miRTarBase - #MIRT451713


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pre-miRNA Information
pre-miRNA hsa-mir-4271   
Genomic Coordinates chr3: 49274120 - 49274186
Description Homo sapiens miR-4271 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4271
Sequence 39| GGGGGAAGAAAAGGUGGGG |57
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30481495 1 COSMIC
COSN31532060 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs760829741 1 dbSNP
rs1277951968 2 dbSNP
rs189148716 3 dbSNP
rs757021935 4 dbSNP
rs1285201145 6 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol OLR1   
Synonyms CLEC8A, LOX1, LOXIN, SCARE1, SLOX1
Description oxidized low density lipoprotein receptor 1
Transcript NM_001172632   
Other Transcripts NM_001172633 , NM_002543   
Expression
Putative miRNA Targets on OLR1
3'UTR of OLR1
(miRNA target sites are highlighted)		 
>OLR1|NM_001172632|3'UTR
   1 AGTCCGAGGCGCTGTCTCCCAGACATACCCTTCAGGTACCTGTGCATATATACAACGAGGAGCTGTTTATGCGGAAAACT
  81 GCATTTTAGCTGCCTTCAGTATATGTCAGAAGAAGGCAAACCTAAGAGCACAGTGAATTTGAAGGCTCTGGAAGAAAAGA
 161 AAAAAGTCTTTGAGTTTTATTCTGGAATTTAAGCTATTCTTTGTCACTTGGGTGCCAAACATGAGAGCCCAGAAAACTGT
 241 CATTTAGCTGGCTGCAGAACTCCTTTGCAGAAACTGGGGTTCCAGGTGCCTGGCACCTTTATGTCAACATTTTTGATTCT
 321 AGCTACCTGTATTATTTCACCTAGCTTGTCCCAAGCTTCCCTGCCAGCCTGAAGTCCATTTTCCCCTTTTTATTTTAAAA
 401 TTTGACTCCTCTTCAAGCTTGAAAACCCTCTGAACTCAGTCTTCTTTACCTCATTATCACCTTCCCCTCACACTCCTAAA
 481 ATTGCATGAAAGACAGAACATGGAGAACTTGCTCAAGTGCAGGCAGAGAGCAAAAAGGGGAAATATGTCTGGGAAAAAGT
 561 GCACGTGAAGAAACAAAGAAGGACAGAGGCCATTCCGAAATCAAGAAACTCATGTTCTTAACTTTAAAAAAGGTATCAAT
 641 CCTTGGTTTTTAAACTGTGGTCCATCTCCAGACTCTACCACTTACGGACAGACAGACAGACAGACACACACACACACACA
 721 CACACACATTTTGGGACAAGTGGGGAGCCCAAGAAAGTAATTAGTAAGTGAGTGGTCTTTTCTGTAAGCTAATCCACAAC
 801 CTGTTACCACTTCCTGAATCAGTTATTATTTCTTCATTTTTTTTTCTACCAGAGGACAGATTAATAGATTTAACCCTTCA
 881 CAACAGTTCTTGTTAGAATCATGGGATGTGTGGCCCAGAGGTAAGAATAGAATTTCTTTCCCTAAAGAACATACCTTTTG
 961 TAGATGAACTCTTCTCAACTCTGTTTTGCTATGCTATAATTCCGAAACATACAAGACAAAAAAAATGAAGACACTCAATC
1041 TAGAACAAACTAAGCCAGGTATGCAAATATCGCTGAATAGAAACAGATGGAATTAGAAATATATCTTCTATTTTTAGGCT
1121 TCTATTTCCTTTCCACCCACTCTTCACAGGCTATTCTACTTTAAAGGAAGCCTTTTTATTTTGCTGCACACAATCTAGCA
1201 GGAATCTTTTTTTTTTTTTAAGAGCTGTGTCATCCTTATGTAGGCAAGAGATGTTTGCTTTTGTTAAAAGCTTTATTGAG
1281 ATATAATTAACATAAAATAAACTGAACATATTTAAAGTGTACTATTTGATAAGTTTTCACACCTTGTGGAGAACATGCAT
1361 ACTACAATTAAGAGAGTGAACATATCCATCATCCCTCAAAGTGTCACAATGCTCCTCCTGATGACTCCTCCCCAGAAAAC
1441 CACCAATCGGCTTTCATTTTGCATTTTGTAGTTTTATGTGAATGGAATCATATAGTATGTCTTTTTTTTTTGTCTGGCTT
1521 CTTTCACTTTGCATAATTATTTTGAGATTCATATGTCTCCATCTTGATGCTCGTATGAATTCATTCTTTTAAATGTTGAA
1601 TATTCCCTTGTATGGATATACCACAATTCATTTACCCATTTACTTGTTGATGACATTTGGGTTGTTTTAGTTTTGGGATA
1681 TTACAAATAAAGCTGCTGTGAACATTTGTGTACAAGAAAAAAAAAAAAAAAAA
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' ggGGUGGAAAA---GAAGGGGg 5'
            || | || |   ||||||| 
Target 5' taCCTCATTATCACCTTCCCCt 3'
 447 - 468 149.00 -19.90
2 
miRNA  3' gggguggaAAAGAAGGGGg 5'
                  ||||||:||| 
Target 5' gaatagaaTTTCTTTCCCt 3'
 925 - 943 139.00 -12.90
3 
miRNA  3' ggGGUGGAAAA------GAAGGGGg 5'
            |:| ||| |      ||||||: 
Target 5' acCTAGCTTGTCCCAAGCTTCCCTg 3'
