pre-miRNA Information
pre-miRNA hsa-mir-6799   
Genomic Coordinates chr19: 49791866 - 49791934
Description Homo sapiens miR-6799 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6799-5p
Sequence 6| GGGGAGGUGUGCAGGGCUGG |25
Evidence Experimental
Experiments Meta-analysis
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1439869964 1 dbSNP
rs1206286688 3 dbSNP
rs767550469 6 dbSNP
rs1471732220 9 dbSNP
rs986966775 11 dbSNP
rs754316096 12 dbSNP
rs757819623 15 dbSNP
rs1473089544 16 dbSNP
Putative Targets

Gene Information
Gene Symbol RFT1   
Synonyms CDG1N
Description RFT1 homolog
Transcript NM_052859   
Expression
Putative miRNA Targets on RFT1
3'UTR of RFT1
(miRNA target sites are highlighted)
>RFT1|NM_052859|3'UTR
   1 CTTCAGGGAAGCCTGGACACCCGAGGCACCTGGACCAGCTATGGGTAGTTCTGTGGGTGGAACACATTCTGTGTAAGAGC
  81 CCCACTGAGGGCTCTGCAGCGGAGTGACAGCAACCCCAGAGATGAGGCACCAGAGAGTGCCACTGCATGAGACACCTGTG
 161 ACCATTCGAAGTCTGAAATGCGGGGGGGGAGTTTCATTTTTAAGTGAAGACCAAAAGCCCTTTAAAAATAATAGTTTTTT
 241 ATCATTTTATAGTAATCAGCATTTTCTCTTTTACTAATATACTCATTCCTTTTGCGTATGATTGGCCTTTGGAGCTACAT
 321 GCTCCAACAAACTATATCTTAATTGTTAACTGTTAATAATTATCTGGCCCAGAAAAAGAGATGCAGTGATTTTACCCTTC
 401 ACAGGAATATTGAACTTCTTCTGTAAAAGAGAGAGAGAAACCTCTCTCTCTCATGCACCACATGGAAACAGAGTGTGGCC
 481 CTGAAGTTGTGGCTTTCTTTGTGTCAAAACTGTGGTCTGAGTTTTTAGAGAAGGAAAAATGCTACTCAGTGAGAAATCCA
 561 AGAAATGAAACCAGGAAGGTTTTCAGATCACATTTCCCAGAGTGAGTTCGGGAGAATCTTGCCTGTCGTGATCACACTGT
 641 TCCCCGCCGCCCCAGGTCAGCACATACTTGACCCAGAGTGGGCTCTCAGGATTTGTTGATTGAAGGGTGGGTGAAAGCTG
 721 GCTGGAGACTCCTGGCCTGGCCACCTGCAAGAGGCGGACTTTGAAGAAAACTGTGATCCAGTTGAGCCACTTTGTCCCTG
 801 AGGGGAATGCTGCTTTGCAGCTTTCTGTAACTTCTCACATGGGAATTGCACTGGTGACAGATAAGGTTTAACAGATGTAC
 881 TTTTTTATCCTCAGAATAAGACAAGGCAAACTCTATATGGCTAGTATTACTGAGTCAGGTCCCTCCCGTTGACCCATTAA
 961 TTCCAGCATTGATCAATACAACCAAATTCCAGCCCCAGGACAAGAGTGGCAGGCATGGGGGCCTGGTACTCCAGGCTACA
1041 GTGTGAGCCCAGGTGTTCTGCACCTTGCAGCCTGCACACTGCAGGTGAAATCATGAGCAGTGTTCTGGAGTGTGAAGTGT
1121 TTTTATTTTTTTGTTAATGTATTAATTCCTTTTAGATATTAACCCCCCTCAGAACTATATGCACAAACTATAACTTGGAT
1201 GTTAATAATCCTGTCACTCAGTGCCCCAAACCTTCTGTGTCTACACCTAGAGAGAGGGCCAGTAAGGGCAACTCCTATCA
1281 TGCATTAAAATGCATGTATTTAAATCTGCTTGCCCAGAGCCAGTACCCAGGGGCTAAGGATTAAGACCTGTCAGTACACC
1361 AAGACTGGGGCCCAGTCACCTGGCAGGTTTTTATCTACTCAGAGGGAGAATGCTTTGCACTAAGTGGGAGAAAAGCAGCT
1441 AAATGCAAGGTGTCCTGAGCAATTAGAGGACCTCCAAAGCATGGCCTCAGTCATGCCTTCATCGGGCAAGGTCAGGCCAG
1521 CTCAGAAAAATGGATGGTCCCATAGGGTCAAGTGGAGCACACACGGAAGGCAGTCCTCCTTCCCTCCCATGTCCTTTCTC
1601 TGTCCCTGGCATCCACAGAAAGGGACCTTCAGTCCTCATGAGCTGCTTCTCTGCAGCTGCTGATCACCCTCCCGGAACCC
1681 TGCACCTATCCCGTGCCCACCTGACCCCAGACTCAAGCATGATCCTCATTCTACCTGCCTCGGAATCACCTGGATTGCAA
1761 GTCAGAACATGGCTTCCCAGGACCCACTCCAGGCCTTCAGGGTCTGTGTCTCCCAGGAGGAGGGCTCTGAGATTGGCTTT
1841 TCTGGCAAGCCCACGTGGCTTTGATGCCACCAAGGTTGGCATGCCCCATTGTCTTCCTTCGTGACAGGCCCAGGACCATC
1921 ATGCTCATGCTCACAGTGCCTGTTCTCTGCTCCAGGAACAGAGCTGCTGCTCTACAAGCAGCCTTGTGACTCCGGGGTCT
2001 CTGGGAGCAGGACTCCCCAGGCTTGTGCTCTCTCAGCTTGAGAGAGGCTCTATGTCTGAAGGCAGTGCTCACTCTCTCAT
2081 CCCTCCCCTGCTGTTCGCCCAGTGCTGCTGTCAGGGCCAGCTCCTCTTGAAAGACAGCCAGCCGCAAAGGCAGCCCAGGG
2161 CTTCTTCCGGTGTCCTGCTTCCCTGTATCTAGGGAGAGTTGTACATGTGGCTGCGTGTTTTCCCAGGACTAGCCCTGCCG
2241 CCTGGGCTGTCAGCACTTTGGCAGCAGGTCCTCTGTGGTTCTCTGCCTCTGGTGCCTCCCTAAAGCTCAGCTGGACCTGA
