pre-miRNA Information
pre-miRNA hsa-mir-6787   
Genomic Coordinates chr17: 82236668 - 82236728
Description Homo sapiens miR-6787 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6787-5p
Sequence 6| UGGCGGGGGUAGAGCUGGCUGC |27
Evidence Experimental
Experiments Meta-analysis
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs778888046 4 dbSNP
rs772018061 5 dbSNP
rs760886644 6 dbSNP
rs776925052 7 dbSNP
rs760060985 8 dbSNP
rs1432528063 9 dbSNP
rs778772390 10 dbSNP
rs924024166 11 dbSNP
rs201523090 13 dbSNP
rs1451075810 17 dbSNP
rs1378844609 18 dbSNP
Putative Targets

Gene Information
Gene Symbol NEUROD2   
Synonyms NDRF, bHLHa1
Description neuronal differentiation 2
Transcript NM_006160   
Expression
Putative miRNA Targets on NEUROD2
3'UTR of NEUROD2
(miRNA target sites are highlighted)
>NEUROD2|NM_006160|3'UTR
   1 GACTTCGCGCCGGCTCCCTTCTTTTTCTTTTGCCTTTGCCCGCCCCCCTGTCCCCAGCCCCCAGAGCGCAGGGACACCCC
  81 CATCCTACCCCGGCGCCGGGCGCGGGGAGCGGGCCACCGGTCCTGCCGCTCTCCTGGGGCAGCGCAGTCCTGTTACCTGT
 161 GGGTGGCCTGTCCCAGGGGCCTCGCTTCCCCCAGGGGACTCGCCTTCTCTCTCCCCAAGGGGTTCCCTCCTCCTCTCTCC
 241 CAAGGAGTGCTTCTCCAGGGACCTCTCTCCGGGGGCTCCCTGGAGGCACCCCTCCCCCATTCCCAATATCTTCGCTGAGG
 321 TTTCCTCCTCCCCCTCCTCCCTGCAGGCCCAAGGCGTTGGTAAGGGGGCAGCTGAGCAATGGAACGCGTTTCCCCCTCTC
 401 ATTATTATTTTAAAAACAGACACCCAGCTGCCGAGGCAAAAAGGAGCCAGGCGCTCCCTCTTTCTTGAAGAGGGTAGAAG
 481 TTAGGGCGCCGGAGCCCGGGCCTGGAACGCCCTCACCCCCAACCTCCAGTCTCCGCGTTTTGCGATTTTAATTTTGGCGG
 561 GAGGGGAAGTGGATTGAGAGGAAAGAGAGAGGCCAAGACAATTTGTAACTAGAATCCGTTTTTCCCTTTTCCTTTTTTTA
 641 AACAAACAAACATACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCTAAGAGGCGACGGAAGCCGAACG
 721 CAGAGTCCGGATCGGAGAGAAAACGCAGTAAGGACTTTTAGAAGCAATAAAAGGCAAAAAAAACAAAAAACAAAAAAACA
 801 AACAAAAAAAAACCACTACTACCAATAATCAAAGACACAAATATCTATGCAAGGAGGCTCCACTGAGCCTCGCGGCCCGG
 881 CCCGGCCCCGGGATGCCCCGCCCGGCCTGCGGGCCGCCCCGCCCGAGCGCGGATCTGTGCACTTTGGTGAAGTGGGGGCC
 961 CGCGCCGCCCCCTCCCCCTCCCCAGGTTCTTACAATCAGTGACTCGGAGATTTGGGGCCCCAGTGCCACTGCCCTCCCCC
1041 GCCCCGTCCCCGTTGTGCGTCATGCTGTTTTTTAAAAACCTGTTTCCAAATTTGTATGGAATGGCAAACTGTTGGGGGGT
1121 CGGTTTGGGGAGGGAGGGTTTGCATGAAAGACACACGCACACCACACCGCACGCACAAGCAGGCCCGGCGCCGGCGTCCG
1201 GGGGGCAGAAGGAGGTGAGCTCGCCGGCTCCTCCTCCCCGCGGCCATTCTGTCCCCTCCTGGGGTGAGGGGTGGGGATGG
1281 AGACCTGGGGGCAGCCCCACCCCTGCCCGGACTGTGCCTCGGTGGGTGCCACCTGGCGATTTCCGGTGTCTGGAGAGAGT
1361 ATTTTTTGGTCCAAGGAGTCCTCTTGGCTTTAGCTGGTGGGTGGGCGGGGAGAGGTCTGAGGGCTCCTACTGGAGGTTCC
1441 CCCAAAAAGGGGCAAAAGGAGACCCTCTGCCCACCGGAGGCAGGGGATCAGGCATCCAAATACACGATGCAAAAATGCAA
1521 TCCCACAGGCGACACACCCACACACTCACCCACACACACGCAATTTTACCTTCCTCTTGTAGCGAAGATGAAACTCCCGT
1601 CGGACACCCGAAGTGCATTGCGTGTTTCTGTTCAGTTTAATGACGATTAATAAATATTTATGTAAATGAGATGCAAAGCC
1681 GGAAAAAAAAAAAAAAAAA
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' cguCGGU--CGAGAUGGGGGCGGu 5'
             ||||  || || |||||||| 
Target 5' agtGCCACTGCCCT-CCCCCGCCc 3'
1022 - 1044 164.00 -25.50
2
miRNA  3' cgUCGGUCGAGAUGGGGGCGGu 5'
