miRTarBase - #MIRT314032


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pre-miRNA Information
pre-miRNA hsa-mir-6839   
Genomic Coordinates chr7: 64679064 - 64679176
Description Homo sapiens miR-6839 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6839-3p
Sequence 92| UUGGGUUUUCUCUUCAAUCCAG |113
Evidence Experimental
Experiments Meta-analysis
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN15661209 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1426245091 3 dbSNP
rs533324498 6 dbSNP
rs1169594864 16 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PAPD7   
Synonyms LAK-1, LAK1, POLK, POLS, TRF4, TRF4-1, TRF41, TUTASE5
Description poly(A) RNA polymerase D7, non-canonical
Transcript NM_001171805   
Other Transcripts NM_001171806 , NM_006999   
Expression
Putative miRNA Targets on PAPD7
3'UTR of PAPD7
(miRNA target sites are highlighted)		 
>PAPD7|NM_001171805|3'UTR
   1 TGGCTCCTGGCTGCGTCAGCCTCCCCCACCCCTCTGCAGACTGCCCCGCGGCCTCGGCCACCGGCAGGGGAACCGAGACC
  81 AGCACCCCGCACGTCAGCCGGGCTCGCGGCACGCCCGCCGCTGATCACTCTGCATGTTTCTTCGTGTGGTGGTCGCGTCC
 161 ATCTTCAAGAACAGCTCGTTGTGCTCATCTGTGAAGCCTTATTAAACGTGGACGTTGTTTTCTGCCTTCCCAGGATTCTT
 241 CCTTCAGTGCTGAGGCAGGTCGGGCTCAGGAACTGCAGGGACGTGAACATGCGCTTGCGGTTTGAGGTAGCCGTGTCTGT
 321 TCCTTCGCGGTTTGCTATTTTCATTTCCTGTTCGTCAAAGCAGCAGAGGAGATCAAACCCCGTTCGTGTGTCTTTCCTCC
 401 ACGGATAAGCTTGGGAGGTCATTGTTTTACTGCCCTCACATTTTGTTTGAAATTTCAGAACTGTTTTTCTATGTAAATAT
 481 TGAAAACTTATGATTTGTGCAATAACTCAGATATTTTTTATTTAATTTCCTATTTTCACATAAGTTATATTTAAGGGAGG
 561 AGGGAATTTTTTTTAAACAAGCTTAGGTCCTTTCCCGAGCTGCATTTTCTAAGTTGGGTCATCGTGTCGGCTGGTTGTCT
 641 GACGAGCATCGTTACAAACACCATGATGAGGGGTTTGGGGTTTTATTTTGATGTCTTTTCTTTTGGTCGGAAGTGAGTGA
 721 AGGAGCCAGGTCGCCCTGAAGGTTTTCCAAAGGGCTTGGCTCCAGAGCCACCTGGCAGACTGCCCGTGGCCCTGCTGTCG
 801 GGCCCCAGGCCGTTGTCCTGCTCTGACCACAGAGTTTTAATGTTTTGGTTTTCACTTCTTTTAAACTGGACAACAAATCC
 881 AGCATTTCAAGTGCCAGAAGTATAACTTTCTAAGGAGAGAAGGGTTGTCACATTATAAAATCTTTAGGAAAATGTGAACT
 961 GGAAAACGCTTCGGTCAGTTTTAGTGACATAGCCTGTGATGATGGGTCTGGTGACTATTATTGCGGACCGTGGTACCCAG
1041 TTTTAGGAATGTGGAGAAAGGAATTCTGTTGATTCCGTTGAGGAATCTGTAGCGTATGCATTCGTTCTGTTAAGAGCAAA
1121 TCTAGGAGAAGTGCTTCAGCTGCCCAGTGCGCCGTGGGGAGTGTTTTAACGGATCGTGTCGCAGGAGAGCACAGCCCAGC
1201 GTTGGGGCCGGGACCGCTGGCGCCCGACGTCGGAAGCATACAGGTATACTATGCAAGTGTATTCTGCCACAACAACCACT
1281 GTCTTTGTTACCTTTTTTTGAACAAGAATATATCCATCCTGCCTAACCCTGAGTTTTTGGAGCACCACAGTTGTCCTGGG
1361 AGTTGGTTGCATCTTGTAGGCCATCTGACTTCCTGTTTTTAAAACGGGGGTCTGGTCTTGCTAAACACTACAGGTAGGTT
1441 GGTCTTTGAAGTCCACTAGTGGAGAATGTCAAGACAAGATACTTATTACCATGACATCTGATGCATGTGCAGCAGTGGGG
1521 AGTTCTAGATTGATCTCTGAATGTGATCGACGCCCAGCAAGGACAAGCTTTAAAATGTCTGCGGTCTGCCCTTTTGAAGC
1601 AGGACTGGCTCACTCTGTCATTGGGAGCTGTCAGCTGCGACTGCAGGTTCTCTAGGAGGCATTCCAGAATAGAGTAGCAC
