miRTarBase - #MIRT453760


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pre-miRNA Information
pre-miRNA hsa-mir-3689d-1   
Genomic Coordinates chr9: 134849609 - 134849682
Description Homo sapiens miR-3689d-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3689d-2   
Genomic Coordinates chr9: 134850277 - 134850356
Description Homo sapiens miR-3689d-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3689d
Sequence 2| GGGAGGUGUGAUCUCACACUCG |23
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs551722268 8 dbSNP
rs143142996 8 dbSNP
rs1236297052 12 dbSNP
rs573148947 14 dbSNP
rs1210004979 14 dbSNP
rs1217460444 14 dbSNP
rs762590109 18 dbSNP
rs574332265 18 dbSNP
rs1164353021 21 dbSNP
rs963741171 21 dbSNP
rs1177416877 22 dbSNP
rs765777344 22 dbSNP
Putative Targets

Gene Information
Gene Symbol RANGAP1   
Synonyms Fug1, RANGAP, SD
Description Ran GTPase activating protein 1
Transcript NM_002883   
Expression
Putative miRNA Targets on RANGAP1
3'UTR of RANGAP1
(miRNA target sites are highlighted)		 
>RANGAP1|NM_002883|3'UTR
   1 ACTCAAAGCCTCTCCCATCCCTTGGCCTGGACCAGTGAGCTGGGGAGGGACTCGGATGAACTGAGGCGCAGCCTACGCCA
  81 TTGCCTTGGACAGGACTCTGGCCACAGGCAGGGCGGGTCTGTGTCCCATGTGTCCTGTCAGTCCCCTGAGTATGTGTGTG
 161 GGTGTGGCGCATGTGCAGGTCTGTGCCTCCTGTCGGGATTTGGGTTTTAACGTCTTCTGCTGGCCCAGCCCTGCTCTGTT
 241 GTGGGGAGTTGGCCCCCAGGGGAAAGGGCTGTGAGCTGCTCCGCCATTAAACTCACCTCCACCTGAGGGCGCTCTGCTGA
 321 TCTCCGCCTGGGCCCTGATGGCCGTCCCCACCCACCTGCCTTCCGGCCCGGCTCCCTGGCGGAGCCAGAACCCAGGGAGT
 401 TGCCCGCGTGCTGTCCTTCCCCTCTGTGTTGTGATTGGGTTGTTTCCTGCCCTGCCTGGGGCTGCTTCTCGTCACCAAGC
 481 CCTGGTCCTGCGGCAGCTGTCACCCCTACCATCCATACCACTGTGCTGACCGCTCAGCCTGAAGAGCAGAGAATGCCATG
 561 GGTGGGACTGTGGGGGTCGGATCGTGGGGTTGTTGGCAGAGGGCAACCCTGGGCCCCACACCGTGTGGACAGGCAGACAC
 641 CAGATTGTCCAGGAGCAGGAGCTGCTGGGACTGCGCTGGCCCCGGACCTAGTGGGCCTTCTCCTGGCTGCTGAGATGTCG
 721 TCTGTGACTGGCCTGGCTGGAGGGGGAGTGTTGACAACCCAAAGCTGTTCTCCAGTCTGGGGAGGGAGAGGCAGGGTCCC
 801 CAATGTCCGAGCTGCATCTGGACGCTGCTCTTAAAGGACCTCCTGGGGCAGGGGAGCGGTAGGGTCTGGACTGGGCAGAT
 881 GCTGTATGACCTCCCTGAGCACCCGTGACTGCCCCATGCTTTCCCCTTTGTGCTCTGTGTGTGTCTGGGCTGTGCCCGGG
 961 GGCTTCACAAATAAAGTCGTGTGGCAGCTTCAGAGACTCAGAAACTCTCACTGAAAGCGGGATAGTCTCGGGGGCCGTTG
1041 TACGTGGAGTCCCACCTCGGCAGAGCATGCGGCCCCGCAGCAGTCTGTGGGGCAGTCAGCCCTGCAGAAGGGCCCGGCCT
1121 CGGCCTCAGGCCACTACCTGGGAAGTGGCAGTCCTGAGTGGGGGCCCATTTTCCTGCCTGGCCACACCTCACCCAGCACC
1201 CTGCCTTTGGGCTGCAGCTCGCTTGGCTTCTGCGTTGCTCCTTCACTATGGAAGCCACCTCCCTTGGGATCCTTTGCTCC
1281 ACTGCCACATATGTGAGGACAGCCCAGCCAACCTTCCTTACCTCCTACCCTACACCATGTATGTGCTTTGGGAGCCCATG
1361 TCCCCCACAAACGGCCTCCAAGAAGTCCCTCCAAGGTTTCTTAGAGGGCAATATTTTCTCATTGGCAGTCGGCCACGTAG
1441 GTGACCAGGTGGCAGAGGATACTGCTGGCCCTGTCCCCTGTCTTCTGTGTGAGTTGATACGGTAGGGGGTGGGTGTGGGG
1521 CTGGCATTAAGTTCTGATGCCAGCTACAACGTGGATGAACTTTGAAAACATGTTAAATGAAATAAGCCAGACACAAAAGG
1601 ACAAATATGATTCCATTTAGATGAGGCATCTAGAATAAGCAAATTCAGAGACAAGAAGGTAGAGGTTGCCAGGGCTAGGG
1681 GAAGGGTGGAATAGGGAGTGAGGCTGCAAACAGATTCTCTGGGATGATGAAGATGTTCTGGAAATGGAGAGTGGTGATGG
1761 TTGCATAACATTGTGAATGTACTTAATGCACTGAATTGTACACATAAAAATGGTTAAAATGATAGAAAAAAAAAAAAAA
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' gcUCACACUCUAGUGUGGAGGg 5'
            | | ||: | | ||||||| 
Target 5' tcACTATGGAAGC-CACCTCCc 3'
 1243 - 1263 151.00 -16.90
2 
miRNA  3' gcucACACUC----------UAGU----GUGGAGGg 5'
              ||||||          ||:|    ||||||| 
Target 5' gggcTGTGAGCTGCTCCGCCATTAAACTCACCTCCa 3'
 266 - 301 146.00 -21.20
3 
miRNA  3' gcucaCACUCUAGUGUGGAGgg 5'
               |||: :|| ||||||  