 339 - 363 131.00 -15.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
6995 324 ClinVar
COSM2063892 6 COSMIC
COSM5764029 10 COSMIC
COSM5535967 18 COSMIC
COSM3455191 20 COSMIC
COSM3870565 29 COSMIC
COSM9868864 35 COSMIC
COSM6577067 50 COSMIC
COSM8414884 55 COSMIC
COSM3383975 56 COSMIC
COSM6071191 60 COSMIC
COSM6874527 65 COSMIC
COSM7828832 68 COSMIC
COSM8572872 72 COSMIC
COSM6733321 73 COSMIC
COSM9466257 74 COSMIC
COSM5778955 89 COSMIC
COSM6071192 89 COSMIC
COSM4038082 91 COSMIC
COSM6733322 101 COSMIC
COSM8806900 105 COSMIC
COSM7319227 106 COSMIC
COSM6000205 107 COSMIC
COSM4749843 117 COSMIC
COSM5725976 126 COSMIC
COSM163081 127 COSMIC
COSN31542501 146 COSMIC
COSN30459011 148 COSMIC
COSN19699868 159 COSMIC
COSN31538871 159 COSMIC
COSN31573474 177 COSMIC
COSN30488879 185 COSMIC
COSN31580688 189 COSMIC
COSN31522199 190 COSMIC
COSN16580558 192 COSMIC
COSN31495270 195 COSMIC
COSN31601982 199 COSMIC
COSN7307657 222 COSMIC
COSN30112595 263 COSMIC
COSN31610403 294 COSMIC
COSN28707705 326 COSMIC
COSN31578787 377 COSMIC
COSN31527854 381 COSMIC
COSN31539884 382 COSMIC
COSN8585174 386 COSMIC
COSN8585173 391 COSMIC
COSN23880975 408 COSMIC
COSN5314378 413 COSMIC
COSN31541513 428 COSMIC
COSN31523266 568 COSMIC
COSN31596789 621 COSMIC
COSN24294675 626 COSMIC
COSN19337509 684 COSMIC
COSN23706840 699 COSMIC
COSN20109210 702 COSMIC
COSN24731251 703 COSMIC
COSN27221039 703 COSMIC
COSN22258462 885 COSMIC
COSN20758540 1086 COSMIC
COSN8692020 1193 COSMIC
COSN20109207 1206 COSMIC
COSN29767199 1501 COSMIC
COSN10096335 1669 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1056125322 2 dbSNP
rs199989233 5 dbSNP
rs986422401 6 dbSNP
rs1255753047 7 dbSNP
rs140400766 10 dbSNP
rs535180296 11 dbSNP
rs778185706 14 dbSNP
rs763828543 17 dbSNP
rs1434673386 18 dbSNP
rs1327080047 19 dbSNP
rs1320415681 22 dbSNP
rs146768121 28 dbSNP
rs765325570 31 dbSNP
rs1401481108 44 dbSNP
rs1174203633 46 dbSNP
rs1045169061 48 dbSNP
rs374394285 56 dbSNP
rs1388126264 64 dbSNP
rs897928133 65 dbSNP
rs753886560 70 dbSNP
rs374494106 72 dbSNP
rs370707474 73 dbSNP
rs1189764015 77 dbSNP
rs1184848638 79 dbSNP
rs1441345415 81 dbSNP
rs771828476 93 dbSNP
rs577739742 99 dbSNP
rs1477039270 101 dbSNP
rs1350439609 103 dbSNP
rs1272993571 106 dbSNP
rs1421643708 109 dbSNP
rs1410024324 112 dbSNP
rs143492178 113 dbSNP
rs1227908282 118 dbSNP
rs368924076 120 dbSNP
rs1340404592 124 dbSNP
rs557756840 126 dbSNP
rs1436152952 129 dbSNP
rs759534798 129 dbSNP
rs1339953580 130 dbSNP
rs1313134582 131 dbSNP
rs1313373404 132 dbSNP
rs1416569692 133 dbSNP
rs1340184018 136 dbSNP
rs775134477 139 dbSNP
rs1307252179 141 dbSNP
rs747491547 145 dbSNP
rs778031576 157 dbSNP
rs1161095451 159 dbSNP
rs758714127 160 dbSNP
rs1035542814 165 dbSNP
rs773946372 166 dbSNP
rs748491543 167 dbSNP
rs770787725 167 dbSNP
rs779149604 171 dbSNP
rs1227734693 172 dbSNP
rs574510080 175 dbSNP
rs753926543 179 dbSNP
rs1250060613 183 dbSNP
rs374709504 184 dbSNP
rs1438768383 187 dbSNP
rs1279899571 194 dbSNP
rs1441624839 196 dbSNP
rs1185211259 212 dbSNP
rs1243750059 222 dbSNP
rs1475721516 225 dbSNP
rs1449230326 232 dbSNP
rs905240653 248 dbSNP
rs575452645 260 dbSNP
rs1387732168 261 dbSNP
rs946641968 266 dbSNP
rs772122949 268 dbSNP
rs1260342489 275 dbSNP
