miRTarBase - #MIRT465320


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pre-miRNA Information
pre-miRNA hsa-mir-383   
Genomic Coordinates chr8: 14853438 - 14853510
Synonyms MIRN383, hsa-mir-383, MIR383
Description Homo sapiens miR-383 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-383-5p
Sequence 7| AGAUCAGAAGGUGAUUGUGGCU |28
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26994512 7 COSMIC
COSN30109318 22 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs112302475 1 dbSNP
rs756858316 1 dbSNP
rs757040124 3 dbSNP
rs1419085595 4 dbSNP
rs912771170 5 dbSNP
rs1190491141 6 dbSNP
rs986831934 7 dbSNP
rs1471946963 9 dbSNP
rs1237080909 10 dbSNP
rs757526216 11 dbSNP
rs1431645579 13 dbSNP
rs763747200 13 dbSNP
rs184836993 15 dbSNP
rs913343525 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TRAF5   
Synonyms MGC:39780, RNF84
Description TNF receptor associated factor 5
Transcript NM_001033910   
Other Transcripts NM_004619 , NM_145759   
Expression
Putative miRNA Targets on TRAF5
3'UTR of TRAF5
(miRNA target sites are highlighted)		 
>TRAF5|NM_001033910|3'UTR
   1 TCACTGTTATGGGGTGATAAGAGGACTTCTTGGGGCCAGAACTGTGGAGGAGAGCACATTTGATTATCATATTGACCTGG
  81 ATTTAGACTCAAAGCACATTTGTATTTGCCTTTTTCCTTAACGTTTGAAGTCAGTTTAAAACTTCTGAAGTGCTGTCTTT
 161 TTACATTTTACTCTGTCCCAGTTTGAAACTTAAAACTCTTAGAATATTCTCTTATTATTTATATTTTTATATTTCTTGAA
 241 AGATGGTAAGTTTCTTGAAGTTTTTGGGGCGTTTCTCTTTTACTGGTGCTTAGCGCAGTGTCTCGGGCACTCTAAATATT
 321 GAGTGTTATGGAGGACACAGAGGTAGCAGAATCCCAGTTGAAAATGTTTTGATATTTTATTGTTTGGCCTATTGATTCTA
 401 GACCTGGCCTTAAGTCTGCAAAAGCCATCTTTATAAGGTAGGCTGTTCCAGTTAAGTAGTGGGTGATGTAGTTACAAAGA
 481 TAATATGCTCAGTTTGGACCTTTTTTTCAGTTAAATGCTAAATATATGAAAATTACTATACCTCTAAGTATTTTCATGAA
 561 ATTCACCAGCAGTTTGCAAGCACAGTTTTGCAAGGCTGCATAAGAACTGGTGAATGGGGTAAGCATTTTCATTCTTCCTG
 641 CTGAAGTAAAGCAGAAAGTACTGCATAGTATATGAGATATAGCCAGCTAGCTAAAGTTCAGATTTTGTTAGGTTCAACCC
 721 TATGAAAAAAACTATTTTCATAGGTCAAAAATGGTAAAAAATTAGCAGTTTCATAAGATTCAACCAAATAAATATATATA
 801 TACACACACACATACATATACACCTATATATGTGTGTATACAAACAGTTCGAATGTATTTTGGTGACAGTAATAAATCAA
 881 TGTGAGGATGGATAGAATTTAGTATATGATAGAGAAAATGTCATAAATGGATAAAAGGAATTTACAACTTGAGGAGAAAA
 961 CCTTTACAATTTCCTATGGGTGTCAGAAGTACTCTCAGCGAAAACTGATGGCTAAAACAGTATCTACTATTCTCTGATAA
1041 CTTTTTTTTTGAGACAGAGTTTCATTGTCACCCAGGCTGGAGTACAGTGGCATGATCTCAGCTCACTGCAAACTCTGCCT
1121 CCCGAATTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGCCCGTCACCACACCCAGGTAATTT
1201 TTGTATTTTTAGTAGAGACGGAGTTTTGCCATGTTGGCCAAGCTGATCTCAAACTCCTGACCTCAAGTGATCTGCCCGCC
1281 TCGGCCTCCCAAAGTGCTGAGATTACAGGCATGACCCACCGCGTCAAGCCTCTGACAACTATTGAATTTGTAAGCTGCTA
1361 TGCAAATGGGCATTTATATAAACTTGTGATGTTTCTTGTCAGAATTCTGAGTACTCTGTGAAGAACAGAAATGATCATAT
1441 TCTTATGCATCTATCTGTATGGGTCTGAAGGTGTATATACAAACTGAGATGAGTCCTTATGACTCTTGATAAGCCTGAGT
1521 TTAACAACAACAAAAATGCCAAGTTGTCCTGAGCCCTTCTGCGTTGTTATGCCACTTCCCTACTGCTCATATGCACGCTG