Target 5' tgtacGTGGAGTCCCACCTCgg 3'
 1039 - 1060 141.00 -15.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN15626085 2 COSMIC
COSN30547721 7 COSMIC
COSN231159 24 COSMIC
COSN30510263 30 COSMIC
COSN30136973 36 COSMIC
COSN30135693 67 COSMIC
COSN31564311 68 COSMIC
COSN31959848 76 COSMIC
COSN31586100 168 COSMIC
COSN9166367 376 COSMIC
COSN26323132 481 COSMIC
COSN17005111 623 COSMIC
COSN25906040 805 COSMIC
COSN20650317 815 COSMIC
COSN32063642 928 COSMIC
COSN31961982 941 COSMIC
rs3171692 395 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs776261990 2 dbSNP
rs1345497058 4 dbSNP
rs768691544 8 dbSNP
rs1249057284 9 dbSNP
rs1055919032 10 dbSNP
rs1195791455 12 dbSNP
rs372644088 17 dbSNP
rs1386605684 19 dbSNP
rs779779748 22 dbSNP
rs1448565580 23 dbSNP
rs771712470 24 dbSNP
rs979166295 29 dbSNP
rs370550540 30 dbSNP
rs1486403016 32 dbSNP
rs778657857 36 dbSNP
rs1220937495 37 dbSNP
rs1490978005 38 dbSNP
rs756829159 43 dbSNP
rs1221043738 53 dbSNP
rs1264084373 62 dbSNP
rs1318488608 63 dbSNP
rs950055457 67 dbSNP
rs557412992 68 dbSNP
rs917349786 70 dbSNP
rs1247946500 73 dbSNP
rs913769544 76 dbSNP
rs1186102399 77 dbSNP
rs1415275554 86 dbSNP
rs539022421 99 dbSNP
rs987954175 100 dbSNP
rs989275415 101 dbSNP
rs965823256 105 dbSNP
rs956213028 108 dbSNP
rs926136587 111 dbSNP
rs978915219 114 dbSNP
rs571505287 115 dbSNP
rs1360470746 119 dbSNP
rs953245929 129 dbSNP
rs1027357583 132 dbSNP
rs546983348 135 dbSNP
rs1310832727 137 dbSNP
rs898078378 148 dbSNP
rs1229362019 156 dbSNP
rs534776259 162 dbSNP
rs1014442526 167 dbSNP
rs1159446788 168 dbSNP
rs142951047 169 dbSNP
rs139374732 170 dbSNP
rs1189449972 171 dbSNP
rs745478746 173 dbSNP
rs529878660 178 dbSNP
rs1238710897 181 dbSNP
rs1483259405 186 dbSNP
rs373963890 194 dbSNP
rs568808714 195 dbSNP
rs9611526 196 dbSNP
rs1203308516 201 dbSNP
rs3180782 208 dbSNP
rs757514891 211 dbSNP
rs993230119 212 dbSNP
rs1261066765 213 dbSNP
rs1243729959 214 dbSNP
rs780074492 219 dbSNP
rs532443949 233 dbSNP
rs898906427 234 dbSNP
rs1359829126 255 dbSNP
rs1037531334 262 dbSNP
rs1001991195 270 dbSNP
rs1301357380 272 dbSNP
rs905112493 276 dbSNP
rs564689535 278 dbSNP
rs540244285 282 dbSNP
rs528174736 283 dbSNP
rs1288157494 286 dbSNP
rs1327442872 288 dbSNP
rs1221451446 289 dbSNP
rs1339938148 292 dbSNP
rs561001755 294 dbSNP
rs946015708 308 dbSNP
rs1316892521 310 dbSNP
rs1225982493 311 dbSNP
rs1384397706 321 dbSNP
rs950094713 323 dbSNP
rs1386254985 325 dbSNP
rs73428601 326 dbSNP
rs1250805627 327 dbSNP
rs1053109303 330 dbSNP
rs1471454133 335 dbSNP
rs934764249 338 dbSNP
rs988045915 342 dbSNP
rs944606832 343 dbSNP
rs926022508 344 dbSNP
rs1475286908 347 dbSNP
rs767002434 348 dbSNP
rs985919005 353 dbSNP
rs958831014 356 dbSNP
rs953162488 360 dbSNP
rs978927098 361 dbSNP
rs1448682379 363 dbSNP
rs1275998276 364 dbSNP
rs1367485831 365 dbSNP
rs778184519 367 dbSNP
rs1262289208 369 dbSNP
rs964838317 370 dbSNP
rs961984713 376 dbSNP
rs1466962452 379 dbSNP
rs1275363658 380 dbSNP
rs910817949 381 dbSNP
rs1247021233 382 dbSNP
rs1317427713 387 dbSNP
rs1189332777 389 dbSNP
rs3171692 395 dbSNP
rs752829724 403 dbSNP
rs954964883 404 dbSNP
rs1026427851 405 dbSNP
rs773739578 406 dbSNP
rs767739376 407 dbSNP
rs1349619822 413 dbSNP
rs1434951275 415 dbSNP
rs1300371234 416 dbSNP
rs1034527429 419 dbSNP
rs1296480675 421 dbSNP
rs1337067848 423 dbSNP
rs557534354 425 dbSNP
rs963138419 429 dbSNP
rs1397137164 430 dbSNP
rs141198880 431 dbSNP
rs1002070144 435 dbSNP
rs767576320 436 dbSNP
rs904625353 437 dbSNP