1681 ACTGTGTCTGCAGTTCTCGATGACCGAAAGTTATCAAAAATATTTAAAATATTTAAATTGTGAACCTATTGATAAAGAAT
1761 ATTTATAAAAACTGATCTGTAGGCCTGTACTAATCTCTACGCATTAGCAATATTGACTGTAAACCCACATTAAGGAAACC
1841 ACTACGGGTCTGGCAGTGCGTGTCCCGTGGGGTGTGCATTTTAAAACTCGATTCATAGACACAGGTACCATGTTCCATTT
1921 CCGTCATGGTGAAGCAAATGAATTGGCCTGGCTACCACTGTGGTCGCGTGCTACAGGTTTGACAAAAAGATATCATGTTT
2001 CGATTTTTTTGTGTGTGGACAACAATATGGAAGCTAAAATTGACATATTTTTATGTAAAGTTTTTCTATTCTTTGATTTT
2081 TAATAAACTTTGGAAACCAGTTTAAAAAAAAAA
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' gaccUAACUUCUCUUUUGGGUu 5'
              |||| |  | ||||||| 
Target 5' caatATTG-ACTGTAAACCCAc 3'
 1808 - 1828 153.00 -9.70
2 
miRNA  3' gaccuaaCUUCUCU--UUUGGGuu 5'
                 ||:||||  ||||||  
Target 5' agcagcaGAGGAGATCAAACCCcg 3'
 359 - 382 141.00 -14.20
3 
miRNA  3' gaccUAACUUCUCUUUUGGGUu 5'
              | ||:| |  |||:||| 
Target 5' ttaaACTGGACAACAAATCCAg 3'
 861 - 882 138.00 -11.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30107879 6 COSMIC
COSN20057503 15 COSMIC
COSN31507891 26 COSMIC
COSN18729826 28 COSMIC
COSN26437093 51 COSMIC
COSN28836387 89 COSMIC
COSN31577005 156 COSMIC
COSN31545050 215 COSMIC
COSN30172228 223 COSMIC
COSN28801921 262 COSMIC
COSN30176223 305 COSMIC
COSN6925736 329 COSMIC
COSN9309692 402 COSMIC
COSN31536023 444 COSMIC
COSN31515047 541 COSMIC
COSN29468635 556 COSMIC
COSN31588094 564 COSMIC
COSN31545391 575 COSMIC
COSN19002552 622 COSMIC
COSN31491222 633 COSMIC
COSN28758284 640 COSMIC
COSN29274780 687 COSMIC
COSN30541713 725 COSMIC
COSN25757973 849 COSMIC
COSN24534152 954 COSMIC
COSN32062309 1017 COSMIC
COSN31594153 1089 COSMIC
COSN31569723 1144 COSMIC
COSN31480398 1171 COSMIC
COSN31577786 1173 COSMIC
COSN32058509 1223 COSMIC
COSN14980162 1247 COSMIC
COSN30542866 1319 COSMIC
COSN30543068 1320 COSMIC
COSN31482808 1533 COSMIC
COSN19067371 1542 COSMIC
COSN26752206 1641 COSMIC
COSN26567140 1694 COSMIC
COSN31486121 1720 COSMIC
COSN9955969 1743 COSMIC
COSN23706648 1891 COSMIC
COSN31543349 1939 COSMIC
COSN31555852 1957 COSMIC
COSN22616845 1969 COSMIC
COSN31569006 2067 COSMIC
COSN31529771 2090 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs537954282 2 dbSNP
rs989644580 4 dbSNP
rs763607292 6 dbSNP
rs1299116562 7 dbSNP
rs1340762865 9 dbSNP
rs1330073622 14 dbSNP
rs374273741 15 dbSNP
rs368438275 16 dbSNP
rs966963490 20 dbSNP
rs766622423 22 dbSNP
rs1233797682 23 dbSNP
rs3822436 24 dbSNP
rs1232935958 26 dbSNP
rs372015045 28 dbSNP
rs957266568 30 dbSNP
rs778024726 31 dbSNP
rs749437135 32 dbSNP
rs911799388 33 dbSNP
rs771231370 34 dbSNP
rs762194546 35 dbSNP
rs940628853 40 dbSNP
rs921028880 42 dbSNP
rs971922229 47 dbSNP
rs745739473 48 dbSNP
rs375445893 49 dbSNP
rs368724278 50 dbSNP