            :| |||| | |||||:||| 
Target 5' ggGGGCAGCCCCACCCCTGCCc 3'
1287 - 1308 156.00 -25.80
3
miRNA  3' cgucGGUCGAGAUG------GGGGCGGu 5'
              ||:|| ||:|      ||||||| 
Target 5' ccgcCCGGC-CTGCGGGCCGCCCCGCCc 3'
898 - 924 151.00 -26.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26650131 75 COSMIC
COSN16951837 97 COSMIC
COSN17611565 270 COSMIC
COSN7166178 482 COSMIC
COSN8836167 619 COSMIC
COSN20093264 643 COSMIC
COSN20093261 647 COSMIC
COSN20093259 651 COSMIC
COSN20113886 653 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1186275470 1 dbSNP
rs763861049 4 dbSNP
rs762645051 6 dbSNP
rs762307909 8 dbSNP
rs952983762 15 dbSNP
rs1264672377 19 dbSNP
rs1295675771 23 dbSNP
rs764646721 25 dbSNP
rs951462020 25 dbSNP
rs1216062660 34 dbSNP
rs1341798325 41 dbSNP
rs114472862 43 dbSNP
rs1244243430 44 dbSNP
rs1356162207 47 dbSNP
rs1210337825 48 dbSNP
rs756693947 49 dbSNP
rs745820470 50 dbSNP
rs753048184 50 dbSNP
rs997004929 52 dbSNP
rs1181998556 58 dbSNP
rs1262304887 64 dbSNP
rs541303698 67 dbSNP
rs1186346500 74 dbSNP
rs1463337050 75 dbSNP
rs1274673328 77 dbSNP
rs974135725 79 dbSNP
rs1019723740 80 dbSNP
rs1161784783 87 dbSNP
rs1387175862 89 dbSNP
rs11388087 91 dbSNP
rs1303512264 95 dbSNP
rs779287298 99 dbSNP
rs903186815 103 dbSNP
rs1263224574 104 dbSNP
rs1351308751 117 dbSNP
rs577225942 118 dbSNP
rs1018435851 119 dbSNP
rs558744571 127 dbSNP
rs946651069 128 dbSNP
rs1008902074 131 dbSNP
rs893721563 135 dbSNP
rs1257282446 136 dbSNP
rs891337682 138 dbSNP
rs1228937885 139 dbSNP
rs536857164 140 dbSNP
rs1009826826 142 dbSNP
rs892793483 143 dbSNP
rs1054159361 144 dbSNP
rs576234546 155 dbSNP
rs905728000 158 dbSNP
rs554359530 160 dbSNP
rs1045534293 162 dbSNP
rs1326992807 163 dbSNP
rs1410140827 166 dbSNP
rs536382313 167 dbSNP
rs950012535 173 dbSNP
rs939735656 179 dbSNP
rs907761368 183 dbSNP
rs983354460 188 dbSNP
rs908227095 190 dbSNP
rs1388818834 191 dbSNP
rs372941240 193 dbSNP
rs983747076 194 dbSNP
rs1169763560 195 dbSNP
rs408262 197 dbSNP
rs449430 198 dbSNP
rs1372297727 203 dbSNP
rs1028559456 209 dbSNP
rs1303378600 211 dbSNP
rs380373 222 dbSNP
rs976039912 226 dbSNP
rs547013176 231 dbSNP
rs1019754788 236 dbSNP
rs1447435964 242 dbSNP
rs919921294 243 dbSNP
rs998947396 244 dbSNP
rs1480539513 249 dbSNP
rs974187473 251 dbSNP
rs1192108850 253 dbSNP
rs144216348 259 dbSNP
rs1431934152 261 dbSNP
rs1173109611 262 dbSNP
rs1021675446 270 dbSNP
rs1306359770 271 dbSNP
rs1354140037 277 dbSNP
rs1467785880 278 dbSNP
rs1018859558 279 dbSNP
rs986961133 290 dbSNP
rs1295069254 291 dbSNP
rs570821806 292 dbSNP
rs1020565873 298 dbSNP
rs1233401625 308 dbSNP
rs12946177 310 dbSNP
rs1010428684 313 dbSNP
rs892845213 314 dbSNP
rs12946169 315 dbSNP
rs1055065229 319 dbSNP
rs1480640956 326 dbSNP
rs1451815055 330 dbSNP
rs1222843668 332 dbSNP
rs1248758870 333 dbSNP
rs1487792732 334 dbSNP
rs1032633517 344 dbSNP
rs1193513249 348 dbSNP
rs1251248672 349 dbSNP
rs937904151 356 dbSNP
rs1001248621 365 dbSNP