rs112952942 443 dbSNP
rs1395254255 454 dbSNP
rs1371354172 456 dbSNP
rs1165680661 460 dbSNP
rs1002002471 463 dbSNP
rs545336226 470 dbSNP
rs904997540 471 dbSNP
rs1046330179 479 dbSNP
rs891819760 480 dbSNP
rs1452389658 483 dbSNP
rs1041021120 490 dbSNP
rs944659274 491 dbSNP
rs1284415187 492 dbSNP
rs1355467071 493 dbSNP
rs1231188133 494 dbSNP
rs1269989152 499 dbSNP
rs911776292 500 dbSNP
rs1013946622 504 dbSNP
rs371660618 508 dbSNP
rs1053147027 510 dbSNP
rs1444144680 513 dbSNP
rs186662503 518 dbSNP
rs1188578901 520 dbSNP
rs1340137215 526 dbSNP
rs1255992823 528 dbSNP
rs182065081 531 dbSNP
rs1444733276 532 dbSNP
rs1043132874 535 dbSNP
rs943535515 539 dbSNP
rs1457182744 542 dbSNP
rs920368384 558 dbSNP
rs973587908 562 dbSNP
rs879073166 563 dbSNP
rs1304650937 567 dbSNP
rs961790019 575 dbSNP
rs55963927 578 dbSNP
rs529686492 579 dbSNP
rs907576014 583 dbSNP
rs1334805012 584 dbSNP
rs1326432723 585 dbSNP
rs534756849 587 dbSNP
rs35721033 590 dbSNP
rs1258879716 595 dbSNP
rs1347299799 598 dbSNP
rs987643830 603 dbSNP
rs1255499207 604 dbSNP
rs567410846 615 dbSNP
rs960283164 617 dbSNP
rs933602505 622 dbSNP
rs1953 623 dbSNP
rs1180373908 631 dbSNP
rs1379851099 632 dbSNP
rs1396558011 634 dbSNP
rs971707738 635 dbSNP
rs1172992302 641 dbSNP
rs962982449 661 dbSNP
rs1467174527 665 dbSNP
rs1015981511 672 dbSNP
rs980467352 673 dbSNP
rs969148911 674 dbSNP
rs1469386619 675 dbSNP
rs1010775883 677 dbSNP
rs1231451662 680 dbSNP
rs891873435 681 dbSNP
rs73885753 683 dbSNP
rs761451831 684 dbSNP
rs1208753858 685 dbSNP
rs1207637418 688 dbSNP
rs1275619800 689 dbSNP
rs568916592 691 dbSNP
rs1482958784 692 dbSNP
rs1350715853 694 dbSNP
rs1281583953 700 dbSNP
rs1434281024 705 dbSNP
rs890390837 710 dbSNP
rs1393969079 714 dbSNP
rs550764052 719 dbSNP
rs1030887124 720 dbSNP
rs1277453876 723 dbSNP
rs931904411 723 dbSNP
rs1392533594 725 dbSNP
rs1387294737 727 dbSNP
rs998867407 743 dbSNP
rs1368958410 749 dbSNP
rs532276809 762 dbSNP
rs1037533420 774 dbSNP
rs1043058632 777 dbSNP
rs940430439 781 dbSNP
rs943477800 782 dbSNP
rs1202640926 793 dbSNP
rs971658816 797 dbSNP
rs907585623 803 dbSNP
rs992515002 807 dbSNP
rs776647322 808 dbSNP
rs1189913837 809 dbSNP
rs1412310774 812 dbSNP
rs1377215364 814 dbSNP
rs571543946 815 dbSNP
rs57712473 823 dbSNP
rs933465893 824 dbSNP
rs1167806944 825 dbSNP
rs1370032931 836 dbSNP
rs980787299 838 dbSNP
rs1325181290 839 dbSNP
rs1392168877 840 dbSNP
rs1405481771 843 dbSNP
rs773874577 852 dbSNP
rs1437122744 854 dbSNP
rs919518680 855 dbSNP
rs11913689 856 dbSNP
rs528135725 857 dbSNP
rs560964951 858 dbSNP
rs760687346 859 dbSNP
rs1417364091 862 dbSNP
rs540528989 869 dbSNP
rs1244480918 874 dbSNP
rs1271883286 889 dbSNP
rs573520424 890 dbSNP
rs1486659331 893 dbSNP
rs1258915428 896 dbSNP
rs542700457 900 dbSNP
rs1215667717 901 dbSNP
rs969580422 902 dbSNP
rs1248119397 903 dbSNP
rs187859921 904 dbSNP
rs771687486 911 dbSNP
rs1257792577 912 dbSNP
rs1163970461 913 dbSNP
rs956536539 915 dbSNP
rs1458759008 924 dbSNP
rs1159744491 925 dbSNP
rs1428719925 926 dbSNP
rs1304851985 930 dbSNP
rs1380134397 933 dbSNP
rs146895453 935 dbSNP
rs1019633987 945 dbSNP
rs1000806831 946 dbSNP
rs1292230219 957 dbSNP
rs183174209 958 dbSNP
rs1315850836 961 dbSNP
rs1213005083 965 dbSNP
rs1021669335 970 dbSNP
rs1028305718 972 dbSNP
rs774931759 976 dbSNP
rs745557535 978 dbSNP
rs773835727 979 dbSNP
rs889202944 988 dbSNP
rs996531891 991 dbSNP
rs1473445329 996 dbSNP
rs1051823749 1001 dbSNP
rs1407124471 1002 dbSNP
rs1399080032 1003 dbSNP