rs760626895 51 dbSNP
rs1196411604 52 dbSNP
rs28381435 56 dbSNP
rs895122582 57 dbSNP
rs1254456348 59 dbSNP
rs1210639552 62 dbSNP
rs938017149 63 dbSNP
rs1226548859 64 dbSNP
rs948047837 67 dbSNP
rs1270897686 73 dbSNP
rs896598811 75 dbSNP
rs1046462487 76 dbSNP
rs1311996468 78 dbSNP
rs1415187963 81 dbSNP
rs975036100 85 dbSNP
rs554075757 86 dbSNP
rs372277358 89 dbSNP
rs902688666 90 dbSNP
rs1265097749 93 dbSNP
rs1000225301 94 dbSNP
rs574007652 100 dbSNP
rs1419563658 101 dbSNP
rs575657775 104 dbSNP
rs1010589010 106 dbSNP
rs1486959737 107 dbSNP
rs375320330 108 dbSNP
rs953163748 109 dbSNP
rs542882975 113 dbSNP
rs1019067390 114 dbSNP
rs562901799 117 dbSNP
rs1468793708 118 dbSNP
rs748037273 120 dbSNP
rs576352088 121 dbSNP
rs920399264 124 dbSNP
rs1357122272 125 dbSNP
rs1453980702 130 dbSNP
rs951986976 131 dbSNP
rs984176151 134 dbSNP
rs916653813 135 dbSNP
rs948140627 145 dbSNP
rs1046428320 146 dbSNP
rs1403098903 146 dbSNP
rs927963708 155 dbSNP
rs746833521 156 dbSNP
rs1475848214 157 dbSNP
rs768809578 158 dbSNP
rs1285705717 159 dbSNP
rs1053135645 162 dbSNP
rs937924903 167 dbSNP
rs545532433 169 dbSNP
rs1272691742 173 dbSNP
rs1055564843 176 dbSNP
rs893946045 178 dbSNP
rs1223009499 179 dbSNP
rs1265950716 179 dbSNP
rs1281441822 184 dbSNP
rs539974549 187 dbSNP
rs1373520831 188 dbSNP
rs1216686895 191 dbSNP
rs1280919612 194 dbSNP
rs1011019335 208 dbSNP
rs1369582910 210 dbSNP
rs1050580979 211 dbSNP
rs781275748 214 dbSNP
rs558112325 215 dbSNP
rs1157305833 219 dbSNP
rs1018576636 225 dbSNP
rs962016248 229 dbSNP
rs993402303 232 dbSNP
rs1400497053 233 dbSNP
rs1027996853 236 dbSNP
rs1269565892 237 dbSNP
rs758135806 247 dbSNP
rs1179159878 256 dbSNP
rs565215182 260 dbSNP
rs274675 262 dbSNP
rs1032490664 263 dbSNP
rs1196723089 266 dbSNP
rs900771934 269 dbSNP
rs71600237 270 dbSNP
rs1157856915 275 dbSNP
rs866753997 277 dbSNP
rs1345006910 281 dbSNP
rs371509469 283 dbSNP
rs1305318144 284 dbSNP
rs1286144816 289 dbSNP
rs1366798617 290 dbSNP
rs915786127 290 dbSNP
rs996427944 293 dbSNP
rs1303439983 294 dbSNP
rs10037633 299 dbSNP
rs529208421 300 dbSNP
rs1287629717 307 dbSNP
rs1430720008 308 dbSNP
rs1301377714 312 dbSNP
rs1375549530 313 dbSNP
rs955021173 314 dbSNP
rs1394714811 316 dbSNP
rs986424269 317 dbSNP
rs1455637212 325 dbSNP
rs190018612 327 dbSNP
rs568873510 328 dbSNP
rs935344412 329 dbSNP
rs1052475983 330 dbSNP
rs915461981 338 dbSNP
rs1490184128 344 dbSNP
rs1485107708 349 dbSNP
rs959586156 350 dbSNP
rs144572996 354 dbSNP
rs551481107 355 dbSNP
rs555282487 358 dbSNP
rs947012111 359 dbSNP
rs1050548045 361 dbSNP
rs889289063 378 dbSNP
rs1008559776 382 dbSNP
rs1040544282 383 dbSNP
rs897458944 386 dbSNP
rs28381436 387 dbSNP
rs1446071319 393 dbSNP
rs1371385459 395 dbSNP
rs1169856442 397 dbSNP