rs893694356 278 dbSNP
rs1436056800 280 dbSNP
rs1173800270 282 dbSNP
rs4237962 287 dbSNP
rs935182876 296 dbSNP
rs1320748735 297 dbSNP
rs1346275719 308 dbSNP
rs1486244882 315 dbSNP
rs12316150 324 dbSNP
rs1220579826 325 dbSNP
rs1050283 326 dbSNP
rs1235123603 329 dbSNP
rs1028408951 335 dbSNP
rs942425571 340 dbSNP
rs1198479159 341 dbSNP
rs1286038381 351 dbSNP
rs1447385613 357 dbSNP
rs1207968205 364 dbSNP
rs753992352 367 dbSNP
rs910894520 371 dbSNP
rs962752685 376 dbSNP
rs1193785349 382 dbSNP
rs553080240 385 dbSNP
rs1476860510 392 dbSNP
rs1159974758 394 dbSNP
rs1293352545 395 dbSNP
rs749954561 397 dbSNP
rs1319054866 404 dbSNP
rs952287098 408 dbSNP
rs181195036 412 dbSNP
rs867663831 415 dbSNP
rs1323013548 418 dbSNP
rs1329444334 426 dbSNP
rs1241390733 439 dbSNP
rs962556349 443 dbSNP
rs1329519369 448 dbSNP
rs1301944369 453 dbSNP
rs1227629359 458 dbSNP
rs1035191354 465 dbSNP
rs887266038 467 dbSNP
rs190216641 472 dbSNP
rs1209882661 482 dbSNP
rs1367116272 498 dbSNP
rs1449405340 516 dbSNP
rs550520331 518 dbSNP
rs1163825184 525 dbSNP
rs1461801437 532 dbSNP
rs1364027568 538 dbSNP
rs1371641594 543 dbSNP
rs969409368 546 dbSNP
rs904902879 548 dbSNP
rs1328566318 551 dbSNP
rs531114395 562 dbSNP
rs1163210025 564 dbSNP
rs1023603158 565 dbSNP
rs1393217885 580 dbSNP
rs1197427842 582 dbSNP
rs1490856392 586 dbSNP
rs1350167170 588 dbSNP
rs1010836297 596 dbSNP
rs1336717209 597 dbSNP
rs1245370487 607 dbSNP
rs1044828971 609 dbSNP
rs1353568657 611 dbSNP
rs1292858329 625 dbSNP
rs1197107972 626 dbSNP
rs1204614835 632 dbSNP
rs946347111 634 dbSNP
rs893787694 636 dbSNP
rs1179602543 642 dbSNP
rs10505755 653 dbSNP
rs1475746746 654 dbSNP
rs1187375429 656 dbSNP
rs935268849 670 dbSNP
rs1168619940 673 dbSNP
rs999443857 674 dbSNP
rs1420758461 675 dbSNP
rs911724498 678 dbSNP
rs901042970 680 dbSNP
rs1282546718 681 dbSNP
rs548589878 685 dbSNP
rs17808009 686 dbSNP
rs781251301 688 dbSNP
rs931840641 689 dbSNP
rs151080645 690 dbSNP
rs1303394904 694 dbSNP
rs1390416623 695 dbSNP
rs1394825573 698 dbSNP
rs76039690 699 dbSNP
rs1462798533 701 dbSNP
rs1801809 703 dbSNP
rs59626458 703 dbSNP
rs58628154 704 dbSNP
rs1189811025 705 dbSNP
rs1491226407 705 dbSNP
rs61523668 705 dbSNP
rs754931154 705 dbSNP
rs113230765 707 dbSNP
rs1447750936 707 dbSNP
rs921316777 707 dbSNP
rs1399833687 709 dbSNP
rs1481460915 709 dbSNP
rs1269621841 717 dbSNP
rs1298255489 721 dbSNP
rs143220784 721 dbSNP
rs1181386315 725 dbSNP
rs35568748 726 dbSNP
rs371184661 727 dbSNP
rs377471306 728 dbSNP
rs1225632096 729 dbSNP
rs34435182 729 dbSNP
rs753989762 729 dbSNP
rs779614686 729 dbSNP
rs1387890384 749 dbSNP
rs1432235106 757 dbSNP
rs1327381390 758 dbSNP
rs1048109964 762 dbSNP
rs975540263 770 dbSNP
rs1197385782 772 dbSNP
rs1298761697 776 dbSNP
rs963016890 777 dbSNP
rs930990112 780 dbSNP
rs982989387 801 dbSNP
rs533021686 811 dbSNP
rs1035238383 821 dbSNP
rs1380944468 827 dbSNP
rs1221551585 838 dbSNP
rs1003634337 846 dbSNP
rs1473442619 846 dbSNP
rs972764606 866 dbSNP
rs1159692274 881 dbSNP
rs962280756 885 dbSNP
rs969597132 888 dbSNP
rs1023781996 901 dbSNP
rs185807023 903 dbSNP
rs1166860151 908 dbSNP
rs1349897100 912 dbSNP
rs1435137135 913 dbSNP
rs1010684674 914 dbSNP
rs893454575 921 dbSNP
rs377485340 930 dbSNP
rs999193802 944 dbSNP