rs1037942209 1006 dbSNP
rs1359772508 1008 dbSNP
rs564519571 1009 dbSNP
rs1434352206 1010 dbSNP
rs1161114535 1016 dbSNP
rs940482695 1018 dbSNP
rs933499882 1019 dbSNP
rs1410788073 1022 dbSNP
rs1056932581 1027 dbSNP
rs897976037 1029 dbSNP
rs1371835386 1030 dbSNP
rs1221393845 1034 dbSNP
rs578172576 1036 dbSNP
rs6002298 1037 dbSNP
rs909462399 1043 dbSNP
rs1045126798 1044 dbSNP
rs947709673 1057 dbSNP
rs947632361 1058 dbSNP
rs917670356 1059 dbSNP
rs1163034326 1061 dbSNP
rs1476252573 1063 dbSNP
rs1418641953 1068 dbSNP
rs991898233 1070 dbSNP
rs575316078 1071 dbSNP
rs573651082 1076 dbSNP
rs1192791926 1077 dbSNP
rs1426031743 1078 dbSNP
rs1019727320 1081 dbSNP
rs555350258 1083 dbSNP
rs1372618072 1085 dbSNP
rs1216977573 1088 dbSNP
rs1328635576 1090 dbSNP
rs986869462 1097 dbSNP
rs979251156 1112 dbSNP
rs967995667 1115 dbSNP
rs537110517 1121 dbSNP
rs899096890 1122 dbSNP
rs1016156707 1136 dbSNP
rs1300869116 1158 dbSNP
rs1336371954 1164 dbSNP
rs375930033 1165 dbSNP
rs1343887299 1168 dbSNP
rs1214755639 1171 dbSNP
rs1018164824 1174 dbSNP
rs1435852892 1182 dbSNP
rs1223761591 1193 dbSNP
rs1253513389 1194 dbSNP
rs1468128933 1199 dbSNP
rs1007981052 1215 dbSNP
rs953378028 1218 dbSNP
rs371174688 1220 dbSNP
rs1450326378 1221 dbSNP
rs1271799260 1223 dbSNP
rs748620053 1225 dbSNP
rs557009492 1233 dbSNP
rs1393422674 1234 dbSNP
rs1324831519 1240 dbSNP
rs897902459 1248 dbSNP
rs1439284044 1249 dbSNP
rs1036525173 1257 dbSNP
rs1006303935 1261 dbSNP
rs1324199025 1275 dbSNP
rs1463235646 1279 dbSNP
rs1366658434 1288 dbSNP
rs570153142 1289 dbSNP
rs1395449262 1292 dbSNP
rs117983667 1296 dbSNP
rs1269224891 1296 dbSNP
rs1045290667 1298 dbSNP
rs1169832408 1305 dbSNP
rs9637339 1325 dbSNP
rs1273524358 1330 dbSNP
rs1408222208 1332 dbSNP
rs1044454845 1334 dbSNP
rs567364018 1338 dbSNP
rs780485954 1339 dbSNP
rs1447646068 1358 dbSNP
rs914822058 1362 dbSNP
rs1056520887 1368 dbSNP
rs1474008557 1370 dbSNP
rs6002297 1372 dbSNP
rs1187612592 1373 dbSNP
rs562754629 1377 dbSNP
rs751813958 1379 dbSNP
rs1390287514 1382 dbSNP
rs1251497682 1392 dbSNP
rs1382266965 1396 dbSNP
rs1195834792 1410 dbSNP
rs571444094 1411 dbSNP
rs967840031 1422 dbSNP
rs1265591297 1430 dbSNP
rs1231434820 1431 dbSNP
rs912768957 1433 dbSNP
rs911142955 1436 dbSNP
rs6002296 1437 dbSNP
rs955453633 1440 dbSNP
rs534921594 1441 dbSNP
rs1444377946 1443 dbSNP
rs1030363080 1445 dbSNP
rs962774118 1448 dbSNP
rs1229029737 1450 dbSNP
rs997920321 1459 dbSNP
rs780084513 1462 dbSNP
rs567230951 1465 dbSNP
rs756986914 1467 dbSNP
rs1453613386 1470 dbSNP
rs1442751472 1471 dbSNP
rs549015382 1476 dbSNP
rs1382056042 1479 dbSNP
rs1415829092 1480 dbSNP
rs1297810217 1483 dbSNP
rs950607189 1485 dbSNP
rs1290194510 1491 dbSNP
rs1035529813 1500 dbSNP
rs1336304462 1500 dbSNP
rs1006356417 1501 dbSNP
rs905625442 1510 dbSNP
rs1044121986 1513 dbSNP
rs1171789743 1514 dbSNP
rs1484923705 1517 dbSNP
rs1207766594 1526 dbSNP
rs1379180843 1530 dbSNP
rs758635155 1543 dbSNP
rs1393765058 1546 dbSNP
rs1361616496 1550 dbSNP
rs887921079 1554 dbSNP
rs1011728219 1555 dbSNP
rs1045621369 1558 dbSNP
rs1374458229 1561 dbSNP
rs1432431797 1562 dbSNP
rs1299699592 1571 dbSNP
rs753644433 1572 dbSNP
rs763951476 1578 dbSNP
rs1396865173 1584 dbSNP
rs1390762583 1587 dbSNP
rs186968705 1599 dbSNP
rs1332947316 1607 dbSNP
rs1267680258 1608 dbSNP
rs1176259484 1609 dbSNP
rs1218459247 1615 dbSNP
rs1302699712 1616 dbSNP
rs1346030269 1619 dbSNP
rs1230797639 1625 dbSNP
rs563426992 1627 dbSNP
rs1479401670 1630 dbSNP
rs1480500926 1633 dbSNP