2321 CCAGGCCTCTGGCATTTCCCCTGCTGGACCCCCTAGAGCCACAGCTGTGCCTCAGGGAGCTTGCATACATGTGGGCCAGC
2401 CTGCCTCACTTTACCCAAGTGGATTTGGGGAGCAGAAATCATACTTTTGGCTTTCAATACCACTTATAGTGAGGCTACTT
2481 CTCCATGGAAACAAGTCTCTGAGGCACAACCTTTATGAAAGGAAGGAGCATTCGTTGGTGAGAAGAACAGTATCGCTGAC
2561 TTCCTGTGCTCCTCTGGCCACAGGTAACTGTTGGTCACTTCAGATTTGGCTTGGGGTCTCTCAGTGAGGAGCTGCTGCTG
2641 TGCTGTTTAATGCTTACCTGATGGCAACTTCTGGCTCTGGAACCGCTACTCTGCCCTGTTCCCAGCCACTTCCCAACCTG
2721 ATTCAAGCAGGGCCCCTCCTTCCTCCTGTCTTTATTTATTTATTTATTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGG
2801 AGTGCAGTAGCGCGATCTCGGCTCACTGCGAGCTCTGCCTCCTGGGTTCAAGCGATTCTCTTGCCTCAGCCTCCTGAGTA
2881 GCTGGGGCTACAGGCGCCTGCCACCACACCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATATTGGCCA
2961 GGCTGGTCTTGAACTCCTGACCTTGTGATCCGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC
3041 TCCTGGCCTATTCTTTTCTTTTCAGAGACAAGGTCTCACTCTCTCCTCTCGCCCAGGCTGGAGTGCAGTGGTGTCATCAT
3121 AGCTCATTGCAGCCTCAAACTCCTGGGCTCAAGCAATCCTCCCACCTCAGCCTCCTGAGTAGCTGGGATCACAGGTGTGT
3201 GCTACCTCACCCAGCTAATTTCTAATTTTTTTTTGTAGAGACTGGATCTCACTGTTGCCTTGAACTCCTGGGCTCAAGTG
3281 ATCCTCCTGCCTCAGCCTCCCAAAGTGCTGGGATTCCAGACCAGCCATTTTTTTTCCTTAATCATGCATTCCTGTTGCTA
3361 GTTTCACATCAGTCCCCTGGTTTAATAAGAAATAAAATATTTTCTTCACACTTTTGAAAAAAAAAAAAAAAA
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' gguCGGGAC----GU--GUGGAGGGg 5'
             ||||||    ||  |||:|||| 
Target 5' tctGCCCTGTTCCCAGCCACTTCCCa 3'
2690 - 2715 145.00 -23.80
2
miRNA  3' gguCGG-GACGUGUGGAGGGg 5'
             ||| ||| :::|||||| 
Target 5' tctGCCTCTG-GTGCCTCCCt 3'
2282 - 2301 140.00 -21.40
3
miRNA  3' ggucGGGACGUG--UGGAGGGg 5'
              :||||| :  :|||||| 
Target 5' atccTCCTGCCTCAGCCTCCCa 3'
3281 - 3302 138.00 -22.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
902846 84 ClinVar
902845 116 ClinVar
346182 127 ClinVar
346181 146 ClinVar
346180 153 ClinVar
901949 182 ClinVar
346179 184 ClinVar
901948 240 ClinVar
346178 242 ClinVar
901947 295 ClinVar
346177 334 ClinVar
346176 405 ClinVar
901394 423 ClinVar
901393 441 ClinVar
346175 450 ClinVar
346174 490 ClinVar
346173 609 ClinVar
346172 622 ClinVar
346171 645 ClinVar
900240 649 ClinVar
346170 799 ClinVar
346169 861 ClinVar
900239 880 ClinVar
900238 968 ClinVar
902792 972 ClinVar
346168 1009 ClinVar
902791 1117 ClinVar
346167 1124 ClinVar
346166 1271 ClinVar
346165 1533 ClinVar
346164 1693 ClinVar
902790 1693 ClinVar
346163 1803 ClinVar
346162 1804 ClinVar
901893 1900 ClinVar
346161 1901 ClinVar
346160 1975 ClinVar
901892 2052 ClinVar
901891 2076 ClinVar
346159 2161 ClinVar
346158 2165 ClinVar
901338 2187 ClinVar
346157 2214 ClinVar
346156 2215 ClinVar
346155 2255 ClinVar
901337 2280 ClinVar
346154 2350 ClinVar
346153 2366 ClinVar
346152 2427 ClinVar
900175 2428 ClinVar
346151 2433 ClinVar
900174 2453 ClinVar
346150 2457 ClinVar
346149 2646 ClinVar
346148 2655 ClinVar
346147 2706 ClinVar
346146 2787 ClinVar
346145 2789 ClinVar
902727 2790 ClinVar
346144 2820 ClinVar
346143 2840 ClinVar
346142 2887 ClinVar
346141 2950 ClinVar
901824 2991 ClinVar
901823 2992 ClinVar
346140 2995 ClinVar
901822 2996 ClinVar
346139 2997 ClinVar
346138 3056 ClinVar
346137 3068 ClinVar
346136 3093 ClinVar
901277 3093 ClinVar