rs1165937985 398 dbSNP
rs274674 403 dbSNP
rs553965830 404 dbSNP
rs567471697 414 dbSNP
rs1474749828 416 dbSNP
rs1258042929 419 dbSNP
rs924048428 422 dbSNP
rs35781419 426 dbSNP
rs1322091367 429 dbSNP
rs951940183 430 dbSNP
rs936754016 431 dbSNP
rs1054389520 441 dbSNP
rs1443070715 441 dbSNP
rs759979999 444 dbSNP
rs900658740 447 dbSNP
rs1022765585 449 dbSNP
rs1297657391 461 dbSNP
rs181234493 463 dbSNP
rs1454774750 465 dbSNP
rs1315472251 466 dbSNP
rs1308542980 470 dbSNP
rs556578060 472 dbSNP
rs576414257 481 dbSNP
rs971237404 488 dbSNP
rs763794729 492 dbSNP
rs961447952 498 dbSNP
rs995259803 503 dbSNP
rs573654063 507 dbSNP
rs959239828 510 dbSNP
rs1462574064 512 dbSNP
rs1275081573 514 dbSNP
rs1162695718 521 dbSNP
rs1035503591 525 dbSNP
rs956837945 533 dbSNP
rs988546417 540 dbSNP
rs1307984687 544 dbSNP
rs915279038 548 dbSNP
rs946938365 550 dbSNP
rs1203280373 558 dbSNP
rs1189820956 560 dbSNP
rs986346498 564 dbSNP
rs1416894011 565 dbSNP
rs1249403440 567 dbSNP
rs990581255 567 dbSNP
rs917847665 584 dbSNP
rs545061609 587 dbSNP
rs1270772612 591 dbSNP
rs970597819 597 dbSNP
rs1462380804 598 dbSNP
rs1334792386 600 dbSNP
rs1274156374 602 dbSNP
rs1183759499 616 dbSNP
rs774977721 616 dbSNP
rs910694179 624 dbSNP
rs944888028 625 dbSNP
rs1161792951 629 dbSNP
rs1053871117 630 dbSNP
rs1422331723 636 dbSNP
rs1411002046 640 dbSNP
rs147882827 644 dbSNP
rs1395161112 645 dbSNP
rs1398116109 649 dbSNP
rs776202781 651 dbSNP
rs572594285 652 dbSNP
rs770389105 655 dbSNP
rs1337595669 656 dbSNP
rs929109020 665 dbSNP
rs1420556698 666 dbSNP
rs1049197366 672 dbSNP
rs1450249104 673 dbSNP
rs1192501487 675 dbSNP
rs1468377281 677 dbSNP
rs1254190813 680 dbSNP
rs1212210580 685 dbSNP
rs1271702703 686 dbSNP
rs1348976836 689 dbSNP
rs541491988 693 dbSNP
rs1239999599 696 dbSNP
rs761367354 699 dbSNP
rs148576717 709 dbSNP
rs896816159 710 dbSNP
rs995542218 717 dbSNP
rs1383946035 718 dbSNP
rs1289255862 727 dbSNP
rs1213852330 733 dbSNP
rs1270290772 734 dbSNP
rs1022901330 736 dbSNP
rs1203938308 742 dbSNP
rs1026744525 743 dbSNP
rs1396429936 747 dbSNP
rs1201603959 751 dbSNP
rs1262160563 760 dbSNP
rs1261407873 765 dbSNP
rs959355626 772 dbSNP
rs567493168 777 dbSNP
rs1489352824 783 dbSNP
rs1012054766 785 dbSNP
rs907148702 786 dbSNP
rs529089388 787 dbSNP
rs1276740484 792 dbSNP
rs749984862 793 dbSNP
rs542953033 794 dbSNP
rs957000988 798 dbSNP
rs988253953 800 dbSNP
rs958067996 801 dbSNP
rs1022211365 802 dbSNP
rs1311890267 805 dbSNP
rs1434990559 806 dbSNP
rs968037198 807 dbSNP
rs1165671448 808 dbSNP
rs1474688559 810 dbSNP
rs562619441 812 dbSNP
rs1186383172 813 dbSNP
rs1421620236 816 dbSNP
rs989854780 819 dbSNP
rs1471022015 821 dbSNP
rs1177219342 826 dbSNP
rs1405702778 829 dbSNP
rs1210416540 836 dbSNP
rs1486136300 841 dbSNP