rs1194656317 1638 dbSNP
rs1270061491 1640 dbSNP
rs1469460930 1656 dbSNP
rs1193745958 1659 dbSNP
rs896722075 1666 dbSNP
rs767167696 1668 dbSNP
rs934923602 1669 dbSNP
rs1373490947 1672 dbSNP
rs1461292682 1676 dbSNP
rs912776027 1683 dbSNP
rs1051223440 1689 dbSNP
rs1396624242 1691 dbSNP
rs932807839 1695 dbSNP
rs141090986 1698 dbSNP
rs1325304007 1702 dbSNP
rs1368801331 1703 dbSNP
rs1205208165 1714 dbSNP
rs921421552 1727 dbSNP
rs533620137 1735 dbSNP
rs1225676564 1744 dbSNP
rs1278027250 1746 dbSNP
rs1056172149 1749 dbSNP
rs758902325 1752 dbSNP
rs1312554390 1754 dbSNP
rs6002295 1757 dbSNP
rs1187969062 1759 dbSNP
rs1261968269 1761 dbSNP
rs541286064 1770 dbSNP
rs1427504168 1773 dbSNP
rs574007715 1774 dbSNP
rs1190799317 1780 dbSNP
rs1389866389 1782 dbSNP
rs1375736960 1786 dbSNP
rs946551286 1787 dbSNP
rs911083007 1798 dbSNP
rs1164107663 1803 dbSNP
rs908579930 1805 dbSNP
rs1455380543 1822 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' gcucacacucUAGUGUGGAGGg 5'
                    | | ||||||| 
Target 5' ----ccauuaAACUCACCUCCa 3'
 		1 - 18
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 ENST00000405486.1 | 3UTR | CCAUUAAACUCACCUCCACCUG
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
231 hsa-miR-3689d Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059166 TXNIP thioredoxin interacting protein 2 4
MIRT080699 KIAA1468 KIAA1468 2 2
MIRT218770 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT278059 KHNYN KH and NYN domain containing 2 2
MIRT345933 EIF4A1 eukaryotic translation initiation factor 4A1 2 2
MIRT366238 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT449689 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT451149 C19orf53 chromosome 19 open reading frame 53 2 2
MIRT451266 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT451375 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451570 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451585 HIRIP3 HIRA interacting protein 3 2 2
MIRT451614 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT451763 ZNF611 zinc finger protein 611 2 6
MIRT452383 LY6E lymphocyte antigen 6 family member E 2 4
MIRT452573 ZFP69B ZFP69 zinc finger protein B 2 2
MIRT452735 PTGES3L prostaglandin E synthase 3 like 2 6
MIRT452867 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT452975 CABP4 calcium binding protein 4 2 2
MIRT453215 CERS1 ceramide synthase 1 2 2
MIRT453259 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT453449 GLG1 golgi glycoprotein 1 2 2
MIRT453479 PITPNM3 PITPNM family member 3 2 2
MIRT453663 CD207 CD207 molecule 2 6
MIRT453724 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 2 2
MIRT453760 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT454181 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454330 PPARA peroxisome proliferator activated receptor alpha 2 2
MIRT454338 CDKL1 cyclin dependent kinase like 1 2 2
MIRT454427 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454665 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT454825 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455130 TBC1D25 TBC1 domain family member 25 2 2
MIRT455166 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT455416 RXRB retinoid X receptor beta 2 2
MIRT455668 GLO1 glyoxalase I 2 2
MIRT455999 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 2
MIRT456446 TMEM81 transmembrane protein 81 2 2
MIRT456642 NOS1AP nitric oxide synthase 1 adaptor protein 2 2