346135 3191 ClinVar
901276 3286 ClinVar
346134 3342 ClinVar
901275 3348 ClinVar
COSN30488344 15 COSMIC
COSN30484353 49 COSMIC
COSN30462689 56 COSMIC
COSN30146055 69 COSMIC
COSN20074698 81 COSMIC
COSN20074700 82 COSMIC
COSN26552571 85 COSMIC
COSN31574564 168 COSMIC
COSN22863002 181 COSMIC
COSN31600667 189 COSMIC
COSN31528948 1503 COSMIC
COSN31486821 1842 COSMIC
COSN31540871 2020 COSMIC
COSN27853205 2067 COSMIC
COSN19127918 2383 COSMIC
COSN22904469 2779 COSMIC
COSN2462765 3153 COSMIC
rs2564921 334 GWAS
rs2564922 450 GWAS
rs62255926 490 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1428784090 2 dbSNP
rs1174840451 5 dbSNP
rs1357802828 8 dbSNP
rs752783410 15 dbSNP
rs765560875 16 dbSNP
rs1310089028 20 dbSNP
rs368020513 22 dbSNP
rs766080123 23 dbSNP
rs1328124867 25 dbSNP
rs994360246 26 dbSNP
rs1387542646 28 dbSNP
rs965505108 29 dbSNP
rs1172871218 32 dbSNP
rs371549083 35 dbSNP
rs1362701596 36 dbSNP
rs1218867853 38 dbSNP
rs760705571 41 dbSNP
rs367639242 44 dbSNP
rs771958164 45 dbSNP
rs1236211393 59 dbSNP
rs961334872 72 dbSNP
rs1019347106 74 dbSNP
rs1213512944 80 dbSNP
rs1006593246 81 dbSNP
rs1243354046 82 dbSNP
rs889484730 83 dbSNP
rs553703050 84 dbSNP
rs1422618820 85 dbSNP
rs1455886645 94 dbSNP
rs760260993 98 dbSNP
rs1053465850 100 dbSNP
rs1000901610 101 dbSNP
rs902448043 111 dbSNP
rs540094410 114 dbSNP
rs1345872918 115 dbSNP
rs1474404507 116 dbSNP
rs1292067740 118 dbSNP
rs1371949356 120 dbSNP
rs1193330895 124 dbSNP
rs1429922493 125 dbSNP
rs570767824 127 dbSNP
rs1442889966 130 dbSNP
rs949221376 133 dbSNP
rs1303924631 137 dbSNP
rs1352631559 139 dbSNP
rs113494789 145 dbSNP
rs72965388 146 dbSNP
rs886058723 153 dbSNP
rs1490268987 156 dbSNP
rs753091164 159 dbSNP
rs537172287 163 dbSNP
rs568521172 167 dbSNP
rs767843839 168 dbSNP
rs1250806424 181 dbSNP
rs550906487 182 dbSNP
rs1338066691 183 dbSNP
rs548020075 184 dbSNP
rs1404877135 186 dbSNP
rs751577328 187 dbSNP
rs952792926 188 dbSNP
rs1036015103 190 dbSNP
rs1330870758 190 dbSNP
rs564047932 190 dbSNP
rs1375956015 191 dbSNP
rs1328415545 196 dbSNP
rs1281553081 212 dbSNP
rs918873931 217 dbSNP
rs1281255756 219 dbSNP
rs1373941622 220 dbSNP
rs1404576905 231 dbSNP
rs534506262 240 dbSNP
rs903190754 241 dbSNP
rs565490076 242 dbSNP
rs1257014597 272 dbSNP
rs1395767751 273 dbSNP
rs1436497445 274 dbSNP
rs1011637518 278 dbSNP
rs1167974799 288 dbSNP
rs1234014483 293 dbSNP
rs1050584536 295 dbSNP
rs567674354 296 dbSNP
rs1006980749 298 dbSNP
rs1170321730 308 dbSNP
rs1426592494 310 dbSNP
rs933480407 313 dbSNP
rs1198186056 314 dbSNP
rs1330664725 316 dbSNP
rs763245570 321 dbSNP
rs923423420 326 dbSNP
rs2564921 334 dbSNP
rs1000552998 342 dbSNP
rs1291296520 347 dbSNP
rs532398312 351 dbSNP
rs908224737 358 dbSNP
rs1202099690 368 dbSNP
rs902155637 375 dbSNP
rs1436577733 376 dbSNP
rs952468407 377 dbSNP
rs1197127385 396 dbSNP
rs915655265 398 dbSNP
rs886058722 405 dbSNP
rs1209430063 409 dbSNP
rs960148471 415 dbSNP
rs1475601666 417 dbSNP
rs1193014697 418 dbSNP
rs1035494921 423 dbSNP
rs1476531096 423 dbSNP
rs1168642466 425 dbSNP
rs1020907854 427 dbSNP
rs1013499903 429 dbSNP
rs1396963103 431 dbSNP
rs1341482075 439 dbSNP
rs1413687410 439 dbSNP
rs896368837 442 dbSNP
rs1054966199 447 dbSNP
rs1377162860 448 dbSNP
rs2564922 450 dbSNP