rs905573868 366 dbSNP
rs1406160999 368 dbSNP
rs1166672011 380 dbSNP
rs552497007 381 dbSNP
rs1233978275 386 dbSNP
rs1321086387 396 dbSNP
rs939810967 398 dbSNP
rs949886623 402 dbSNP
rs1329597351 415 dbSNP
rs1269063705 421 dbSNP
rs886253447 424 dbSNP
rs1356627953 426 dbSNP
rs1047716414 432 dbSNP
rs1229608338 433 dbSNP
rs921441215 447 dbSNP
rs1333081692 452 dbSNP
rs930537991 456 dbSNP
rs1269370345 457 dbSNP
rs1466637627 458 dbSNP
rs1392046730 460 dbSNP
rs919932202 467 dbSNP
rs1186824090 472 dbSNP
rs1395775071 479 dbSNP
rs530999969 491 dbSNP
rs563939216 494 dbSNP
rs866069408 496 dbSNP
rs931005283 498 dbSNP
rs1411384233 499 dbSNP
rs911279021 500 dbSNP
rs11653421 502 dbSNP
rs987274159 504 dbSNP
rs1460764677 507 dbSNP
rs1159621231 516 dbSNP
rs920905506 518 dbSNP
rs11078918 519 dbSNP
rs965978485 520 dbSNP
rs1019827384 524 dbSNP
rs530232603 528 dbSNP
rs977584191 534 dbSNP
rs11653416 536 dbSNP
rs1282115187 542 dbSNP
rs112686862 551 dbSNP
rs1477548522 554 dbSNP
rs989058801 558 dbSNP
rs1233132482 559 dbSNP
rs957585754 561 dbSNP
rs1032643173 565 dbSNP
rs1331861570 568 dbSNP
rs1203836598 578 dbSNP
rs1001132716 580 dbSNP
rs528702688 587 dbSNP
rs1212308983 589 dbSNP
rs1255756458 591 dbSNP
rs1474995556 593 dbSNP
rs1202383570 596 dbSNP
rs1413815375 599 dbSNP
rs1486962731 601 dbSNP
rs1281618366 602 dbSNP
rs1157874927 603 dbSNP
rs1210642538 605 dbSNP
rs764577112 611 dbSNP
rs958754433 625 dbSNP
rs1331624535 627 dbSNP
rs1374538732 633 dbSNP
rs1417284126 637 dbSNP
rs1281490237 638 dbSNP
rs1240107453 639 dbSNP
rs1248141235 641 dbSNP
rs1335382202 643 dbSNP
rs1286581099 644 dbSNP
rs1034727399 646 dbSNP
rs1416660526 647 dbSNP
rs1377225670 649 dbSNP
rs559748741 650 dbSNP
rs1413705119 651 dbSNP
rs1055287381 653 dbSNP
rs1279537713 653 dbSNP
rs8081945 654 dbSNP
rs1170337764 655 dbSNP
rs1259111996 656 dbSNP
rs1485468951 657 dbSNP
rs1160073736 659 dbSNP
rs67001366 660 dbSNP
rs1206085591 670 dbSNP
rs1470337130 683 dbSNP
rs1410728223 687 dbSNP
rs11650045 695 dbSNP
rs1002136329 696 dbSNP
rs1170313855 696 dbSNP
rs1195072205 696 dbSNP
rs1229199541 696 dbSNP
rs1267722739 696 dbSNP
rs1273111404 696 dbSNP
rs1277082442 696 dbSNP
rs1301378534 696 dbSNP
rs1309419082 696 dbSNP
rs1328587150 696 dbSNP
rs1332191581 696 dbSNP
rs1337687506 696 dbSNP
rs1347177764 696 dbSNP
rs1368295427 696 dbSNP
rs1390068850 696 dbSNP
rs1393888712 696 dbSNP
rs1430039156 696 dbSNP
rs1439140721 696 dbSNP
rs1478962623 696 dbSNP
rs906453442 696 dbSNP
rs1191630999 698 dbSNP
rs1453263836 698 dbSNP
rs1475874357 699 dbSNP
rs867666920 700 dbSNP
rs1449595450 701 dbSNP
rs1371042705 716 dbSNP
rs1461121539 717 dbSNP
rs1003987867 719 dbSNP
rs1391855512 726 dbSNP
rs886911534 727 dbSNP
rs1324526259 728 dbSNP
rs1370861201 730 dbSNP
rs1258843000 734 dbSNP
rs1187371699 745 dbSNP
rs1299906904 745 dbSNP
rs1441184863 755 dbSNP
rs1048159931 756 dbSNP
rs1226890327 764 dbSNP
rs1265848977 768 dbSNP
rs1358144859 772 dbSNP