MIRT456728 TMEM239 transmembrane protein 239 2 2
MIRT457131 ASPH aspartate beta-hydroxylase 2 2
MIRT457157 MXRA7 matrix remodeling associated 7 2 2
MIRT457358 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457458 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT457619 UPK3BL uroplakin 3B like 1 2 2
MIRT457692 ZNF587 zinc finger protein 587 2 2
MIRT457727 SMOX spermine oxidase 2 2
MIRT457788 VWA1 von Willebrand factor A domain containing 1 2 2
MIRT457875 THEM6 thioesterase superfamily member 6 2 4
MIRT457909 ZNF212 zinc finger protein 212 2 2
MIRT458395 ABCF1 ATP binding cassette subfamily F member 1 2 2
MIRT458496 MARVELD2 MARVEL domain containing 2 2 2
MIRT458544 CYP2B6 cytochrome P450 family 2 subfamily B member 6 2 2
MIRT458577 TCOF1 treacle ribosome biogenesis factor 1 2 2
MIRT458732 CES2 carboxylesterase 2 2 2
MIRT458814 ZNF843 zinc finger protein 843 2 2
MIRT458931 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459341 ZNF17 zinc finger protein 17 2 2
MIRT459365 MPLKIP M-phase specific PLK1 interacting protein 2 6
MIRT459572 NLGN2 neuroligin 2 2 2
MIRT460015 DTX3L deltex E3 ubiquitin ligase 3L 2 4
MIRT460144 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460653 IGFBP4 insulin like growth factor binding protein 4 2 2
MIRT460798 VPS33A VPS33A, CORVET/HOPS core subunit 2 2
MIRT461058 KCNK6 potassium two pore domain channel subfamily K member 6 2 4
MIRT461458 SLC19A3 solute carrier family 19 member 3 2 2
MIRT461572 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461927 TNFSF14 TNF superfamily member 14 2 2
MIRT461953 C3 complement C3 2 2
MIRT462278 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT462744 EFNB1 ephrin B1 2 2
MIRT463136 ZNF451 zinc finger protein 451 2 4
MIRT463566 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT463866 WNT7B Wnt family member 7B 2 2
MIRT464326 UST uronyl 2-sulfotransferase 2 2
MIRT464796 UBE2F ubiquitin conjugating enzyme E2 F (putative) 2 2
MIRT465034 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT466207 TMED10 transmembrane p24 trafficking protein 10 2 2
MIRT467007 SSBP2 single stranded DNA binding protein 2 2 2
MIRT467029 SRSF1 serine and arginine rich splicing factor 1 2 4
MIRT468001 SKI SKI proto-oncogene 2 2
MIRT468031 SIKE1 suppressor of IKBKE 1 2 6
MIRT468575 SERBP1 SERPINE1 mRNA binding protein 1 2 6
MIRT468834 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT468970 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT469450 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT470888 PLXND1 plexin D1 2 2
MIRT470953 PKM pyruvate kinase, muscle 2 2
MIRT471828 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472590 NACC1 nucleus accumbens associated 1 2 2
MIRT472805 MTMR12 myotubularin related protein 12 2 2
MIRT472818 MTMR10 myotubularin related protein 10 2 6
MIRT472914 MSN moesin 2 2
MIRT474558 KLHDC3 kelch domain containing 3 2 2
MIRT474716 KIF13A kinesin family member 13A 2 6
MIRT475279 TOR1AIP2 torsin 1A interacting protein 2 2 2
MIRT475300 IFNLR1 interferon lambda receptor 1 2 2
MIRT475759 HDLBP high density lipoprotein binding protein 2 2
MIRT475786 HDGF heparin binding growth factor 2 2
MIRT475933 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476212 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT476238 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 2 4
MIRT476799 FNDC3B fibronectin type III domain containing 3B 2 2
MIRT477988 DNAL1 dynein axonemal light chain 1 2 2