rs1346442223 455 dbSNP
rs1284953977 456 dbSNP
rs1439824803 458 dbSNP
rs905960621 460 dbSNP
rs1048944003 463 dbSNP
rs373519253 465 dbSNP
rs931354681 472 dbSNP
rs1021604923 473 dbSNP
rs1329379348 477 dbSNP
rs1283148470 478 dbSNP
rs62255926 490 dbSNP
rs889236839 501 dbSNP
rs1448750465 505 dbSNP
rs1194238807 507 dbSNP
rs972994025 511 dbSNP
rs944303164 518 dbSNP
rs912777467 526 dbSNP
rs1171496764 543 dbSNP
rs1175145940 551 dbSNP
rs1469964235 567 dbSNP
rs985613812 571 dbSNP
rs1050471258 574 dbSNP
rs1396605257 599 dbSNP
rs142937957 602 dbSNP
rs376703231 603 dbSNP
rs886058721 609 dbSNP
rs1383412277 610 dbSNP
rs1174669364 618 dbSNP
rs1330129659 620 dbSNP
rs7645611 622 dbSNP
rs979586155 627 dbSNP
rs966434786 628 dbSNP
rs542491294 643 dbSNP
rs909450024 644 dbSNP
rs115646874 645 dbSNP
rs527818382 646 dbSNP
rs915542340 649 dbSNP
rs1467324882 650 dbSNP
rs959788937 655 dbSNP
rs1454542670 672 dbSNP
rs745888856 696 dbSNP
rs778252435 700 dbSNP
rs569032736 703 dbSNP
rs1203186098 706 dbSNP
rs1361965167 711 dbSNP
rs977266751 713 dbSNP
rs1158666734 717 dbSNP
rs1459553609 728 dbSNP
rs892693567 731 dbSNP
rs1327432803 737 dbSNP
rs1033567124 751 dbSNP
rs560651260 755 dbSNP
rs759730185 756 dbSNP
rs1338025039 758 dbSNP
rs989984867 775 dbSNP
rs552352730 788 dbSNP
rs953386659 790 dbSNP
rs1028919020 798 dbSNP
rs148552528 799 dbSNP
rs1444262843 805 dbSNP
rs1468784139 809 dbSNP
rs531112684 813 dbSNP
rs143957220 818 dbSNP
rs901908147 819 dbSNP
rs1335495360 831 dbSNP
rs1452811574 836 dbSNP
rs1416542804 839 dbSNP
rs183106989 849 dbSNP
rs1005043035 858 dbSNP
rs1394726319 860 dbSNP
rs886058720 861 dbSNP
rs1407680037 862 dbSNP
rs1296830612 869 dbSNP
rs557106378 880 dbSNP
rs537443006 889 dbSNP
rs1293149413 892 dbSNP
rs1353719174 893 dbSNP
rs1049345053 897 dbSNP
rs1235185051 909 dbSNP
rs948252581 915 dbSNP
rs894159685 918 dbSNP
rs1202646828 923 dbSNP
rs1048511665 927 dbSNP
rs938455220 931 dbSNP
rs931381367 935 dbSNP
rs897204278 942 dbSNP
rs1256712502 948 dbSNP
rs1399786658 950 dbSNP
rs1473962401 954 dbSNP
rs977694744 966 dbSNP
rs1407658253 967 dbSNP
rs1159558402 968 dbSNP
rs1442056912 972 dbSNP
rs1383984982 976 dbSNP
rs1427584679 981 dbSNP
rs1167795445 983 dbSNP
rs945884761 988 dbSNP
rs1461771234 991 dbSNP
rs1462799797 993 dbSNP
rs1312853058 995 dbSNP
rs914371811 998 dbSNP
rs73840205 1009 dbSNP
rs944019235 1012 dbSNP
rs1446685825 1015 dbSNP
rs1297980677 1016 dbSNP
rs912830143 1019 dbSNP
rs1284654146 1021 dbSNP
rs1242132929 1025 dbSNP
rs1357181147 1026 dbSNP
rs1029431352 1028 dbSNP
rs985666316 1029 dbSNP
rs966559604 1037 dbSNP
rs879433277 1039 dbSNP
rs1429534798 1044 dbSNP
rs1286635830 1047 dbSNP
rs1429567961 1049 dbSNP
rs1393619888 1059 dbSNP
rs932872252 1063 dbSNP
rs925432983 1081 dbSNP
rs748816207 1086 dbSNP
rs1344747658 1098 dbSNP
rs1345460697 1100 dbSNP
rs1015006340 1101 dbSNP
rs979588650 1111 dbSNP
rs966863348 1112 dbSNP
rs1319375211 1114 dbSNP
rs368022201 1115 dbSNP
rs1005338302 1118 dbSNP
rs1362892271 1118 dbSNP
rs1440384120 1119 dbSNP
rs913627356 1121 dbSNP
rs554646046 1124 dbSNP
rs190744142 1132 dbSNP
rs1033619523 1133 dbSNP
rs188309556 1141 dbSNP
rs1315879945 1142 dbSNP
rs1055899714 1143 dbSNP
rs1184893890 1144 dbSNP
rs1486010817 1153 dbSNP
rs35638182 1154 dbSNP
