 CCND1 cyclin D1 2 6
MIRT480352 C5orf24 chromosome 5 open reading frame 24 2 2
MIRT480407 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480859 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT481445 ARRB2 arrestin beta 2 2 2
MIRT481732 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT481824 AP2M1 adaptor related protein complex 2 mu 1 subunit 2 2
MIRT482566 ABHD2 abhydrolase domain containing 2 2 2
MIRT482607 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483144 SYCE1L synaptonemal complex central element protein 1 like 2 2
MIRT483214 APOA1 apolipoprotein A1 2 6
MIRT483878 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483917 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483939 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484420 SNX19 sorting nexin 19 2 2
MIRT484489 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484612 SIX3 SIX homeobox 3 2 6
MIRT484705 RNF11 ring finger protein 11 2 2
MIRT485107 SHISA6 shisa family member 6 2 2
MIRT485354 MYO1C myosin IC 2 4
MIRT485609 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT487311 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487417 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487695 CDK14 cyclin dependent kinase 14 2 2
MIRT487791 GPR20 G protein-coupled receptor 20 2 4
MIRT488042 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 2
MIRT488058 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 2
MIRT488237 DNLZ DNL-type zinc finger 2 4
MIRT488764 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489401 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489777 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490099 FN3K fructosamine 3 kinase 2 2
MIRT490290 ISL2 ISL LIM homeobox 2 2 2
MIRT490378 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491329 GFER growth factor, augmenter of liver regeneration 2 2
MIRT491435 MSX2 msh homeobox 2 2 2
MIRT491769 ZNF385A zinc finger protein 385A 2 2
MIRT491922 WNK2 WNK lysine deficient protein kinase 2 2 2
MIRT491983 UNK unkempt family zinc finger 2 2
MIRT492228 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492404 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT492767 PDGFB platelet derived growth factor subunit B 2 2
MIRT492966 NCS1 neuronal calcium sensor 1 2 2
MIRT493295 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT493650 HDLBP high density lipoprotein binding protein 2 2
MIRT493913 FAM127B retrotransposon Gag like 8A 2 4
MIRT495601 NKX2-5 NK2 homeobox 5 2 2
MIRT496875 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT498514 MYH14 myosin heavy chain 14 2 2
MIRT499178 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT502143 KIF5B kinesin family member 5B 2 8
MIRT502692 CSNK1G1 casein kinase 1 gamma 1 2 4
MIRT508460 HOXB6 homeobox B6 2 4
MIRT510430 ZNF207 zinc finger protein 207 2 6
MIRT511837 GPATCH8 G-patch domain containing 8 2 4
MIRT512368 CPM carboxypeptidase M 2 2
MIRT512506 BTBD19 BTB domain containing 19 2 2
MIRT513065 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513267 SCUBE1 signal peptide, CUB domain and EGF like domain containing 1 2 4
MIRT513575 EVX1 even-skipped homeobox 1 2 2
MIRT515051 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515790 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT521657 PRKD3 protein kinase D3 2 2
MIRT522679 LUZP1 leucine zipper protein 1 2 6
MIRT528845 RAB32 RAB32, member RAS oncogene family 2 2
MIRT533569 TOR1AIP1 torsin 1A interacting protein 1 2 2
MIRT543738 DHCR7 7-dehydrocholesterol reductase 2 2
MIRT544295 TSPYL1 TSPY like 1 2 2
MIRT544857 MYH2 myosin heavy chain 2 2 4
MIRT557323 HIATL1 major facilitator superfamily domain containing 14B 2 4
MIRT560522 TMEM98 transmembrane protein 98 2 2
MIRT561565 SLC6A9 solute carrier family 6 member 9 2 2
MIRT562374 ERI2 ERI1 exoribonuclease family member 2 2 2
MIRT565780 SEMA6D semaphorin 6D 2 2
MIRT569548 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569944 PRRT2 proline rich transmembrane protein 2 2 2
MIRT570016 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572163 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT572322 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573495 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574139 MARVELD1 MARVEL domain containing 1 2 2
MIRT609449 CCDC149 coiled-coil domain containing 149 2 2
MIRT610619 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT623355 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT629854 ACOX1 acyl-CoA oxidase 1 2 2
MIRT630516 CDC73 cell division cycle 73 2 2
MIRT632535 PSMB2 proteasome subunit beta 2 2 2
MIRT633975 SLC35E2 solute carrier family 35 member E2 2 2
MIRT636408 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT641722 LTBR lymphotoxin beta receptor 2 2
MIRT642661 RGS6 regulator of G protein signaling 6 2 2
MIRT649649 MAST3 microtubule associated serine/threonine kinase 3 2 2
MIRT650367 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT651355 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT664840 HUS1 HUS1 checkpoint clamp component 2 2
MIRT667322 MYH9 myosin heavy chain 9 2 2
MIRT670680 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT674922 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT675919 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT676493 GJD3 gap junction protein delta 3 2 2
MIRT680162 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT688008 GSN gelsolin 2 2
MIRT688997 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT700337 RAB4A RAB4A, member RAS oncogene family 2 2
MIRT701344 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT703519 FKBP15 FK506 binding protein 15 2 2
MIRT703901 EPT1 selenoprotein I 2 2
MIRT705565 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 2 2
MIRT709709 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT713108 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT718426 ZNF85 zinc finger protein 85 2 2
MIRT719236 CYSLTR2 cysteinyl leukotriene receptor 2 2 2
MIRT719326 STAC SH3 and cysteine rich domain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4747 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4747-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4747-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4747-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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