MIRT478317 DDN dendrin 2 2
MIRT479257 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT479344 CEP97 centrosomal protein 97 2 2
MIRT479522 CDCA4 cell division cycle associated 4 2 2
MIRT479906 CCDC117 coiled-coil domain containing 117 2 6
MIRT481147 AVL9 AVL9 cell migration associated 2 6
MIRT481735 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482089 ALG8 ALG8, alpha-1,3-glucosyltransferase 2 2
MIRT482389 AEN apoptosis enhancing nuclease 2 2
MIRT483093 TFPI tissue factor pathway inhibitor 2 2
MIRT484246 ANK1 ankyrin 1 2 2
MIRT484342 EPN1 epsin 1 2 4
MIRT489141 C5orf38 chromosome 5 open reading frame 38 2 2
MIRT489163 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489547 SOX11 SRY-box 11 2 4
MIRT489780 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489799 KRT80 keratin 80 2 6
MIRT490535 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT492198 SOCS1 suppressor of cytokine signaling 1 2 2
MIRT492283 SHISA6 shisa family member 6 2 4
MIRT501059 SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 2 4
MIRT501094 SLC5A6 solute carrier family 5 member 6 2 4
MIRT503870 CBS cystathionine-beta-synthase 2 2
MIRT507981 BCL2L13 BCL2 like 13 2 4
MIRT508125 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT508205 SLC35E1 solute carrier family 35 member E1 2 2
MIRT508385 SPTBN2 spectrin beta, non-erythrocytic 2 2 4
MIRT510308 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT510462 ZDHHC18 zinc finger DHHC-type containing 18 2 2
MIRT512227 ATXN3 ataxin 3 2 8
MIRT512665 STEAP3 STEAP3 metalloreductase 2 2
MIRT514184 PGPEP1 pyroglutamyl-peptidase I 2 2
MIRT515053 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515138 ZNF799 zinc finger protein 799 2 4
MIRT515452 ZNF747 zinc finger protein 747 2 2
MIRT515791 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT515905 AGTPBP1 ATP/GTP binding protein 1 2 2
MIRT516129 MRPS16 mitochondrial ribosomal protein S16 2 6
MIRT516679 ZNF860 zinc finger protein 860 2 4
MIRT516750 ZNF100 zinc finger protein 100 2 2
MIRT516971 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT517491 NPAP1 nuclear pore associated protein 1 2 2
MIRT517774 PROM2 prominin 2 2 2
MIRT517938 ZNF431 zinc finger protein 431 2 4
MIRT518386 ZNF250 zinc finger protein 250 2 2
MIRT520621 TMEM41B transmembrane protein 41B 2 2
MIRT521028 SLC30A5 solute carrier family 30 member 5 2 2
MIRT521454 RAD51 RAD51 recombinase 2 2
MIRT521564 PTPLB 3-hydroxyacyl-CoA dehydratase 2 1 1
MIRT521581 PTBP2 polypyrimidine tract binding protein 2 2 2
MIRT522263 NKRF NFKB repressing factor 2 2
MIRT522410 MXI1 MAX interactor 1, dimerization protein 2 2
MIRT522543 MED28 mediator complex subunit 28 2 6
MIRT522915 KCNE3 potassium voltage-gated channel subfamily E regulatory subunit 3 2 2
MIRT523029 IGF1 insulin like growth factor 1 2 2
MIRT523854 ESPL1 extra spindle pole bodies like 1, separase 2 4
MIRT524184 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT524520 CDK19 cyclin dependent kinase 19 2 2
MIRT524674 C12orf5 TP53 induced glycolysis regulatory phosphatase 2 2
MIRT530257 ZNF620 zinc finger protein 620 2 2
MIRT540691 BMP3 bone morphogenetic protein 3 2 2
MIRT540976 C17orf85 nuclear cap binding subunit 3 2 2
MIRT545505 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT545631 GGCX gamma-glutamyl carboxylase 2 2
MIRT547358 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT550701 MPL MPL proto-oncogene, thrombopoietin receptor 2 4