rs938354163 1163 dbSNP
rs906987551 1165 dbSNP
rs951947234 1170 dbSNP
rs1455844526 1178 dbSNP
rs1242976516 1180 dbSNP
rs1041474593 1197 dbSNP
rs1194878293 1199 dbSNP
rs1399076286 1210 dbSNP
rs1407857190 1210 dbSNP
rs551922839 1215 dbSNP
rs1345821748 1217 dbSNP
rs1461123919 1220 dbSNP
rs1489764924 1223 dbSNP
rs538582575 1230 dbSNP
rs1027910305 1244 dbSNP
rs914422646 1254 dbSNP
rs569915755 1258 dbSNP
rs989921280 1263 dbSNP
rs549553484 1271 dbSNP
rs1275404891 1274 dbSNP
rs1223072326 1277 dbSNP
rs931928308 1279 dbSNP
rs1323482757 1283 dbSNP
rs1292783253 1284 dbSNP
rs921863917 1294 dbSNP
rs1212746510 1304 dbSNP
rs897251826 1308 dbSNP
rs1037050917 1311 dbSNP
rs776509712 1312 dbSNP
rs1222742650 1314 dbSNP
rs149471736 1323 dbSNP
rs1362059287 1327 dbSNP
rs891110184 1329 dbSNP
rs1179394937 1341 dbSNP
rs1408819290 1357 dbSNP
rs1474911419 1361 dbSNP
rs1049997979 1362 dbSNP
rs183423964 1369 dbSNP
rs1402751197 1377 dbSNP
rs907835088 1379 dbSNP
rs1324005128 1380 dbSNP
rs1364052034 1391 dbSNP
rs925516919 1393 dbSNP
rs1044301360 1395 dbSNP
rs777362557 1396 dbSNP
rs952085580 1400 dbSNP
rs1425810748 1411 dbSNP
rs1027848646 1417 dbSNP
rs1012410422 1418 dbSNP
rs1232120164 1422 dbSNP
rs959927035 1424 dbSNP
rs1035278147 1433 dbSNP
rs1004166819 1434 dbSNP
rs1272747980 1435 dbSNP
rs1436374447 1436 dbSNP
rs1207311340 1437 dbSNP
rs1253156868 1439 dbSNP
rs945535700 1444 dbSNP
rs1185867904 1450 dbSNP
rs1420067780 1451 dbSNP
rs906878367 1469 dbSNP
rs755765190 1480 dbSNP
rs1167501523 1493 dbSNP
rs560823839 1503 dbSNP
rs1420326594 1504 dbSNP
rs530126523 1509 dbSNP
rs139197209 1533 dbSNP
rs1054249925 1538 dbSNP
rs931813739 1545 dbSNP
rs960400995 1546 dbSNP
rs1040300579 1548 dbSNP
rs926269306 1549 dbSNP
rs1337928588 1550 dbSNP
rs980430300 1550 dbSNP
rs952059940 1564 dbSNP
rs1209278641 1565 dbSNP
rs527346979 1565 dbSNP
rs1027542618 1571 dbSNP
rs993753615 1573 dbSNP
rs1192830201 1575 dbSNP
rs560010190 1579 dbSNP
rs1240545655 1600 dbSNP
rs961884041 1613 dbSNP
rs530134541 1616 dbSNP
rs1203738870 1639 dbSNP
rs983433289 1644 dbSNP
rs747180289 1645 dbSNP
rs952137908 1668 dbSNP
rs1259452821 1673 dbSNP
rs1434030395 1674 dbSNP
rs546357228 1675 dbSNP
rs1221279076 1677 dbSNP
rs1015657233 1678 dbSNP
rs991028619 1682 dbSNP
rs577503428 1686 dbSNP
rs1008255850 1692 dbSNP
rs146195364 1693 dbSNP
rs543708970 1699 dbSNP
rs1298807521 1703 dbSNP
rs1049727896 1707 dbSNP
rs1232821851 1718 dbSNP
rs1283083773 1719 dbSNP
rs1345857312 1724 dbSNP
rs996832246 1725 dbSNP
rs904122069 1727 dbSNP
rs1370204928 1728 dbSNP
rs1282185184 1733 dbSNP
rs1296890882 1737 dbSNP
rs1442161029 1741 dbSNP
rs1019935242 1742 dbSNP
rs1189378824 1746 dbSNP
rs764652274 1747 dbSNP
rs1043966157 1753 dbSNP
rs945564889 1768 dbSNP
rs141515586 1771 dbSNP
rs892926343 1787 dbSNP
rs1157504322 1793 dbSNP
rs114029473 1803 dbSNP
rs114515847 1804 dbSNP
rs386660972 1805 dbSNP
rs1320799791 1810 dbSNP
rs926325053 1815 dbSNP
rs1306336278 1819 dbSNP
rs1332202020 1831 dbSNP
rs980857720 1833 dbSNP
rs1176869917 1845 dbSNP
rs572185414 1845 dbSNP
rs930301911 1850 dbSNP
rs1238913503 1854 dbSNP
rs558363169 1855 dbSNP
rs538816619 1868 dbSNP
rs920530559 1881 dbSNP
rs971990936 1885 dbSNP
rs1480946480 1887 dbSNP
rs1211561324 1888 dbSNP
