miRTarBase - #MIRT454515


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pre-miRNA Information
pre-miRNA hsa-mir-3179-1   
Genomic Coordinates chr16: 14901508 - 14901591
Description Homo sapiens miR-3179-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-2   
Genomic Coordinates chr16: 16300159 - 16300242
Description Homo sapiens miR-3179-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-3   
Genomic Coordinates chr16: 18411894 - 18411977
Description Homo sapiens miR-3179-3 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-4   
Genomic Coordinates chr16: 18494493 - 18494576
Description Homo sapiens miR-3179-4 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-3179
Sequence 52| AGAAGGGGUGAAAUUUAAACGU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1351100204 1 dbSNP
rs1398613616 4 dbSNP
rs1340262765 20 dbSNP
rs1229893475 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZFYVE27   
Synonyms PROTRUDIN, SPG33
Description zinc finger FYVE-type containing 27
Transcript NM_001002261   
Other Transcripts NM_001002262 , NM_001174119 , NM_001174120 , NM_001174121 , NM_001174122 , NM_144588   
Expression
Putative miRNA Targets on ZFYVE27
3'UTR of ZFYVE27
(miRNA target sites are highlighted)		 
>ZFYVE27|NM_001002261|3'UTR
   1 GAAGAGAGGCCAGGGTCCAACCAGGCACCCGTCCTTGGGACCAGCAGTAGACCCCCCACTCTCCCCACCCCTGGCCCACT
  81 GTGGTGTGTGCTGGGCAAATGTGGCCTGAATGCTAGGTAGGCTTCCCCTTCCTTCCTCACTCTCTCCAGCTGGATTCTGG
 161 AGCTGTTCTCCATCCATGAGAGTGGCTGGCAATGGCTGCTCTCAATCCCTTGAGGGAGAAGAGCCCCTGGAGGGCCTGGC
 241 ATGTTTGTCCTGCTCTGCCTGGGACTGAGCGAGTGGACTTAGGGCTGGGCAGGCAGTAGCCACCAGAGGGCAGCAGCGAA
 321 CTAGGCCAGGCCTGACTGGGGTCTGAAGATCAGGGTCAGTGTGGCTGTGCCTGGGAATTCCAGACCTGAGGTTGGGAAAA
 401 GAGGTTTTTCTCCTGCAGGGTACTGGGCCAGGCCCTCAGCCTCAGAGAGCCTGCAGAAGGGCTTGGGAGTGCCACACCCC
 481 ATCTCTGCTGATTGAATGTCCCTCCAGGCACCAGGATCTCATCATTTCCCCATCAGAGGGTGTGGCCAGGCCTAACAAGA
 561 CCATGGGTGCTTCTAGAAACAGGGTTGAAGTTCCCAGATTCCCTGAGAGGAGAATGTGTATAGGAGGGTTTGGCTGAGTC
 641 CTTCAGCGTTAAGTGGAGGAAAGCTTGGGGAAGCCCCAATAGCTGGACAGACCTCGGCCTCCCCTCGAAGACACCTCAAT
 721 TCACAGACTCTCAGCCCACACAATGCCCCAGTGTCCCCAGCTCCGCTGGAGCAGCTGCAGGGCACTTGGATCACAACTTC
 801 TGCACCCTCTGTCCAGAGTCTAGGGCAGTCCTCCACTGGCCCAGCACTCCAGTTTCCTTTCCCTGCCTCTTGTCCAATGG
 881 AGTGGGAGGCCAGGTGAGTGGAGCAGAGGTCCTGAAGCCCTTGACCCCTGGGGGCCTGGGTAGTGTAGGATCTCGCTGGG
 961 CTGGGTCCTGGATTCCAGGGCTATTCCCTGGAGGACAGTCTCAGTTATGGGATAAGGCCCCCTGGGGGTCTCCATTTCTT
1041 TCCAACAGTTTCATGTTCACTACTGGACTCTTACGGGCTCAGTATCTCTCCCTTAGCCATGAGCTGGCTCAGGCATCCCT
1121 TCCCTTCCCTGGAGCTGCCCTGCCTTTCTCAAGTATTTATTTATTTATTGCATGGTTCCTGGGAACATGTGGCACAAGTA
1201 ATGGGATGAGGAGGAATTGGGGGTGGGGGTCTTCTACCTAGGACTCTTCCCTGGAGTCATGGGCTGCCTGGGACCCAGGA
1281 CCCATGAGGGGGCTGAGAGGTTTCTACACTCGAGGAGCAGGGGTCCAGAGAGGCAGGCTGGGGAGGCAAGGGACCCATCC
1361 TAGGCCCGCTTTCTTGCCGAGCCAAGCAGCTTAGCTGGGGCTGTGCAGCCAGGGGCTTACCCAGGCCAGTGGAGGTGCCA
1441 CAGCCCTGGGGAGCCAGACAGGCTTTGGTATCGTATCGCCTCTGTGTCCTTTTAAGAGAGGAGAGTTCAGTACCCCGTGC
1521 TTTCTTTACACTGGAGAGGAACTAAAAGGATCTCTGTGTCTATGGAGAATTGTCAATAAAAAGGCCTCAAGCTTCTTGTT