MIRT550717 PMPCA peptidase, mitochondrial processing alpha subunit 2 4
MIRT551203 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT553999 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 2 4
MIRT561081 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT563523 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT564463 SLC35E2 solute carrier family 35 member E2 2 2
MIRT565233 TRAF6 TNF receptor associated factor 6 2 2
MIRT566618 NKAP NFKB activating protein 2 2
MIRT569527 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569639 QPCT glutaminyl-peptide cyclotransferase 2 2
MIRT570253 SSPN sarcospan 2 2
MIRT570570 OTUD7B OTU deubiquitinase 7B 2 2
MIRT570621 MTF2 metal response element binding transcription factor 2 2 2
MIRT571098 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 2
MIRT575196 Entpd4 ectonucleoside triphosphate diphosphohydrolase 4 2 2
MIRT575554 Cd99 CD99 antigen 2 2
MIRT575634 Gnl3l guanine nucleotide binding protein-like 3 (nucleolar)-like 2 2
MIRT608267 NOP14 NOP14 nucleolar protein 2 2
MIRT609314 FXYD6 FXYD domain containing ion transport regulator 6 2 2
MIRT627670 RPL28 ribosomal protein L28 2 2
MIRT631185 TSPAN14 tetraspanin 14 2 2
MIRT631964 YIPF5 Yip1 domain family member 5 2 2
MIRT632885 GINM1 glycoprotein integral membrane 1 2 2
MIRT642618 CDKN3 cyclin dependent kinase inhibitor 3 2 2
MIRT645609 TSPAN6 tetraspanin 6 2 2
MIRT662227 PGBD4 piggyBac transposable element derived 4 2 2
MIRT662329 MYLK3 myosin light chain kinase 3 2 2
MIRT662725 LRRC3C leucine rich repeat containing 3C 2 2
MIRT665520 USP14 ubiquitin specific peptidase 14 2 2
MIRT666634 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT668969 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT670925 DESI1 desumoylating isopeptidase 1 2 2
MIRT673939 ZNF500 zinc finger protein 500 2 2
MIRT674675 PLCE1 phospholipase C epsilon 1 2 2
MIRT675230 MAK male germ cell associated kinase 2 2
MIRT680864 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT681047 ZDBF2 zinc finger DBF-type containing 2 2 2
MIRT681105 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT683553 HAVCR1 hepatitis A virus cellular receptor 1 2 2
MIRT684508 C1orf174 chromosome 1 open reading frame 174 2 2
MIRT684812 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT685981 CCDC77 coiled-coil domain containing 77 2 2
MIRT686709 TBC1D19 TBC1 domain family member 19 2 2
MIRT686867 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688908 C11orf84 chromosome 11 open reading frame 84 2 2
MIRT691208 KLHL30 kelch like family member 30 2 2
MIRT692298 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT694380 MTA1 metastasis associated 1 2 2
MIRT696497 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT700686 POLR3D RNA polymerase III subunit D 2 2
MIRT701088 PAPOLG poly(A) polymerase gamma 2 2
MIRT703373 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT706189 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT706648 SMIM19 small integral membrane protein 19 2 2
MIRT709466 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT709699 DMWD DM1 locus, WD repeat containing 2 2
MIRT710693 LYRM4 LYR motif containing 4 2 2
MIRT713457 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT722409 RARS2 arginyl-tRNA synthetase 2, mitochondrial 2 2
MIRT725391 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT725548 DNMT3A DNA methyltransferase 3 alpha 2 2

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