rs1211567550 773 dbSNP
rs1272513500 774 dbSNP
rs1465289428 784 dbSNP
rs551444488 784 dbSNP
rs1258973774 785 dbSNP
rs1350272240 788 dbSNP
rs1024081875 791 dbSNP
rs1187750390 791 dbSNP
rs796298977 793 dbSNP
rs1235235737 794 dbSNP
rs541446644 795 dbSNP
rs1292745312 798 dbSNP
rs1458178974 798 dbSNP
rs1014417166 799 dbSNP
rs1039768004 799 dbSNP
rs944342535 800 dbSNP
rs1313766352 803 dbSNP
rs184228621 803 dbSNP
rs1231299022 807 dbSNP
rs1292384450 807 dbSNP
rs1329780333 809 dbSNP
rs753230107 812 dbSNP
rs967552549 813 dbSNP
rs977616710 813 dbSNP
rs754639255 814 dbSNP
rs914722734 818 dbSNP
rs1257915367 823 dbSNP
rs1387480745 826 dbSNP
rs532399831 839 dbSNP
rs1417512325 843 dbSNP
rs990256054 847 dbSNP
rs1161854921 855 dbSNP
rs1343927351 866 dbSNP
rs1453198779 869 dbSNP
rs1156426474 871 dbSNP
rs1377565869 872 dbSNP
rs1331860414 873 dbSNP
rs1462563817 878 dbSNP
rs1418027216 879 dbSNP
rs1350829768 883 dbSNP
rs1304834139 890 dbSNP
rs959009397 898 dbSNP
rs1034390223 900 dbSNP
rs1257180846 902 dbSNP
rs1472122116 905 dbSNP
rs378062 910 dbSNP
rs377678800 911 dbSNP
rs1209662991 912 dbSNP
rs1024858532 913 dbSNP
rs1464685787 919 dbSNP
rs1179288933 922 dbSNP
rs1418992275 926 dbSNP
rs975589007 926 dbSNP
rs1215866768 931 dbSNP
rs1176884478 945 dbSNP
rs1396924316 950 dbSNP
rs1352734783 954 dbSNP
rs1433115708 958 dbSNP
rs1173299145 963 dbSNP
rs1335711024 963 dbSNP
rs886944528 967 dbSNP
rs1272680041 973 dbSNP
rs140330658 976 dbSNP
rs543739980 977 dbSNP
rs1345058413 978 dbSNP
rs1271807586 979 dbSNP
rs1039396475 983 dbSNP
rs1343853231 984 dbSNP
rs1231478271 985 dbSNP
rs1364108000 985 dbSNP
rs1480609800 1003 dbSNP
rs943673175 1005 dbSNP
rs1255416305 1006 dbSNP
rs1318286936 1009 dbSNP
rs576142835 1012 dbSNP
rs912203076 1014 dbSNP
rs1168062274 1016 dbSNP
rs1353670389 1022 dbSNP
rs1442719976 1038 dbSNP
rs899056700 1039 dbSNP
rs1038391575 1040 dbSNP
rs1297678993 1046 dbSNP
rs1363656170 1047 dbSNP
rs1212369526 1049 dbSNP
rs942743127 1051 dbSNP
rs1163506327 1056 dbSNP
rs1403051048 1059 dbSNP
rs911196946 1063 dbSNP
rs1307334509 1073 dbSNP
rs1222734220 1074 dbSNP
rs1275670077 1078 dbSNP
rs554777541 1085 dbSNP
rs1193097632 1092 dbSNP
rs946243906 1097 dbSNP
rs182956042 1105 dbSNP
rs1449395202 1106 dbSNP
rs1419052765 1117 dbSNP
rs1388770253 1138 dbSNP
rs59417645 1144 dbSNP
rs958859275 1148 dbSNP
rs1392273269 1151 dbSNP
rs934064072 1156 dbSNP
rs1346404833 1157 dbSNP
rs756876521 1157 dbSNP
rs1469106279 1160 dbSNP
rs913412491 1163 dbSNP
rs571825429 1168 dbSNP
rs1439576657 1169 dbSNP
rs34115897 1171 dbSNP
rs944293418 1173 dbSNP
rs1379438269 1174 dbSNP
rs1275030808 1184 dbSNP
rs1229136632 1186 dbSNP
rs971386875 1189 dbSNP
rs1014837290 1192 dbSNP
rs1213567459 1198 dbSNP
rs1285076244 1200 dbSNP
rs982670832 1200 dbSNP
rs866788448 1201 dbSNP
rs190361988 1203 dbSNP
rs995728470 1205 dbSNP
rs538253115 1209 dbSNP
rs1415311575 1211 dbSNP
rs1371315547 1212 dbSNP
rs980749637 1224 dbSNP
rs1410032149 1225 dbSNP