1601 GCTCCCCTGGGCACGCAAGGATGAGTATGGGCCATGGGCCCCTGTAGAGCTGCTTACCTGGTGATGACCATGCACCTTAC
1681 AATTTCTGAACAGTTAACCCTATAGAAGCATGCTTTATATGAGTGTCTTCTGGGAAGAGGAACCTTCTTAATCTCTTCTG
1761 TGGGATTTTCAAAATGCTAAAGACTCACACTGCAGCAATCATCCCAGATGATTAAATTCAAAGAAATAGGTTCACAACAG
1841 GAATATACTGAAGAACTAGAGTGTCACTGCTGGTGAACTGTGGCACGGTTGCTCAACACATCACCTCGGACAAATTCAGG
1921 AAGCATTTCTTTAGCCCACAAGTCCAGACCCAGGTGCTCTGTATGTTTGTTTTTAATATTCATCATATCCAAGTTCACTC
2001 TGTCTTCCTGAGCAGTGGAAGATCATATTGCTGTAACTTCTTTTAAGTAGTTGATGTGGAAAACATTTTAAAGTGAATTT
2081 GTCAAAATGCTGGTTTTGTGTTTTATCCAACTTTTGTGCATATATATAAAGTATGTCATGGCATGGTTTGCTTAGGAGTT
2161 CAGAGTTCCTTCATCATCGAAATAGTGATTAAGTGATCCCAGAACAAGGAATACTAGAGTAAAAAGCACCTCTTTTTCAC
2241 AAAAAAAAAAAAAA
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' ucGGUGUUAGUGGAAGACUAga 5'
            |:|| ||  :| ||||||  
Target 5' atCTACTAT--TC-TCTGATaa 3'
 1022 - 1040 131.00 -9.20
2 
miRNA  3' ucgGUGUUA-GUGGAAGACUAGa 5'
             |||  | || :|||||| | 
Target 5' atgCACCTTACAATTTCTGAACa 3'
 1670 - 1692 127.00 -9.52
3 
miRNA  3' ucGGUGUUAGUGG-AAGACUAGa 5'
            |||:: | :||   |||||| 
Target 5' tgCCATGTTGGCCAAGCTGATCt 3'
 1227 - 1249 124.00 -19.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30167681 30 COSMIC
COSN7984391 51 COSMIC
COSN30145277 73 COSMIC
COSN22473666 239 COSMIC
COSN1429314 246 COSMIC
COSN19457082 286 COSMIC
COSN20090456 539 COSMIC
COSN6021312 1088 COSMIC
COSN7201239 1098 COSMIC
COSN6021313 1171 COSMIC
COSN6440528 1177 COSMIC
COSN29190628 2238 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs765833700 4 dbSNP
rs753167716 5 dbSNP
rs1443534519 7 dbSNP
rs371227861 10 dbSNP
rs777934981 11 dbSNP
rs746706505 12 dbSNP
rs542729528 13 dbSNP
rs780807611 25 dbSNP
rs544270027 30 dbSNP
rs750652467 31 dbSNP
rs1317409185 35 dbSNP
rs745354891 36 dbSNP
rs183601818 45 dbSNP
rs1431032245 48 dbSNP
rs775395971 53 dbSNP
rs1479855240 60 dbSNP
rs573131564 61 dbSNP
rs1187691577 62 dbSNP
rs950993205 64 dbSNP
rs1240811559 71 dbSNP
rs540570162 73 dbSNP
rs753207609 77 dbSNP
rs1016670540 88 dbSNP
rs964803838 89 dbSNP
rs974777310 98 dbSNP
rs1359845161 112 dbSNP
rs921122805 115 dbSNP
rs1473125818 117 dbSNP
rs1453194322 120 dbSNP
rs1350332340 123 dbSNP
rs565614512 124 dbSNP
rs1468968835 130 dbSNP
rs1354709100 151 dbSNP
rs577701565 151 dbSNP
rs1260495862 153 dbSNP
rs933838088 172 dbSNP
rs1486418613 176 dbSNP
rs188266749 184 dbSNP
rs1188482625 185 dbSNP
rs957866746 215 dbSNP
rs1445706940 218 dbSNP
rs986570807 236 dbSNP
rs763524290 245 dbSNP
rs1188775585 264 dbSNP
rs913828845 271 dbSNP
rs945280327 272 dbSNP
rs1305837814 280 dbSNP
rs1272281705 284 dbSNP
rs1246635409 290 dbSNP
rs563099824 296 dbSNP
rs903501093 305 dbSNP
rs771328463 306 dbSNP
rs937772598 307 dbSNP
rs1020486414 309 dbSNP
rs966435505 315 dbSNP
rs1398579658 321 dbSNP
rs1054895275 324 dbSNP
rs1163596230 326 dbSNP