rs1239432498 1890 dbSNP
rs1269136452 1894 dbSNP
rs202235284 1900 dbSNP
rs752158709 1901 dbSNP
rs766819390 1920 dbSNP
rs955471079 1922 dbSNP
rs1159496884 1924 dbSNP
rs1028385963 1926 dbSNP
rs930629696 1928 dbSNP
rs1263311272 1929 dbSNP
rs920557681 1956 dbSNP
rs1391819666 1971 dbSNP
rs1391333806 1974 dbSNP
rs75112182 1975 dbSNP
rs1314271030 1978 dbSNP
rs1305342792 1987 dbSNP
rs1229046005 1988 dbSNP
rs1292955286 1993 dbSNP
rs938067822 1994 dbSNP
rs1445146319 2002 dbSNP
rs1235321155 2007 dbSNP
rs1267009230 2011 dbSNP
rs903841222 2016 dbSNP
rs750538313 2020 dbSNP
rs1009819080 2021 dbSNP
rs892683264 2027 dbSNP
rs1378345135 2036 dbSNP
rs765501493 2046 dbSNP
rs1056653676 2051 dbSNP
rs762188099 2052 dbSNP
rs1416475895 2054 dbSNP
rs1474025272 2061 dbSNP
rs138775144 2076 dbSNP
rs536116661 2079 dbSNP
rs567289966 2082 dbSNP
rs1303602849 2083 dbSNP
rs920263659 2090 dbSNP
rs150160243 2096 dbSNP
rs1467794415 2097 dbSNP
rs1297001395 2098 dbSNP
rs1372921797 2101 dbSNP
rs1410921695 2123 dbSNP
rs544264351 2143 dbSNP
rs972427396 2144 dbSNP
rs957043502 2160 dbSNP
rs180693200 2161 dbSNP
rs141744872 2165 dbSNP
rs987285871 2168 dbSNP
rs1181687344 2169 dbSNP
rs759365609 2175 dbSNP
rs1018809172 2183 dbSNP
rs1249353870 2187 dbSNP
rs1344269234 2195 dbSNP
rs1205703442 2206 dbSNP
rs1256209409 2209 dbSNP
rs886058719 2214 dbSNP
rs886058718 2215 dbSNP
rs886397126 2222 dbSNP
rs552540330 2225 dbSNP
rs1428339401 2227 dbSNP
rs774292834 2240 dbSNP
rs886058717 2255 dbSNP
rs1430956873 2261 dbSNP
rs1173550420 2262 dbSNP
rs968493629 2265 dbSNP
rs372522153 2266 dbSNP
rs1009537068 2272 dbSNP
rs1361560451 2275 dbSNP
rs190988002 2280 dbSNP
rs1035245805 2289 dbSNP
rs1312026502 2292 dbSNP
rs1367024094 2308 dbSNP
rs1229124174 2322 dbSNP
rs930515171 2340 dbSNP
rs1003735219 2342 dbSNP
rs1382061050 2344 dbSNP
rs543785188 2349 dbSNP
rs886058716 2350 dbSNP
rs1256023386 2351 dbSNP
rs1485357887 2353 dbSNP
rs1184334936 2356 dbSNP
rs1250303075 2365 dbSNP
rs575340631 2366 dbSNP
rs930405138 2367 dbSNP
rs938136614 2375 dbSNP
rs1416607528 2385 dbSNP
rs898877920 2408 dbSNP
rs1176927230 2412 dbSNP
rs1344617394 2413 dbSNP
rs928029256 2418 dbSNP
rs1322789387 2425 dbSNP
rs886058715 2427 dbSNP
rs1036043688 2428 dbSNP
rs746181216 2431 dbSNP
rs1078968 2433 dbSNP
rs1288051913 2451 dbSNP
rs755371328 2453 dbSNP
rs560974236 2457 dbSNP
rs1301366126 2458 dbSNP
rs1315749093 2466 dbSNP
rs931851338 2467 dbSNP
rs921786926 2468 dbSNP
rs867467479 2483 dbSNP
rs867356348 2484 dbSNP
rs1385293293 2486 dbSNP
rs1269597144 2487 dbSNP
rs978963595 2500 dbSNP
rs968167427 2524 dbSNP
rs915283422 2526 dbSNP
rs988158221 2534 dbSNP
rs375480909 2535 dbSNP
rs958259802 2538 dbSNP
rs1192226809 2542 dbSNP
rs769422762 2543 dbSNP
rs956672347 2551 dbSNP
rs1417395003 2555 dbSNP
rs1161694190 2567 dbSNP
rs1488784332 2580 dbSNP
rs557700653 2584 dbSNP
rs1220874121 2592 dbSNP
rs1003787619 2594 dbSNP
rs969997671 2595 dbSNP
rs1438538882 2603 dbSNP
rs1359406789 2614 dbSNP
rs1294026313 2615 dbSNP
rs1284845760 2616 dbSNP
rs1247151104 2623 dbSNP
rs1372034218 2624 dbSNP
rs1226017461 2628 dbSNP
rs1023805231 2631 dbSNP
rs995388225 2632 dbSNP
rs898935364 2640 dbSNP
rs891368 2646 dbSNP
rs1004535094 2648 dbSNP
rs148022607 2655 dbSNP
rs1223028020 2660 dbSNP