rs147160288 1225 dbSNP
rs1316999524 1227 dbSNP
rs748946068 1230 dbSNP
rs1433685128 1233 dbSNP
rs145178826 1238 dbSNP
rs1024381950 1241 dbSNP
rs1233035612 1247 dbSNP
rs1353468442 1249 dbSNP
rs1222195391 1250 dbSNP
rs1014012723 1254 dbSNP
rs950478617 1255 dbSNP
rs374010186 1258 dbSNP
rs1026169020 1259 dbSNP
rs1041372701 1268 dbSNP
rs1255640835 1269 dbSNP
rs1369215107 1270 dbSNP
rs1182252810 1273 dbSNP
rs868649310 1276 dbSNP
rs1454941033 1277 dbSNP
rs898983474 1280 dbSNP
rs1054656513 1284 dbSNP
rs1436220141 1288 dbSNP
rs1171422078 1290 dbSNP
rs1374447073 1293 dbSNP
rs1414630085 1305 dbSNP
rs1038990966 1309 dbSNP
rs1007889139 1318 dbSNP
rs1189625039 1321 dbSNP
rs889829070 1322 dbSNP
rs537774536 1323 dbSNP
rs1236547534 1324 dbSNP
rs1278537202 1332 dbSNP
rs981491778 1337 dbSNP
rs950104036 1338 dbSNP
rs1482709265 1343 dbSNP
rs1180933484 1346 dbSNP
rs1253526856 1349 dbSNP
rs907915030 1357 dbSNP
rs529684056 1360 dbSNP
rs1272333902 1363 dbSNP
rs1168857688 1369 dbSNP
rs1212774842 1378 dbSNP
rs1328820961 1397 dbSNP
rs983413154 1400 dbSNP
rs1051503926 1404 dbSNP
rs1443273210 1407 dbSNP
rs1301266264 1408 dbSNP
rs1370529918 1409 dbSNP
rs934095941 1427 dbSNP
rs1337257944 1436 dbSNP
rs570121183 1437 dbSNP
rs548779036 1440 dbSNP
rs951322938 1442 dbSNP
rs1300331216 1444 dbSNP
rs1211299159 1445 dbSNP
rs1027304926 1453 dbSNP
rs1428781156 1458 dbSNP
rs1217180797 1463 dbSNP
rs530689671 1464 dbSNP
rs530098119 1465 dbSNP
rs561989444 1470 dbSNP
rs1369270821 1471 dbSNP
rs1395872568 1472 dbSNP
rs1315284087 1474 dbSNP
rs1324003134 1475 dbSNP
rs1393764640 1480 dbSNP
rs755016617 1481 dbSNP
rs936203443 1482 dbSNP
rs1298054594 1485 dbSNP
rs1324908638 1489 dbSNP
rs1226503974 1495 dbSNP
rs926106790 1498 dbSNP
rs1435731951 1504 dbSNP
rs566181170 1509 dbSNP
rs980412508 1518 dbSNP
rs1359015545 1522 dbSNP
rs1174381204 1523 dbSNP
rs1272014929 1525 dbSNP
rs377593425 1527 dbSNP
rs1206374672 1530 dbSNP
rs369924961 1531 dbSNP
rs916923842 1533 dbSNP
rs1446004206 1535 dbSNP
rs150879748 1538 dbSNP
rs1418972311 1539 dbSNP
rs1020002714 1549 dbSNP
rs1009890177 1559 dbSNP
rs565314331 1560 dbSNP
rs1181587131 1570 dbSNP
rs950458351 1574 dbSNP
rs1290698403 1581 dbSNP
rs1026096177 1583 dbSNP
rs973129954 1597 dbSNP
rs1313294630 1598 dbSNP
rs543331390 1609 dbSNP
rs937566776 1610 dbSNP
rs531657682 1618 dbSNP
rs1017849012 1621 dbSNP
rs1007486451 1627 dbSNP
rs1190069249 1633 dbSNP
rs890332795 1638 dbSNP
rs1483531493 1644 dbSNP
rs1258364506 1649 dbSNP
rs1029682771 1661 dbSNP
rs76347134 1666 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A HITS-CLIP data was present in Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
Experimental Support 2 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.

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 Chi_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000302584.4 | 3UTR | CCGGGAUGCCCCGCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset Chi_124B_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + B