rs1425881214 329 dbSNP
rs922257452 330 dbSNP
rs544146447 334 dbSNP
rs1423565268 342 dbSNP
rs1251594559 374 dbSNP
rs1323755793 375 dbSNP
rs1179152470 380 dbSNP
rs1479750109 385 dbSNP
rs1251182502 392 dbSNP
rs1223269829 394 dbSNP
rs1370199538 409 dbSNP
rs1289479535 428 dbSNP
rs1245027209 434 dbSNP
rs1046690 458 dbSNP
rs1308771263 462 dbSNP
rs1026863422 463 dbSNP
rs1304278211 472 dbSNP
rs1372107257 479 dbSNP
rs886727048 482 dbSNP
rs1406221682 489 dbSNP
rs751678066 498 dbSNP
rs1016289548 499 dbSNP
rs941263566 501 dbSNP
rs1457766059 507 dbSNP
rs964667278 510 dbSNP
rs529776899 511 dbSNP
rs1417594335 523 dbSNP
rs548336357 526 dbSNP
rs1200293114 527 dbSNP
rs1317844419 529 dbSNP
rs1218419675 533 dbSNP
rs1209153070 537 dbSNP
rs781584528 542 dbSNP
rs1468437666 545 dbSNP
rs954752387 554 dbSNP
rs75241000 557 dbSNP
rs1236551854 569 dbSNP
rs1328107626 581 dbSNP
rs75076283 585 dbSNP
rs1045774714 586 dbSNP
rs1301923134 604 dbSNP
rs1386715576 610 dbSNP
rs146769184 611 dbSNP
rs1388233982 615 dbSNP
rs780825578 615 dbSNP
rs1176245121 616 dbSNP
rs1001575152 638 dbSNP
rs1481493803 644 dbSNP
rs1427304680 645 dbSNP
rs1198202818 655 dbSNP
rs1408298789 656 dbSNP
rs1429070093 657 dbSNP
rs1263735670 658 dbSNP
rs1420615198 666 dbSNP
rs1464267645 669 dbSNP
rs1162537766 670 dbSNP
rs945339031 671 dbSNP
rs1393570711 678 dbSNP
rs979745958 681 dbSNP
rs1034748641 688 dbSNP
rs925195430 694 dbSNP
rs1440136136 696 dbSNP
rs937679353 703 dbSNP
rs1227462611 708 dbSNP
rs893412486 714 dbSNP
rs1054757243 719 dbSNP
rs1020474939 721 dbSNP
rs372987588 724 dbSNP
rs1337738324 725 dbSNP
rs552177351 732 dbSNP
rs896243511 733 dbSNP
rs1471081441 741 dbSNP
rs1404116148 744 dbSNP
rs1462532162 747 dbSNP
rs147929313 755 dbSNP
rs1029449022 756 dbSNP
rs976246422 756 dbSNP
rs1047931353 762 dbSNP
rs1185162827 763 dbSNP
rs886588900 772 dbSNP
rs1459722728 777 dbSNP
rs71640009 784 dbSNP
rs985166304 786 dbSNP
rs1006500608 790 dbSNP
rs1226854794 792 dbSNP
rs1253657053 792 dbSNP
rs910854995 792 dbSNP
rs1038371183 795 dbSNP
rs962614301 796 dbSNP
rs900737906 802 dbSNP
rs1454894823 803 dbSNP
rs996135018 804 dbSNP
rs79012864 805 dbSNP
rs929849587 808 dbSNP
rs954833506 810 dbSNP
rs1233030620 812 dbSNP
rs1045966218 814 dbSNP
rs1166162015 816 dbSNP
rs1010720618 822 dbSNP
rs1385737400 832 dbSNP
rs1165295403 837 dbSNP
rs1442516625 843 dbSNP
rs1236608648 844 dbSNP
rs150478547 851 dbSNP
rs1185430063 852 dbSNP
rs1413142128 856 dbSNP
rs111307232 866 dbSNP
rs893109722 871 dbSNP
rs1293097184 883 dbSNP
rs1248711103 885 dbSNP
rs1354669103 888 dbSNP
rs1475439000 894 dbSNP
rs1283909737 905 dbSNP
rs370926928 909 dbSNP
rs1011839881 911 dbSNP
rs1042031980 915 dbSNP
rs1409267888 918 dbSNP
rs756763959 921 dbSNP
rs149568330 922 dbSNP
rs778594211 930 dbSNP
rs997724690 932 dbSNP
rs1412819691 941 dbSNP
rs745578810 945 dbSNP
rs1030897807 950 dbSNP