rs1019109686 2663 dbSNP
rs1482140640 2679 dbSNP
rs545126921 2685 dbSNP
rs755321558 2688 dbSNP
rs886284156 2694 dbSNP
rs1026125164 2695 dbSNP
rs994777528 2696 dbSNP
rs1423897004 2702 dbSNP
rs186393432 2706 dbSNP
rs1165459913 2707 dbSNP
rs1055164343 2723 dbSNP
rs1459975383 2729 dbSNP
rs1372005697 2733 dbSNP
rs1350510767 2737 dbSNP
rs1193869985 2755 dbSNP
rs1478625535 2756 dbSNP
rs1413853322 2762 dbSNP
rs921809602 2766 dbSNP
rs1265756787 2769 dbSNP
rs1358952717 2769 dbSNP
rs1197796425 2773 dbSNP
rs938007088 2777 dbSNP
rs1340696355 2778 dbSNP
rs373750297 2779 dbSNP
rs886058714 2787 dbSNP
rs371144725 2789 dbSNP
rs866438979 2790 dbSNP
rs1185770129 2791 dbSNP
rs1250854869 2799 dbSNP
rs1239410742 2800 dbSNP
rs1473221516 2806 dbSNP
rs1182267109 2811 dbSNP
rs536573296 2813 dbSNP
rs1427759904 2814 dbSNP
rs758989408 2819 dbSNP
rs143710210 2820 dbSNP
rs927946432 2822 dbSNP
rs1331843723 2825 dbSNP
rs1341913155 2828 dbSNP
rs181833853 2829 dbSNP
rs969682622 2830 dbSNP
rs1363397917 2835 dbSNP
rs1231328944 2838 dbSNP
rs9875573 2840 dbSNP
rs1347310777 2845 dbSNP
rs1331486238 2847 dbSNP
rs754135193 2854 dbSNP
rs964736539 2855 dbSNP
rs1325371006 2856 dbSNP
rs571213903 2858 dbSNP
rs995042089 2867 dbSNP
rs911530465 2871 dbSNP
rs987642902 2872 dbSNP
rs1395114487 2883 dbSNP
rs1170818591 2884 dbSNP
rs2099162 2887 dbSNP
rs1014662231 2889 dbSNP
rs1403631403 2892 dbSNP
rs1004587422 2895 dbSNP
rs1317180179 2896 dbSNP
rs370653475 2899 dbSNP
rs890164831 2903 dbSNP
rs1386990119 2909 dbSNP
rs1051386425 2911 dbSNP
rs1477864853 2912 dbSNP
rs1231627092 2932 dbSNP
rs1370951915 2932 dbSNP
rs996216173 2940 dbSNP
rs1201587293 2941 dbSNP
rs1345797438 2948 dbSNP
rs2082093 2950 dbSNP
rs1034015528 2951 dbSNP
rs1463419003 2953 dbSNP
rs1210378897 2955 dbSNP
rs1248364299 2958 dbSNP
rs1043346442 2961 dbSNP
rs947269302 2967 dbSNP
rs1378916466 2977 dbSNP
rs1199426839 2978 dbSNP
rs930686494 2980 dbSNP
rs906540667 2981 dbSNP
rs1458454307 2983 dbSNP
rs920581224 2989 dbSNP
rs891624907 2991 dbSNP
rs1390396374 2992 dbSNP
rs886058713 2995 dbSNP
rs1223140817 2996 dbSNP
rs886058712 2997 dbSNP
rs1331796676 2998 dbSNP
rs935403055 2999 dbSNP
rs1345406491 3002 dbSNP
rs1276447023 3003 dbSNP
rs1286477509 3012 dbSNP
rs1331522724 3015 dbSNP
rs570250284 3028 dbSNP
rs927998853 3029 dbSNP
rs1355359677 3031 dbSNP
rs757135640 3038 dbSNP
rs1451723495 3039 dbSNP
rs1180869462 3041 dbSNP
rs886058711 3056 dbSNP
rs948034065 3058 dbSNP
rs1009630912 3063 dbSNP
rs571109920 3068 dbSNP
rs1053916105 3069 dbSNP
rs1165561614 3071 dbSNP
rs936839954 3073 dbSNP
rs974056240 3075 dbSNP
rs963620632 3077 dbSNP
rs1015049921 3081 dbSNP
rs1414702417 3083 dbSNP
rs1306260116 3088 dbSNP
rs1426286950 3090 dbSNP
rs1174721782 3091 dbSNP
rs1410729282 3091 dbSNP
rs552560218 3092 dbSNP
rs886058710 3093 dbSNP
rs1242308921 3107 dbSNP
rs954474058 3115 dbSNP
rs1356972235 3116 dbSNP
rs1204282722 3119 dbSNP
rs1179829317 3123 dbSNP
rs1271931968 3129 dbSNP
rs1030013155 3131 dbSNP
rs1182505629 3134 dbSNP
rs1241395202 3140 dbSNP
rs1255023479 3148 dbSNP
rs530359415 3149 dbSNP
rs1421642376 3156 dbSNP
rs1190082036 3163 dbSNP
rs995879688 3177 dbSNP
rs1429686332 3187 dbSNP
rs886058709 3191 dbSNP
rs561235953 3195 dbSNP
rs1021574868 3196 dbSNP