rs922054173 848 dbSNP
rs1194158705 855 dbSNP
rs1338603063 880 dbSNP
rs986315566 884 dbSNP
rs112187753 885 dbSNP
rs1353295463 889 dbSNP
rs758287300 891 dbSNP
rs1320049203 892 dbSNP
rs1345507316 905 dbSNP
rs945000267 913 dbSNP
rs1414964444 916 dbSNP
rs1429963603 918 dbSNP
rs544243996 921 dbSNP
rs1326198616 922 dbSNP
rs1408873317 923 dbSNP
rs117255937 924 dbSNP
rs919466965 933 dbSNP
rs748934515 936 dbSNP
rs1187718776 941 dbSNP
rs1475621408 942 dbSNP
rs912057219 944 dbSNP
rs929013623 946 dbSNP
rs1437310457 949 dbSNP
rs551102447 949 dbSNP
rs1273853588 951 dbSNP
rs1048861974 954 dbSNP
rs1036617197 959 dbSNP
rs887412820 968 dbSNP
rs766318395 969 dbSNP
rs1044108008 973 dbSNP
rs534913207 974 dbSNP
rs1441083002 979 dbSNP
rs1282071786 981 dbSNP
rs1335813630 989 dbSNP
rs1332820583 997 dbSNP
rs1449605973 1000 dbSNP
rs1392926955 1017 dbSNP
rs1002827291 1018 dbSNP
rs527385382 1020 dbSNP
rs1048510280 1022 dbSNP
rs1321052605 1025 dbSNP
rs142992752 1026 dbSNP
rs891630844 1030 dbSNP
rs567568922 1031 dbSNP
rs1215485214 1034 dbSNP
rs1010041295 1039 dbSNP
rs1022347077 1055 dbSNP
rs1467027590 1059 dbSNP
rs968131591 1060 dbSNP
rs562564089 1068 dbSNP
rs751289625 1076 dbSNP
rs906376182 1077 dbSNP
rs151083904 1078 dbSNP
rs1428605042 1079 dbSNP
rs1030927473 1083 dbSNP
rs1017597555 1094 dbSNP
rs556852682 1095 dbSNP
rs989515489 1097 dbSNP
rs1437855757 1098 dbSNP
rs28381437 1100 dbSNP
rs879140259 1105 dbSNP
rs1381153303 1108 dbSNP
rs553332854 1113 dbSNP
rs1408480378 1114 dbSNP
rs781465229 1132 dbSNP
rs1399934116 1139 dbSNP
rs919380834 1147 dbSNP
rs987551610 1148 dbSNP
rs1394621297 1151 dbSNP
rs911940229 1152 dbSNP
rs186140867 1155 dbSNP
rs984986843 1161 dbSNP
rs1240105115 1162 dbSNP
rs972612153 1167 dbSNP
rs908944872 1168 dbSNP
rs539291941 1171 dbSNP
rs1287704245 1172 dbSNP
rs141069275 1176 dbSNP
rs930870814 1177 dbSNP
rs1044078912 1181 dbSNP
rs928330240 1182 dbSNP
rs938559942 1189 dbSNP
rs370072952 1191 dbSNP
rs1430475293 1192 dbSNP
rs1361637014 1200 dbSNP
rs1053059174 1201 dbSNP
rs947849220 1202 dbSNP
rs577697322 1203 dbSNP
rs1374880850 1208 dbSNP
rs1176925084 1210 dbSNP
rs891591840 1211 dbSNP
rs1417315058 1214 dbSNP
rs1011394391 1215 dbSNP
rs1042891741 1216 dbSNP
rs903943359 1217 dbSNP
rs1007630619 1222 dbSNP
rs777664936 1223 dbSNP
rs1485153430 1225 dbSNP
rs906259768 1226 dbSNP
rs541579832 1227 dbSNP
rs1314393060 1229 dbSNP
rs1284320351 1232 dbSNP
rs551550607 1233 dbSNP
rs1223801900 1234 dbSNP
rs771493733 1242 dbSNP
rs1268298138 1247 dbSNP
rs998147903 1248 dbSNP
rs1303446527 1249 dbSNP
rs1467637557 1250 dbSNP
rs1169620018 1254 dbSNP
rs1466122566 1257 dbSNP
rs1425439389 1259 dbSNP
rs1026554753 1262 dbSNP
rs190465975 1267 dbSNP
rs1184041555 1281 dbSNP
rs1233713453 1282 dbSNP