rs781407804 951 dbSNP
rs1355244752 961 dbSNP
rs771975768 963 dbSNP
rs1311333264 977 dbSNP
rs1450320273 999 dbSNP
rs949186448 1000 dbSNP
rs1415807612 1020 dbSNP
rs554692954 1022 dbSNP
rs202021817 1034 dbSNP
rs907586533 1035 dbSNP
rs1227938144 1040 dbSNP
rs573095150 1042 dbSNP
rs750622824 1042 dbSNP
rs1285208783 1053 dbSNP
rs1434221422 1056 dbSNP
rs1349189102 1057 dbSNP
rs1213420533 1065 dbSNP
rs1273084299 1070 dbSNP
rs1402201061 1086 dbSNP
rs534363911 1093 dbSNP
rs1308822336 1096 dbSNP
rs1480525093 1107 dbSNP
rs1208243291 1110 dbSNP
rs1256391444 1111 dbSNP
rs942208964 1120 dbSNP
rs1188904473 1125 dbSNP
rs779937178 1133 dbSNP
rs558890685 1139 dbSNP
rs1037833291 1147 dbSNP
rs1246618803 1149 dbSNP
rs900769092 1153 dbSNP
rs755889110 1158 dbSNP
rs746804218 1172 dbSNP
rs577436179 1176 dbSNP
rs143220164 1177 dbSNP
rs192988383 1180 dbSNP
rs574511393 1181 dbSNP
rs1217500366 1188 dbSNP
rs1366871026 1191 dbSNP
rs1270692904 1193 dbSNP
rs1432703598 1196 dbSNP
rs1362784957 1198 dbSNP
rs748229298 1203 dbSNP
rs541942112 1215 dbSNP
rs138874475 1220 dbSNP
rs769833787 1221 dbSNP
rs1425172850 1223 dbSNP
rs1187603729 1229 dbSNP
rs1336574930 1232 dbSNP
rs1032168412 1238 dbSNP
rs1430641330 1244 dbSNP
rs1056245702 1245 dbSNP
rs1188284410 1252 dbSNP
rs1461956856 1273 dbSNP
rs184674809 1275 dbSNP
rs1231474539 1279 dbSNP
rs1311665380 1281 dbSNP
rs1279079422 1283 dbSNP
rs990716412 1284 dbSNP
rs1396902333 1291 dbSNP
rs552301503 1295 dbSNP
rs377712073 1301 dbSNP
rs141997541 1303 dbSNP
rs970810839 1316 dbSNP
rs749118102 1321 dbSNP
rs907617715 1322 dbSNP
rs58510761 1323 dbSNP
rs1354629134 1324 dbSNP
rs1037874708 1334 dbSNP
rs549835829 1339 dbSNP
rs903461066 1343 dbSNP
rs1388806244 1347 dbSNP
rs190349032 1349 dbSNP
rs368281988 1363 dbSNP
rs531595678 1367 dbSNP
rs1180347895 1371 dbSNP
rs1483009843 1377 dbSNP
rs1233552019 1379 dbSNP
rs1051982728 1394 dbSNP
rs1273782584 1397 dbSNP
rs536291154 1397 dbSNP
rs372838455 1425 dbSNP
rs1006642840 1427 dbSNP
rs1310246358 1438 dbSNP
rs1394645500 1453 dbSNP
rs1227392519 1460 dbSNP
rs1373561259 1466 dbSNP
rs1299408308 1472 dbSNP
rs1407430303 1476 dbSNP
rs12143280 1479 dbSNP
rs962426672 1485 dbSNP
rs1041686875 1487 dbSNP
rs1370568542 1496 dbSNP
rs571384355 1497 dbSNP
rs181563780 1499 dbSNP
rs1423479760 1500 dbSNP
rs904640678 1506 dbSNP
rs1184485405 1510 dbSNP
rs534054133 1520 dbSNP
rs1471651058 1523 dbSNP
rs1000282282 1529 dbSNP
rs1391470403 1547 dbSNP
rs1485166475 1558 dbSNP
rs1438004538 1563 dbSNP
rs559071850 1564 dbSNP
rs1263488879 1570 dbSNP
rs750203132 1574 dbSNP
rs1234920958 1576 dbSNP
rs1226099851 1579 dbSNP
rs981733871 1580 dbSNP
rs1283295225 1581 dbSNP
rs146257194 1593 dbSNP
rs538506596 1597 dbSNP
rs774661923 1598 dbSNP
rs1292194751 1605 dbSNP
rs1269869206 1607 dbSNP
rs759843598 1608 dbSNP
rs1346080112 1612 dbSNP
rs534007908 1615 dbSNP
rs1024913481 1616 dbSNP