rs147287871 949 dbSNP
rs890342284 951 dbSNP
rs1235616621 953 dbSNP
rs544245192 954 dbSNP
rs921813417 969 dbSNP
rs1237668504 970 dbSNP
rs1333675652 977 dbSNP
rs1483526888 984 dbSNP
rs1181768770 987 dbSNP
rs143980830 996 dbSNP
rs1183458665 1001 dbSNP
rs1392398940 1002 dbSNP
rs181429704 1003 dbSNP
rs34938789 1004 dbSNP
rs1371991555 1008 dbSNP
rs1335330189 1010 dbSNP
rs1471213984 1012 dbSNP
rs1430108466 1015 dbSNP
rs1307039101 1016 dbSNP
rs1158109973 1017 dbSNP
rs1348940847 1026 dbSNP
rs958068096 1037 dbSNP
rs1285287773 1040 dbSNP
rs1031000466 1043 dbSNP
rs1379142581 1048 dbSNP
rs1050286 1052 dbSNP
rs901057240 1059 dbSNP
rs1182717512 1061 dbSNP
rs1204632457 1062 dbSNP
rs552716540 1071 dbSNP
rs36051049 1072 dbSNP
rs1242254459 1076 dbSNP
rs1237966525 1083 dbSNP
rs1180080554 1088 dbSNP
rs1201731329 1088 dbSNP
rs1462630464 1089 dbSNP
rs75688283 1098 dbSNP
rs1449544816 1105 dbSNP
rs557031762 1109 dbSNP
rs1368376746 1122 dbSNP
rs1023839474 1123 dbSNP
rs957734255 1124 dbSNP
rs766688088 1130 dbSNP
rs1300464325 1137 dbSNP
rs931047379 1144 dbSNP
rs918248595 1147 dbSNP
rs1295664096 1150 dbSNP
rs35738181 1161 dbSNP
rs568346386 1170 dbSNP
rs940950941 1171 dbSNP
rs1313321210 1183 dbSNP
rs900328681 1186 dbSNP
rs1207844559 1192 dbSNP
rs1249891594 1193 dbSNP
rs1464944360 1201 dbSNP
rs1407533462 1204 dbSNP
rs1387901899 1205 dbSNP
rs201636631 1206 dbSNP
rs1399031033 1207 dbSNP
rs1037580454 1216 dbSNP
rs1172821628 1220 dbSNP
rs1449821884 1220 dbSNP
rs35678209 1220 dbSNP
rs373801260 1220 dbSNP
rs1387159690 1225 dbSNP
rs1332943348 1231 dbSNP
rs928212585 1232 dbSNP
rs1159390688 1244 dbSNP
rs1274486574 1265 dbSNP
rs1344022264 1270 dbSNP
rs1221519310 1274 dbSNP
rs757567609 1276 dbSNP
rs1269917294 1280 dbSNP
rs1329818069 1288 dbSNP
rs1444195875 1290 dbSNP
rs1245614758 1293 dbSNP
rs941862859 1302 dbSNP
rs1245839683 1303 dbSNP
rs948250438 1308 dbSNP
rs149011911 1317 dbSNP
rs528749641 1322 dbSNP
rs566290994 1324 dbSNP
rs138695853 1328 dbSNP
rs1446219204 1329 dbSNP
rs1392884858 1342 dbSNP
rs1238052024 1356 dbSNP
rs1323124261 1364 dbSNP
rs929955921 1365 dbSNP
rs1402837773 1367 dbSNP
rs1289937714 1371 dbSNP
rs1350907023 1374 dbSNP
rs927992878 1376 dbSNP
rs1258898464 1381 dbSNP
rs982763910 1383 dbSNP
rs1209978841 1391 dbSNP
rs1288675334 1392 dbSNP
rs1489745341 1393 dbSNP
rs969706948 1396 dbSNP
rs1031430070 1401 dbSNP
rs978089788 1409 dbSNP
rs1472478398 1411 dbSNP
rs1180639023 1414 dbSNP
rs1458452464 1417 dbSNP
rs1162778153 1426 dbSNP
rs916819721 1427 dbSNP
rs144993624 1430 dbSNP
rs958204361 1432 dbSNP
rs1019566399 1433 dbSNP
rs1006799142 1446 dbSNP
rs1285685937 1448 dbSNP
rs1050289 1449 dbSNP
rs1244846243 1451 dbSNP
rs1026780218 1462 dbSNP
rs1356677729 1466 dbSNP
rs1289110960 1467 dbSNP
rs1248700005 1468 dbSNP
rs1030034360 1472 dbSNP
rs1194486074 1483 dbSNP
rs372674682 1484 dbSNP
rs1380265633 1488 dbSNP
rs995262617 1490 dbSNP
rs1187487019 1491 dbSNP
rs35555206 1493 dbSNP
rs1429180943 1494 dbSNP
rs1037120761 1496 dbSNP
rs1370252355 1497 dbSNP
rs938383353 1503 dbSNP
rs1246301188 1506 dbSNP
rs534039079 1508 dbSNP
rs886291715 1511 dbSNP
rs1379861826 1512 dbSNP
rs201512084 1512 dbSNP
rs930095062 1512 dbSNP
rs530557200 1514 dbSNP
rs1424076409 1516 dbSNP
rs1364015165 1517 dbSNP