rs573806891 1283 dbSNP
rs1183292880 1286 dbSNP
rs1011227944 1293 dbSNP
rs1231849308 1293 dbSNP
rs1479367319 1293 dbSNP
rs1029033880 1297 dbSNP
rs1260326144 1298 dbSNP
rs1231863881 1304 dbSNP
rs984955765 1320 dbSNP
rs953361472 1331 dbSNP
rs909415761 1334 dbSNP
rs1398050072 1338 dbSNP
rs1371249952 1345 dbSNP
rs1297701385 1361 dbSNP
rs969763793 1363 dbSNP
rs78323632 1376 dbSNP
rs1162456521 1378 dbSNP
rs1460714080 1381 dbSNP
rs962096562 1384 dbSNP
rs1166430230 1393 dbSNP
rs1416986903 1400 dbSNP
rs1162794376 1404 dbSNP
rs1178722387 1406 dbSNP
rs1388452993 1406 dbSNP
rs562665806 1407 dbSNP
rs928268288 1414 dbSNP
rs952361569 1433 dbSNP
rs1212441789 1445 dbSNP
rs1328935697 1451 dbSNP
rs1359853656 1452 dbSNP
rs1488341746 1457 dbSNP
rs1247201821 1459 dbSNP
rs938371998 1460 dbSNP
rs1306294531 1465 dbSNP
rs1240982337 1467 dbSNP
rs1379283636 1468 dbSNP
rs531526464 1478 dbSNP
rs1334876547 1484 dbSNP
rs373447716 1487 dbSNP
rs1440127382 1491 dbSNP
rs1391153965 1492 dbSNP
rs916126882 1500 dbSNP
rs1451095451 1501 dbSNP
rs947344132 1505 dbSNP
rs1158939557 1506 dbSNP
rs1247386159 1506 dbSNP
rs1046019096 1507 dbSNP
rs1392767586 1514 dbSNP
rs1265411052 1516 dbSNP
rs1192286240 1537 dbSNP
rs1354835085 1538 dbSNP
rs544855561 1549 dbSNP
rs1268444012 1550 dbSNP
rs889623356 1552 dbSNP
rs181992032 1553 dbSNP
rs1007560315 1555 dbSNP
rs527290450 1558 dbSNP
rs935057214 1563 dbSNP
rs1039137580 1583 dbSNP
rs547120395 1584 dbSNP
rs1355902117 1587 dbSNP
rs1244764998 1592 dbSNP
rs1233406857 1593 dbSNP
rs1331618719 1602 dbSNP
rs560636604 1603 dbSNP
rs1380302893 1604 dbSNP
rs1026772993 1608 dbSNP
rs1052306649 1611 dbSNP
rs1421193361 1621 dbSNP
rs529763890 1629 dbSNP
rs746219336 1636 dbSNP
rs550128982 1638 dbSNP
rs1016403576 1639 dbSNP
rs970234022 1640 dbSNP
rs979817253 1648 dbSNP
rs1201721115 1651 dbSNP
rs1427104745 1655 dbSNP
rs1010701074 1658 dbSNP
rs1035430790 1660 dbSNP
rs889006469 1668 dbSNP
rs527566417 1673 dbSNP
rs1018937245 1678 dbSNP
rs1199959567 1680 dbSNP
rs1345881721 1683 dbSNP
rs1257688667 1686 dbSNP
rs960081425 1694 dbSNP
rs186330577 1699 dbSNP
rs1401419577 1700 dbSNP
rs28381438 1700 dbSNP
rs1027859179 1704 dbSNP
rs552895496 1706 dbSNP
rs566124314 1707 dbSNP
rs1403804975 1715 dbSNP
rs991640585 1733 dbSNP
rs978650882 1735 dbSNP
rs911031250 1740 dbSNP
rs942523547 1749 dbSNP
rs1478893736 1751 dbSNP
rs1339295202 1755 dbSNP
rs534993747 1761 dbSNP
rs971599560 1775 dbSNP
rs1258411270 1785 dbSNP
rs981767053 1790 dbSNP
rs1317253924 1791 dbSNP
rs761335385 1792 dbSNP
rs1220248851 1794 dbSNP
rs901924529 1801 dbSNP
rs1283231236 1802 dbSNP
rs933436257 1806 dbSNP
rs1251975495 1811 dbSNP
rs914961436 1823 dbSNP
rs1197016852 1824 dbSNP
rs146440814 1825 dbSNP
rs1400215756 1830 dbSNP