rs970629495 1617 dbSNP
rs1467094671 1618 dbSNP
rs977438678 1624 dbSNP
rs1213058591 1625 dbSNP
rs924578427 1627 dbSNP
rs74137663 1629 dbSNP
rs1052407363 1630 dbSNP
rs1014582393 1631 dbSNP
rs963483609 1633 dbSNP
rs1201257396 1634 dbSNP
rs1190449982 1635 dbSNP
rs1486070468 1653 dbSNP
rs1269722014 1668 dbSNP
rs35232266 1668 dbSNP
rs1206442947 1669 dbSNP
rs973116088 1680 dbSNP
rs889371669 1681 dbSNP
rs921659176 1682 dbSNP
rs1263243471 1683 dbSNP
rs932173110 1692 dbSNP
rs987561873 1694 dbSNP
rs912139415 1696 dbSNP
rs946313445 1715 dbSNP
rs376828636 1717 dbSNP
rs1386625121 1719 dbSNP
rs139298194 1720 dbSNP
rs904504269 1724 dbSNP
rs1455874786 1726 dbSNP
rs936098490 1733 dbSNP
rs1460331507 1736 dbSNP
rs541804938 1742 dbSNP
rs1325871981 1744 dbSNP
rs1375927634 1749 dbSNP
rs566505571 1778 dbSNP
rs560192743 1779 dbSNP
rs995191471 1783 dbSNP
rs1025275040 1787 dbSNP
rs1326400296 1789 dbSNP
rs886737840 1793 dbSNP
rs1002542104 1799 dbSNP
rs1243338048 1804 dbSNP
rs1201741222 1807 dbSNP
rs186323245 1808 dbSNP
rs894537532 1814 dbSNP
rs1342242021 1820 dbSNP
rs1254849092 1827 dbSNP
rs1233169047 1839 dbSNP
rs1343455602 1845 dbSNP
rs1300297868 1850 dbSNP
rs545616415 1860 dbSNP
rs1364785033 1865 dbSNP
rs79204495 1866 dbSNP
rs1024778092 1867 dbSNP
rs531454050 1879 dbSNP
rs546852360 1885 dbSNP
rs906475386 1887 dbSNP
rs370923000 1888 dbSNP
rs529155842 1892 dbSNP
rs548152806 1898 dbSNP
rs1391924893 1908 dbSNP
rs189164345 1909 dbSNP
rs973019999 1914 dbSNP
rs1385537745 1918 dbSNP
rs749963887 1937 dbSNP
rs1189209908 1951 dbSNP
rs1440276096 1952 dbSNP
rs1254915279 1964 dbSNP
rs1195824619 1966 dbSNP
rs1483697029 1970 dbSNP
rs1277358002 1975 dbSNP
rs1226738645 1976 dbSNP
rs1341883360 1980 dbSNP
rs1028704626 1982 dbSNP
rs1211715651 1986 dbSNP
rs1248611537 1987 dbSNP
rs879080834 1990 dbSNP
rs1437444465 1991 dbSNP
rs1183246694 2001 dbSNP
rs1414607127 2016 dbSNP
rs1247296934 2018 dbSNP
rs1338874110 2024 dbSNP
rs953100602 2025 dbSNP
rs181868298 2031 dbSNP
rs1372397872 2040 dbSNP
rs1164772763 2063 dbSNP
rs933355930 2066 dbSNP
rs987481088 2069 dbSNP
rs987634575 2078 dbSNP
rs912063401 2085 dbSNP
rs552416333 2094 dbSNP
rs542017884 2097 dbSNP
rs946314199 2111 dbSNP
rs568279904 2118 dbSNP
rs1165665474 2119 dbSNP
rs538096528 2120 dbSNP
rs936003382 2124 dbSNP
rs1055764877 2144 dbSNP
rs74137664 2151 dbSNP
rs1309516619 2152 dbSNP
rs1473284724 2155 dbSNP
rs6690648 2156 dbSNP
rs1203653864 2171 dbSNP
rs1046698470 2179 dbSNP
rs906353990 2180 dbSNP
rs1046838118 2197 dbSNP
rs1323442410 2201 dbSNP
rs1354559136 2211 dbSNP
rs1229149124 2230 dbSNP
rs886855336 2230 dbSNP
rs141801188 2234 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' ucGGUGUUAGUGGAAGACUAGa 5'
            :| ||| | |   |||| | 
Target 5' -aUCUCAAACUC---CUGACCu 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 ENST00000261464.5 | 3UTR | AUCUCAAACUCCUGACCUCAAG