rs1165701950 1518 dbSNP
rs1426318055 1521 dbSNP
rs1046661827 1533 dbSNP
rs759152806 1534 dbSNP
rs948306010 1541 dbSNP
rs1224823171 1551 dbSNP
rs1258082537 1559 dbSNP
rs774385114 1568 dbSNP
rs916753005 1572 dbSNP
rs771043948 1573 dbSNP
rs990155780 1576 dbSNP
rs1185878383 1583 dbSNP
rs936802846 1585 dbSNP
rs1426924642 1593 dbSNP
rs866667095 1598 dbSNP
rs1178537787 1602 dbSNP
rs1379099006 1605 dbSNP
rs1466368930 1615 dbSNP
rs1171909929 1618 dbSNP
rs1403875545 1621 dbSNP
rs924133706 1626 dbSNP
rs1474361112 1627 dbSNP
rs1465330611 1629 dbSNP
rs1302959887 1635 dbSNP
rs977830938 1658 dbSNP
rs561499464 1661 dbSNP
rs954485031 1664 dbSNP
rs1261793011 1668 dbSNP
rs1331895279 1671 dbSNP
rs989574892 1674 dbSNP
rs1193813843 1683 dbSNP
rs1484943683 1684 dbSNP
rs1193070257 1701 dbSNP
rs974403688 1706 dbSNP
rs1490039822 1709 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' gggguggaaaaGAAGGGGg 5'
                     ||||||| 
Target 5' --------cacCUUCCCCu 3'
 		1 - 11
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 ENST00000543993.1 | 3UTR | CACCUUCCCCUCACACUCCUAAAAUUG
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
181 hsa-miR-4271 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066209 MARCH9 membrane associated ring-CH-type finger 9 2 2
MIRT079367 CCDC137 coiled-coil domain containing 137 2 2
MIRT081183 MIDN midnolin 2 4
MIRT083278 ZCCHC3 zinc finger CCHC-type containing 3 2 6
MIRT086207 HOXD13 homeobox D13 2 2
MIRT133713 SKI SKI proto-oncogene 2 4
MIRT150653 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159166 NRBP1 nuclear receptor binding protein 1 2 2
MIRT160059 TET3 tet methylcytosine dioxygenase 3 2 4
MIRT180856 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT181931 MARK2 microtubule affinity regulating kinase 2 2 2
MIRT190628 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190654 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196107 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT263248 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT321168 EIF4H eukaryotic translation initiation factor 4H 2 2
MIRT338624 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT366301 GDI1 GDP dissociation inhibitor 1 2 4
MIRT375172 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 2
MIRT441488 NCEH1 neutral cholesterol ester hydrolase 1 2 2
MIRT442333 WNT9B Wnt family member 9B 2 2
MIRT443889 CNKSR3 CNKSR family member 3 2 2
MIRT445880 WBP1L WW domain binding protein 1 like 2 2
MIRT449312 MRO maestro 2 2
MIRT449844 BCL2L13 BCL2 like 13 2 2
MIRT450304 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT450515 EMX1 empty spiracles homeobox 1 2 2
MIRT451243 ZNF444 zinc finger protein 444 2 2
MIRT451713 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451792 TLR5 toll like receptor 5 2 2
MIRT451823 ALDH3B1 aldehyde dehydrogenase 3 family member B1 2 2
MIRT451906 ILK integrin linked kinase 2 2
MIRT452181 KIAA1456 KIAA1456 2 4
MIRT452242 TRAM1 translocation associated membrane protein 1 2 2
MIRT452544 ZNF467 zinc finger protein 467 2 2
MIRT452605 REPIN1 replication initiator 1 2 2
MIRT454505 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT454657 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT455354 KDM5C lysine demethylase 5C 2 2