rs1172090985 1831 dbSNP
rs1467509607 1833 dbSNP
rs1416202311 1835 dbSNP
rs1162868689 1839 dbSNP
rs1473262317 1845 dbSNP
rs772655979 1846 dbSNP
rs1461933384 1847 dbSNP
rs191917215 1848 dbSNP
rs1253739617 1853 dbSNP
rs889059159 1854 dbSNP
rs944590890 1860 dbSNP
rs1430251328 1861 dbSNP
rs762455069 1868 dbSNP
rs1016541030 1873 dbSNP
rs1200524398 1879 dbSNP
rs1466946892 1883 dbSNP
rs766300327 1890 dbSNP
rs182965603 1891 dbSNP
rs1277192334 1896 dbSNP
rs1476578727 1900 dbSNP
rs1377089293 1908 dbSNP
rs556084648 1910 dbSNP
rs1001682817 1913 dbSNP
rs1348451088 1913 dbSNP
rs754782588 1923 dbSNP
rs377165283 1924 dbSNP
rs988973161 1927 dbSNP
rs767175071 1928 dbSNP
rs1302639485 1939 dbSNP
rs1157105087 1953 dbSNP
rs752557593 1954 dbSNP
rs978619773 1956 dbSNP
rs879124845 1966 dbSNP
rs942659701 1967 dbSNP
rs756232869 1968 dbSNP
rs956581492 1969 dbSNP
rs922437261 1973 dbSNP
rs1285269758 1977 dbSNP
rs1324546816 1986 dbSNP
rs187586511 1994 dbSNP
rs1254053080 1997 dbSNP
rs914992138 2002 dbSNP
rs28381439 2003 dbSNP
rs1242901258 2004 dbSNP
rs946467492 2005 dbSNP
rs1048297634 2008 dbSNP
rs567238436 2010 dbSNP
rs941999212 2012 dbSNP
rs1352047909 2019 dbSNP
rs564818762 2020 dbSNP
rs191587694 2024 dbSNP
rs1419381277 2027 dbSNP
rs1361188371 2030 dbSNP
rs1487259386 2033 dbSNP
rs1201041226 2036 dbSNP
rs767426889 2041 dbSNP
rs1479911786 2045 dbSNP
rs1173453677 2046 dbSNP
rs1191768197 2053 dbSNP
rs757467427 2058 dbSNP
rs1376313804 2069 dbSNP
rs1057265404 2072 dbSNP
rs895974007 2079 dbSNP
rs1488431236 2100 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' gaccUAACUUCUCUUUUGGGUu 5'
              |||| |  | ||||||| 
Target 5' caauAUUG-ACUGUAAACCCAc 3'
 		7 - 27
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 ENST00000230859.6 | 3UTR | CAUUAGCAAUAUUGACUGUAAACCCACAUUAAG
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
62 hsa-miR-6839-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059162 TXNIP thioredoxin interacting protein 2 2
MIRT064872 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT065802 HOXC8 homeobox C8 2 4
MIRT106005 SDCBP syndecan binding protein 2 2
MIRT275773 TFDP1 transcription factor Dp-1 2 2
MIRT314032 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 2
MIRT360277 HIST1H2BE histone cluster 1 H2B family member e 2 8
MIRT360301 HIST1H2BH histone cluster 1 H2B family member h 2 2
MIRT450086 OR2A4 olfactory receptor family 2 subfamily A member 4 2 2
MIRT468815 RSRC2 arginine and serine rich coiled-coil 2 2 6
MIRT475093 IRF2BP2 interferon regulatory factor 2 binding protein 2 2 4
MIRT477575 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
MIRT483926 LCORL ligand dependent nuclear receptor corepressor like 2 6