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
PAAD -0.901 0.14 -1.000 0.5 3 Click to see details
LUSC -0.532 0.18 -0.500 0.2 5 Click to see details
CHOL -0.375 0.23 0.086 0.44 6 Click to see details
STAD 0.158 0.27 0.110 0.33 18 Click to see details
PRAD -0.073 0.32 -0.048 0.38 44 Click to see details
HNSC 0.116 0.37 0.209 0.27 11 Click to see details
LIHC -0.064 0.37 -0.014 0.47 28 Click to see details
BLCA -0.108 0.38 -0.127 0.35 11 Click to see details
BRCA -0.052 0.39 -0.046 0.4 30 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
UCEC -0.048 0.48 -0.200 0.4 4 Click to see details
96 hsa-miR-383-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT004443 VEGFA vascular endothelial growth factor A 5 2
MIRT006137 DIO1 iodothyronine deiodinase 1 3 1
MIRT006535 IRF1 interferon regulatory factor 1 3 1
MIRT007246 IGF1R insulin like growth factor 1 receptor 1 1
MIRT007305 PRDX3 peroxiredoxin 3 1 1
MIRT054359 CCND1 cyclin D1 4 2
MIRT057087 DDIT4 DNA damage inducible transcript 4 2 2
MIRT086536 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 2
MIRT086544 MOB4 MOB family member 4, phocein 2 2
MIRT438194 PPP1R10 protein phosphatase 1 regulatory subunit 10 3 1
MIRT448282 ZMYM2 zinc finger MYM-type containing 2 2 2
MIRT451601 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT453387 RHD Rh blood group D antigen 2 2
MIRT458521 C5orf22 chromosome 5 open reading frame 22 2 2
MIRT459720 SGK494 uncharacterized serine/threonine-protein kinase SgK494 2 2
MIRT461491 KIAA1009 centrosomal protein 162 1 1
MIRT463261 ZIC5 Zic family member 5 2 2
MIRT464237 VCP valosin containing protein 2 2
MIRT465320 TRAF5 TNF receptor associated factor 5 2 2
MIRT465774 TMOD3 tropomodulin 3 2 2
MIRT467879 SLC22A23 solute carrier family 22 member 23 2 2
MIRT469636 RAD21 RAD21 cohesin complex component 2 6
MIRT472041 NPAT nuclear protein, coactivator of histone transcription 2 2
MIRT476568 GABARAPL1 GABA type A receptor associated protein like 1 2 2
MIRT478586 CTDSPL2 CTD small phosphatase like 2 2 2
MIRT478870 CREBRF CREB3 regulatory factor 2 2
MIRT482202 AHR aryl hydrocarbon receptor 2 2
MIRT484237 IER2 immediate early response 2 2 2
MIRT487480 NRF1 nuclear respiratory factor 1 2 6
MIRT493746 GRAP2 GRB2-related adaptor protein 2 2 2
MIRT496836 ZNF460 zinc finger protein 460 2 2
MIRT497234 APOL2 apolipoprotein L2 2 2
MIRT499424 PLCG2 phospholipase C gamma 2 2 9
MIRT500598 UBN2 ubinuclein 2 2 10
MIRT502859 CHEK2 checkpoint kinase 2 2 6
MIRT507727 CLIC4 chloride intracellular channel 4 2 4
MIRT510509 YOD1 YOD1 deubiquitinase 2 6
MIRT511901 FNBP1L formin binding protein 1 like 2 6
MIRT514393 CLUAP1 clusterin associated protein 1 2 2
MIRT520180 WBP2 WW domain binding protein 2 2 4
MIRT531214 PLA2G4D phospholipase A2 group IVD 2 2
MIRT532846 ZNF699 zinc finger protein 699 2 2