MIRT455452 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455587 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT456501 PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 2 2
MIRT456815 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457425 NOL10 nucleolar protein 10 2 2
MIRT457468 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457660 SERINC1 serine incorporator 1 2 2
MIRT458231 NXPH3 neurexophilin 3 2 2
MIRT458374 ITM2C integral membrane protein 2C 2 2
MIRT458667 GPR35 G protein-coupled receptor 35 2 2
MIRT459665 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT459825 TPP1 tripeptidyl peptidase 1 2 2
MIRT460564 FEM1A fem-1 homolog A 2 2
MIRT460725 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT461121 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461529 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461750 DDX11 DEAD/H-box helicase 11 2 2
MIRT462570 STS steroid sulfatase 2 2
MIRT462798 NTN1 netrin 1 2 2
MIRT463030 ZNF689 zinc finger protein 689 2 2
MIRT463991 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464684 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465439 TP53 tumor protein p53 2 2
MIRT465512 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465649 TNPO2 transportin 2 2 10
MIRT465947 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466028 TMEM189 transmembrane protein 189 2 2
MIRT468076 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT468131 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468498 SESN2 sestrin 2 2 2
MIRT468879 RREB1 ras responsive element binding protein 1 2 2
MIRT469318 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469558 RARA retinoic acid receptor alpha 2 2
MIRT469793 RAB15 RAB15, member RAS oncogene family 2 2
MIRT469896 PTRF caveolae associated protein 1 2 2
MIRT470235 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470808 PLXND1 plexin D1 2 2
MIRT471597 PAQR5 progestin and adipoQ receptor family member 5 2 10
MIRT471710 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT471752 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT472978 MRRF mitochondrial ribosome recycling factor 2 2
MIRT473538 MAX MYC associated factor X 2 2
MIRT473581 MAT2A methionine adenosyltransferase 2A 2 2
MIRT473970 LRRC58 leucine rich repeat containing 58 2 2
MIRT474223 LCOR ligand dependent nuclear receptor corepressor 2 4
MIRT474553 KLHDC3 kelch domain containing 3 2 2
MIRT474777 KIAA0895L KIAA0895 like 2 2
MIRT476042 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476438 GBA2 glucosylceramidase beta 2 2 2
MIRT477773 E2F3 E2F transcription factor 3 2 4
MIRT477946 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT478782 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479320 VPS72 vacuolar protein sorting 72 homolog 2 2
MIRT480405 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480593 BTRC beta-transducin repeat containing E3 ubiquitin protein ligase 2 2
MIRT480963 BBC3 BCL2 binding component 3 2 2
MIRT481127 AZIN1 antizyme inhibitor 1 2 4
MIRT481444 ARRB2 arrestin beta 2 2 2
MIRT481687 AR androgen receptor 2 2