rs1011904757 3200 dbSNP
rs891675803 3202 dbSNP
rs944276329 3206 dbSNP
rs541073115 3208 dbSNP
rs1302535783 3209 dbSNP
rs911567973 3212 dbSNP
rs1397938759 3228 dbSNP
rs201061318 3235 dbSNP
rs1227662780 3237 dbSNP
rs1203221097 3238 dbSNP
rs1052945371 3239 dbSNP
rs1349705912 3243 dbSNP
rs1205285906 3250 dbSNP
rs1254867649 3251 dbSNP
rs1482072168 3252 dbSNP
rs987139190 3257 dbSNP
rs950479569 3261 dbSNP
rs1242261100 3264 dbSNP
rs1379874808 3275 dbSNP
rs1313806249 3278 dbSNP
rs1187270655 3284 dbSNP
rs1448264772 3285 dbSNP
rs766245126 3286 dbSNP
rs1336548945 3288 dbSNP
rs1399262962 3305 dbSNP
rs906642546 3306 dbSNP
rs1046906991 3310 dbSNP
rs948115274 3319 dbSNP
rs371114428 3320 dbSNP
rs973108862 3327 dbSNP
rs1159738692 3335 dbSNP
rs1442113071 3336 dbSNP
rs886058708 3342 dbSNP
rs916566285 3343 dbSNP
rs1295072870 3344 dbSNP
rs1367312625 3346 dbSNP
rs1383425042 3348 dbSNP
rs1033489111 3352 dbSNP
rs527683198 3353 dbSNP
rs1235040518 3354 dbSNP
rs942285156 3357 dbSNP
rs1263342875 3367 dbSNP
rs970652407 3368 dbSNP
rs1025426277 3371 dbSNP
rs908106084 3375 dbSNP
rs565093798 3384 dbSNP
rs142330220 3389 dbSNP
rs1250244298 3392 dbSNP
rs1465757142 3396 dbSNP
rs1473241049 3397 dbSNP
rs1009516449 3402 dbSNP
rs1434952059 3404 dbSNP
rs892591770 3416 dbSNP
rs1487814057 3419 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' ggUCGGG-ACGUGUGGAGGGg 5'
            :||:|  |||  |||||| 
Target 5' ugGGCUCAAGCAAUCCUCCCa 3'
12 - 32
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 ENST00000296292.3 | 3UTR | CCUCAAACUCCUGGGCUCAAGCAAUCCUCCCACCUCAG
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
495 hsa-miR-6799-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT057844 SLC30A7 solute carrier family 30 member 7 2 2
MIRT180622 CRY2 cryptochrome circadian clock 2 2 2
MIRT254627 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT294657 ZNF548 zinc finger protein 548 2 2
MIRT386443 CCL22 C-C motif chemokine ligand 22 2 2
MIRT441466 BEST3 bestrophin 3 2 2
MIRT446753 ZNF491 zinc finger protein 491 2 2
MIRT449226 RAD51B RAD51 paralog B 2 2
MIRT451096 ZNF584 zinc finger protein 584 2 2
MIRT451563 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451685 C1RL complement C1r subcomponent like 2 2
MIRT451739 CES3 carboxylesterase 3 2 2
MIRT451761 ZNF611 zinc finger protein 611 2 6
MIRT452415 QDPR quinoid dihydropteridine reductase 2 2
MIRT452566 ZFP69B ZFP69 zinc finger protein B 2 2
MIRT452860 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT452925 DISC1 disrupted in schizophrenia 1 2 2
MIRT453051 TANGO2 transport and golgi organization 2 homolog 2 4
MIRT453102 HOXC4 homeobox C4 2 2
MIRT453256 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT453299 ZNF394 zinc finger protein 394 2 2
MIRT453474 PITPNM3 PITPNM family member 3 2 2
MIRT453542 PRR12 proline rich 12 2 2
MIRT453597 ZNF557 zinc finger protein 557 2 2
MIRT453798 KBTBD12 kelch repeat and BTB domain containing 12 2 2
MIRT453939 XRCC6 X-ray repair cross complementing 6 2 6
MIRT453990 CECR1 adenosine deaminase 2 2 2
MIRT454087 TMEM209 transmembrane protein 209 2 2
MIRT454658 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT454756 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 2 2
MIRT454846 AC