MIRT533461 TRIM71 tripartite motif containing 71 2 2
MIRT539263 ANKRD44 ankyrin repeat domain 44 2 2
MIRT539380 ADSS adenylosuccinate synthase 2 6
MIRT548129 GAS1 growth arrest specific 1 2 2
MIRT550662 ZFP37 ZFP37 zinc finger protein 2 2
MIRT551499 CENPN centromere protein N 2 2
MIRT553778 TAF13 TATA-box binding protein associated factor 13 2 2
MIRT554376 SFPQ splicing factor proline and glutamine rich 2 2
MIRT555821 PCDH11Y protocadherin 11 Y-linked 2 4
MIRT557558 GOSR1 golgi SNAP receptor complex member 1 2 2
MIRT557694 GATA6 GATA binding protein 6 2 2
MIRT561383 TWF1 twinfilin actin binding protein 1 2 2
MIRT561414 TSN translin 2 2
MIRT561867 MSH6 mutS homolog 6 2 2
MIRT567383 GTPBP3 GTP binding protein 3, mitochondrial 2 2
MIRT569272 PCDH11X protocadherin 11 X-linked 2 2
MIRT569556 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569760 RIMBP3C RIMS binding protein 3C 2 5
MIRT573387 GGA2 golgi associated, gamma adaptin ear containing, ARF binding protein 2 2 2
MIRT573456 RPL41 ribosomal protein L41 2 2
MIRT573968 DDX21 DExD-box helicase 21 2 2
MIRT574163 ATG10 autophagy related 10 2 2
MIRT574659 KLHL15 kelch like family member 15 2 2
MIRT574907 Plcg2 phospholipase C, gamma 2 2 6
MIRT607496 HEBP2 heme binding protein 2 2 2
MIRT612840 KCNJ12 potassium voltage-gated channel subfamily J member 12 2 4
MIRT613962 TMEM59 transmembrane protein 59 2 2
MIRT621125 PCNXL2 pecanex homolog 2 2 2
MIRT625216 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT643337 MICA MHC class I polypeptide-related sequence A 2 2
MIRT646342 CLIC6 chloride intracellular channel 6 2 2
MIRT647361 WDR5B WD repeat domain 5B 2 2
MIRT650308 SLC35E2 solute carrier family 35 member E2 2 2
MIRT651372 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT655301 PEAR1 platelet endothelial aggregation receptor 1 2 2
MIRT681918 SLC11A2 solute carrier family 11 member 2 2 2
MIRT684165 ALDH1B1 aldehyde dehydrogenase 1 family member B1 2 2
MIRT688053 GLUL glutamate-ammonia ligase 2 2
MIRT690210 C5orf45 MRN complex interacting protein 2 2
MIRT691024 CRTC3 CREB regulated transcription coactivator 3 2 2
MIRT697699 WAC WW domain containing adaptor with coiled-coil 2 2
MIRT698201 TMEM30A transmembrane protein 30A 2 2
MIRT698857 SRSF2 serine and arginine rich splicing factor 2 2 2
MIRT702292 LDHA lactate dehydrogenase A 4 2
MIRT703341 GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 2 2
MIRT704082 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT713729 SUCO SUN domain containing ossification factor 2 2
MIRT719487 RBM27 RNA binding motif protein 27 2 2
MIRT722080 SMC2 structural maintenance of chromosomes 2 2 2
MIRT724102 TMEM199 transmembrane protein 199 2 2
MIRT725124 SYNRG synergin gamma 2 2
MIRT725601 CAPN6 calpain 6 2 2
MIRT737186 RBM3 RNA binding motif (RNP1, RRM) protein 3 4 0