MIRT504381 HIST1H1C histone cluster 1 H1 family member c 2 4
MIRT506970 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT507028 HIST1H3B histone cluster 1 H3 family member b 2 6
MIRT511561 HIST3H2BB histone cluster 3 H2B family member b 2 4
MIRT511650 HIST1H3D histone cluster 1 H3 family member d 2 6
MIRT511696 HIST1H2BL histone cluster 1 H2B family member l 2 4
MIRT511737 HIST1H2BB histone cluster 1 H2B family member b 2 6
MIRT511746 HIST1H2BA histone cluster 1 H2B family member a 2 8
MIRT515260 CSNK1E casein kinase 1 epsilon 2 2
MIRT516220 RAB3B RAB3B, member RAS oncogene family 2 4
MIRT523281 HIST1H1E histone cluster 1 H1 family member e 2 2
MIRT524121 DMXL1 Dmx like 1 2 2
MIRT530744 GPR82 G protein-coupled receptor 82 2 2
MIRT532214 CCDC117 coiled-coil domain containing 117 2 2
MIRT546182 TPRG1L tumor protein p63 regulated 1 like 2 2
MIRT558638 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT559562 ARF1 ADP ribosylation factor 1 2 4
MIRT560680 HIST1H1T histone cluster 1 H1 family member t 2 2
MIRT570746 AAK1 AP2 associated kinase 1 2 2
MIRT609518 RAB3IP RAB3A interacting protein 2 2
MIRT612583 SYNGAP1 synaptic Ras GTPase activating protein 1 2 4
MIRT615733 RIOK3 RIO kinase 3 2 2
MIRT616068 SIX1 SIX homeobox 1 2 2
MIRT617903 SGCD sarcoglycan delta 2 2
MIRT620851 SERPING1 serpin family G member 1 2 2
MIRT625107 SLC1A5 solute carrier family 1 member 5 2 2
MIRT625120 NUP93 nucleoporin 93 2 2
MIRT625893 LINC00632 long intergenic non-protein coding RNA 632 2 2
MIRT626569 MED7 mediator complex subunit 7 2 2
MIRT626694 ZFP14 ZFP14 zinc finger protein 2 4
MIRT626808 PRR11 proline rich 11 2 2
MIRT628131 HM13 histocompatibility minor 13 2 2
MIRT636596 DCAF5 DDB1 and CUL4 associated factor 5 2 2
MIRT649866 SLFN12L schlafen family member 12 like 2 2
MIRT652133 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652663 TIMELESS timeless circadian clock 2 2
MIRT658335 FAM83D family with sequence similarity 83 member D 2 2
MIRT660615 ANKS4B ankyrin repeat and sterile alpha motif domain containing 4B 2 2
MIRT666304 SLC22A3 solute carrier family 22 member 3 2 2
MIRT668528 ERGIC2 ERGIC and golgi 2 2 2
MIRT692510 PARD3 par-3 family cell polarity regulator 2 2
MIRT694784 DHFRL1 dihydrofolate reductase 2 2 2
MIRT700510 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT701438 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT710155 MTRF1L mitochondrial translational release factor 1 like 2 2
MIRT711436 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT716979 GPR155 G protein-coupled receptor 155 2 2
MIRT720155 POU2F2 POU class 2 homeobox 2 2 2
MIRT722512 DSTYK dual serine/threonine and tyrosine protein kinase 2 2

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