Location of target site ENST00000302584.4 | 3UTR | CCGGGAUGCCCCGCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset Chi_ControlB_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control B
Location of target site ENST00000302584.4 | 3UTR | CCGGGAUGCCCCGCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000302584.4 | 3UTR | ACUGCCCUCCCCCGCC
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
90 hsa-miR-6787-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT449091 XPO6 exportin 6 2 2
MIRT449991 PSMG1 proteasome assembly chaperone 1 2 2
MIRT454608 MYADM myeloid associated differentiation marker 2 2
MIRT456116 VAV3 vav guanine nucleotide exchange factor 3 2 6
MIRT457064 TOR4A torsin family 4 member A 2 2
MIRT461023 SDF4 stromal cell derived factor 4 2 2
MIRT467197 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT471711 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472566 NACC1 nucleus accumbens associated 1 2 2
MIRT476079 GRB2 growth factor receptor bound protein 2 2 2
MIRT480150 CALR calreticulin 2 2
MIRT483027 KHSRP KH-type splicing regulatory protein 2 4
MIRT483498 STMN3 stathmin 3 2 4
MIRT483728 THSD4 thrombospondin type 1 domain containing 4 2 2
MIRT484550 BARHL1 BarH like homeobox 1 2 6
MIRT484684 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 2 2
MIRT486059 CTDNEP1 CTD nuclear envelope phosphatase 1 2 2
MIRT486116 INO80E INO80 complex subunit E 2 2
MIRT486313 SIPA1 signal-induced proliferation-associated 1 2 2
MIRT486525 CLCN7 chloride voltage-gated channel 7 2 2
MIRT486857 DPF1 double PHD fingers 1 2 2
MIRT487352 PHF15 jade family PHD finger 2 1 1
MIRT487582 FAM83H family with sequence similarity 83 member H 2 4
MIRT487792 GPR20 G protein-coupled receptor 20 2 4
MIRT488104 POU3F1 POU class 3 homeobox 1 2 2
MIRT488786 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT489361 SYNGR1 synaptogyrin 1 2 4
MIRT489387 RAB11B RAB11B, member RAS oncogene family 2 2
MIRT489680 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT489731 GNAI2 G protein subunit alpha i2 2 4
MIRT489750 TACC3 transforming acidic coiled-coil containing protein 3 2 2
MIRT490029 PCSK4 proprotein convertase subtilisin/kexin type 4 2 2
MIRT490379 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490580 SLC47A1 solute carrier family 47 member 1 2 2
MIRT490753 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491187 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 4
MIRT491301 VGF VGF nerve growth factor inducible 2 2
MIRT491462 HOXB8 homeobox B8 2 2
MIRT491702 PDZD4 PDZ domain containing 4 2 2
MIRT491724 RTN4R reticulon 4 receptor 2 2
MIRT491737 SEMA3F semaphorin 3F 2 2
MIRT491984 UNK unkempt family zinc finger 2 2
MIRT492844 NRGN neurogranin 2 2
MIRT492936 NEUROD2 neuronal differentiation 2 2 4
MIRT493713 H2AFX H2A histone family member X 2 2