MIRT755379 NOS3 nitric oxide synthase 3 3 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-383 Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-383 Vorinostat (SAHA) approved 5311 Microarray A549 human non-small cell lung cancer cells 19513533 2009 up-regulated
miR-383 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-383 Doxorubicin approved 31703 Microarray heart 22859947 2012 up-regulated
miR-383 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-383 Tert-butyl hydroperoxide (t-BHP) NULL 6410 Microarray mouse auditory cells 20510889 2010 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-383-5p Vincristine 5978 approved resistant High Lymphoblastic Leukemia tissue
hsa-miR-383-5p Daunorubicin 30323 NSC82151 approved resistant High Lymphoblastic Leukemia tissue
hsa-miR-383-5p Prednisolone 5755 NSC9120 approved resistant High Lymphoblastic Leukemia tissue
hsa-miR-383-5p L-Asparaginase resistant High Lymphoblastic Leukemia tissue
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved resistant High Germ Cell Tumor cell line (NTERA-2)
hsa-miR-383-5p Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (RKO)
hsa-miR-383-5p Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer cell line (HT-29)
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved sensitive High Ovarian Cancer cell line (SKOV3)
hsa-miR-383-5p Docetaxel 148124 NSC628503 approved sensitive High Prostate Cancer cell line (PC-3)
hsa-miR-383-5p Cetuximab sensitive High Colon Cancer cell line
hsa-miR-383-5p Paclitaxel 36314 NSC125973 approved sensitive Low Ovarian Cancer cell line (OVCAR3, A2780)
hsa-miR-383-5p Doxorubicin 31703 NSC123127 approved sensitive Low Hepatocellular Carcinoma cell line (BT-474, SKBR3)
hsa-miR-383-5p Cetuximab + Folfox(Fluorouracil + Leucovorin + Oxaliplatin) resistant High Metastatic Colorectal Cancer tissue
hsa-miR-383-5p Gemcitabine 60750 NSC613327 approved sensitive Low Pancreatic Ductal Adenocarcinoma tissue
hsa-miR-383-5p Fluorouracil 3385 NSC19893 approved sensitive Low Gastric Cancer cell line (AGS)
hsa-miR-383-5p Oxaliplatin 6857599 NSC266046 approved resistant Low Hepatocellular Carcinoma cell line (Hep3B, Huh-7)
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-383-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-383-5p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-383-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-383-5p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-383-5p Sunitinib 5329102 NSC750690 approved resistant tissue (CardA)
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-383-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-383-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-383-5p Cetuximab resistant tissue (colorectal carcinoma)

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