MIRT481730 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482386 AEN apoptosis enhancing nuclease 2 2
MIRT482564 ABHD2 abhydrolase domain containing 2 2 2
MIRT482605 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483256 CITED4 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4 2 4
MIRT483531 TAGLN2 transgelin 2 2 2
MIRT483840 UNC5B unc-5 netrin receptor B 2 4
MIRT483935 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484414 SNX19 sorting nexin 19 2 2
MIRT484487 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484609 SIX3 SIX homeobox 3 2 6
MIRT484703 RNF11 ring finger protein 11 2 2
MIRT485244 POGZ pogo transposable element derived with ZNF domain 2 2
MIRT485607 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT485965 RTBDN retbindin 2 2
MIRT487308 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487329 SREBF1 sterol regulatory element binding transcription factor 1 2 4
MIRT487410 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487607 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487689 CDK14 cyclin dependent kinase 14 2 2
MIRT487787 GPR20 G protein-coupled receptor 20 2 4
MIRT488026 ADO 2-aminoethanethiol dioxygenase 2 2
MIRT488476 B3GALNT2 beta-1,3-N-acetylgalactosaminyltransferase 2 2 2
MIRT488761 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489161 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489529 MRE11A MRE11 homolog, double strand break repair nuclease 2 8
MIRT489774 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489878 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT490094 FN3K fructosamine 3 kinase 2 2
MIRT490202 PKNOX2 PBX/knotted 1 homeobox 2 2 2
MIRT490283 ISL2 ISL LIM homeobox 2 2 2
MIRT490377 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491035 ALPK3 alpha kinase 3 2 2
MIRT491186 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 4
MIRT491766 ZNF385A zinc finger protein 385A 2 2
MIRT491888 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT491981 UNK unkempt family zinc finger 2 2
MIRT492400 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT493647 HDLBP high density lipoprotein binding protein 2 2
MIRT494010 DUSP9 dual specificity phosphatase 9 2 2
MIRT494167 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 2
MIRT495712 PADI1 peptidyl arginine deiminase 1 2 2
MIRT496873 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT499175 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT501652 PHLDA3 pleckstrin homology like domain family A member 3 2 2
MIRT506645 MAPK1 mitogen-activated protein kinase 1 2 4
MIRT510590 TUBB2A tubulin beta 2A class IIa 2 6
MIRT511907 FKBP1A FK506 binding protein 1A 2 2
MIRT513063 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513104 DYNAP dynactin associated protein 2 2
MIRT521804 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT523520 GLUL glutamate-ammonia ligase 2 2
MIRT525085 FRK fyn related Src family tyrosine kinase 2 2
MIRT530930 SCIN scinderin 2 2
MIRT533501 TRIM71 tripartite motif containing 71 2 2
MIRT538560 CECR2 CECR2, histone acetyl-lysine reader 2 2
MIRT544556 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT555912 ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 2 2
MIRT560405 TMEM69 transmembrane protein 69 2 2