MIRT494623 ASB6 ankyrin repeat and SOCS box containing 6 2 4
MIRT494703 ARHGAP31 Rho GTPase activating protein 31 2 2
MIRT495602 NKX2-5 NK2 homeobox 5 2 2
MIRT495750 PDE4C phosphodiesterase 4C 2 4
MIRT500367 ZNF385A zinc finger protein 385A 2 2
MIRT501161 SLC10A7 solute carrier family 10 member 7 2 6
MIRT501702 PCGF3 polycomb group ring finger 3 2 6
MIRT504922 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT517945 TRIM59 tripartite motif containing 59 2 2
MIRT524212 DDI2 DNA damage inducible 1 homolog 2 2 6
MIRT531186 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 2 2
MIRT531972 C12orf49 chromosome 12 open reading frame 49 2 2
MIRT558055 EVI5L ecotropic viral integration site 5 like 2 2
MIRT560482 LACE1 AFG1 like ATPase 2 2
MIRT563217 FXN frataxin 2 2
MIRT569095 FSCN1 fascin actin-bundling protein 1 2 2
MIRT569522 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569531 CTTN cortactin 2 2
MIRT569848 RGS5 regulator of G protein signaling 5 2 2
MIRT570738 ANKRD52 ankyrin repeat domain 52 2 2
MIRT574140 MARVELD1 MARVEL domain containing 1 2 2
MIRT615994 DHTKD1 dehydrogenase E1 and transketolase domain containing 1 2 2
MIRT628493 ZNF556 zinc finger protein 556 2 2
MIRT633451 KLLN killin, p53-regulated DNA replication inhibitor 2 2
MIRT649054 SLC1A2 solute carrier family 1 member 2 2 2
MIRT649340 HEXA hexosaminidase subunit alpha 2 2
MIRT670226 PTCHD1 patched domain containing 1 2 2
MIRT670666 KIAA1551 KIAA1551 2 2
MIRT671452 CDH7 cadherin 7 2 2
MIRT671729 ZNF451 zinc finger protein 451 2 2
MIRT690285 ZNF154 zinc finger protein 154 2 2
MIRT700575 PRSS22 protease, serine 22 2 2
MIRT701411 NKRF NFKB repressing factor 2 2
MIRT711877 VASP vasodilator stimulated phosphoprotein 2 2
MIRT712082 UNC13A unc-13 homolog A 2 2
MIRT712523 CYTH2 cytohesin 2 2 2
MIRT712751 GMDS GDP-mannose 4,6-dehydratase 2 2
MIRT714681 PRX periaxin 2 2
MIRT714718 VPS8 VPS8, CORVET complex subunit 2 2
MIRT717508 HRNR hornerin 2 2
MIRT717650 THBS2 thrombospondin 2 2 2
MIRT719592 PIAS4 protein inhibitor of activated STAT 4 2 2
MIRT720521 PTGR2 prostaglandin reductase 2 2 2
MIRT721295 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT724922 VPS18 VPS18, CORVET/HOPS core subunit 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-6787 Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-6787-5p Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-6787-5p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-6787-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-6787-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-6787-5p Tamoxifen 2733525 NSC180973 approved sensitive cell line (LCC2)
hsa-miR-6787-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-6787-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-6787-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-6787-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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