MIRT560664 RTN3 reticulon 3 2 2
MIRT564061 CDT1 chromatin licensing and DNA replication factor 1 2 2
MIRT565504 SP1 Sp1 transcription factor 2 2
MIRT570014 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572321 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573229 TRIM21 tripartite motif containing 21 2 2
MIRT573487 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574137 MARVELD1 MARVEL domain containing 1 2 2
MIRT574323 ZNF703 zinc finger protein 703 2 2
MIRT620939 OSMR oncostatin M receptor 2 2
MIRT650080 MTL5 testis expressed metallothionein like protein 2 2
MIRT684553 ZNF708 zinc finger protein 708 2 2
MIRT685841 ANGEL1 angel homolog 1 2 2
MIRT688551 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT701985 MIER3 MIER family member 3 2 2
MIRT703899 EPT1 selenoprotein I 2 2
MIRT706388 MC2R melanocortin 2 receptor 2 2
MIRT707487 UGT2B4 UDP glucuronosyltransferase family 2 member B4 2 2
MIRT711885 INSIG2 insulin induced gene 2 2 2
MIRT719164 KIF6 kinesin family member 6 2 2
MIRT721294 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT721775 ARL6IP4 ADP ribosylation factor like GTPase 6 interacting protein 4 2 2
MIRT723763 NKIRAS2 NFKB inhibitor interacting Ras like 2 2 2
MIRT725485 GPR26 G protein-coupled receptor 26 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miR-4271 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive High Gastric Cancer cell line (BGC823)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive High Lung Adenocarcinoma tissue
hsa-miR-4271 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4271 Fluorouracil 3385 NSC19893 approved sensitive High Pancreatic Cancer cell line (PATU8988)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant Low Tongue Squamous Cell Carcinoma cell line (CAL-27, SCC-9)
hsa-miR-4271 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (H460)
hsa-miR-4271 Anlotinib 25017411 NSC832523 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Gefitinib 123631 NSC715055 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Icotinib 22024915 NSC800770 sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-miR-4271 Erlotinib 176870 NSC718781 approved sensitive Low Non-Small Cell Lung Cancer cell line (A549, PDC, H460)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (W1)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-4271 Androstenedione+Anastrozole resistant cell line (MCF-7)
hsa-mir-4271 Androstenedione+Letrozole resistant cell line (MCF-7)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-mir-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (BGC-823)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (cytosolic RNA)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (total RNA)
hsa-miR-4271 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4271 Platinum-based doublet chemotherapy sensitive tissue (lung adenocarcinoma)
hsa-miR-4271 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4271 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4271 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)
hsa-miR-4271 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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