1601 TTTGTCAAAAAAAAAAA
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' ugcaaAUUUAAAGUGGGGAAGa 5'
               ||:: ||  ||||||| 
Target 5' ctaggTAGGCTT--CCCCTTCc 3'
 113 - 132 149.00 -11.60
2 
miRNA  3' ugcaaauuuaaaGUGGGGAAGa 5'
                      ||:|||||| 
Target 5' agctggctcaggCATCCCTTCc 3'
 1102 - 1123 134.00 -14.90
3 
miRNA  3' ugCAAAUUUAAAG---UGGGGAAga 5'
            ||||   ||||   :||:|||  
Target 5' caGTTT-CCTTTCCCTGCCTCTTgt 3'
 850 - 873 119.00 -9.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
574530 1 ClinVar
301841 41 ClinVar
877287 53 ClinVar
877288 58 ClinVar
301842 133 ClinVar
301843 164 ClinVar
301844 164 ClinVar
878326 212 ClinVar
301845 224 ClinVar
301846 249 ClinVar
301847 368 ClinVar
301848 414 ClinVar
878907 493 ClinVar
878908 501 ClinVar
878909 583 ClinVar
301849 679 ClinVar
878910 680 ClinVar
301850 697 ClinVar
878911 734 ClinVar
301851 779 ClinVar
301852 895 ClinVar
301853 946 ClinVar
880129 984 ClinVar
880130 1052 ClinVar
301854 1075 ClinVar
880131 1100 ClinVar
301855 1149 ClinVar
301856 1151 ClinVar
301857 1196 ClinVar
877342 1212 ClinVar
301858 1225 ClinVar
301859 1284 ClinVar
301860 1309 ClinVar
877343 1309 ClinVar
301861 1311 ClinVar
301862 1341 ClinVar
301863 1380 ClinVar
301864 1412 ClinVar
878364 1429 ClinVar
878365 1443 ClinVar
301865 1451 ClinVar
301866 1473 ClinVar
301867 1518 ClinVar
878366 1535 ClinVar
878957 1577 ClinVar
COSN30532216 10 COSMIC
COSN512215 10 COSMIC
COSN30520779 18 COSMIC
COSN19771048 31 COSMIC
COSN6606454 41 COSMIC
COSN28813276 113 COSMIC
COSN28383623 196 COSMIC
COSN27148258 236 COSMIC
COSN17076143 660 COSMIC
COSN28966632 928 COSMIC
COSN29755250 1474 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs140695712 1 dbSNP
rs748000031 3 dbSNP
rs1322077208 10 dbSNP
rs755860145 12 dbSNP
rs777563040 13 dbSNP
rs932903591 14 dbSNP
rs1216170764 19 dbSNP
rs1242876900 21 dbSNP
rs1476606341 22 dbSNP
rs1374859664 25 dbSNP
rs1270726910 27 dbSNP
rs748892716 28 dbSNP
rs368123077 30 dbSNP
rs745358878 31 dbSNP
rs767869701 31 dbSNP
rs201233270 32 dbSNP
rs1981237 41 dbSNP
rs757632237 43 dbSNP
rs948475412 45 dbSNP
rs762223790 47 dbSNP
rs765533781 51 dbSNP
rs750636794 52 dbSNP
rs755945943 52 dbSNP
rs760481213 53 dbSNP
rs907068014 56 dbSNP
rs547223774 58 dbSNP
rs1178938742 59 dbSNP
rs1244427562 65 dbSNP
rs1453234183 69 dbSNP
rs1250648888 71 dbSNP
rs1026190061 75 dbSNP
rs998519601 77 dbSNP
rs1260076492 79 dbSNP
rs1213311066 87 dbSNP
rs565747755 89 dbSNP
rs1200025471 90 dbSNP
rs1056899516 100 dbSNP
rs1241205305 103 dbSNP
rs1422744129 108 dbSNP
rs1370311763 109 dbSNP
rs1463856814 113 dbSNP
rs1299224982 116 dbSNP
rs1388627024 117 dbSNP
rs1392000495 122 dbSNP
rs1288810587 129 dbSNP
rs115982037 133 dbSNP
rs766440166 136 dbSNP
rs1004138480 139 dbSNP
rs1433659845 142 dbSNP
rs1022911850 143 dbSNP
rs1016916434 144 dbSNP
rs376690954 145 dbSNP
rs1433278021 148 dbSNP
rs952732484 151 dbSNP
rs41290464 164 dbSNP
rs1489133362 182 dbSNP
rs1286541114 188 dbSNP
rs762983122 193 dbSNP
rs367888325 196 dbSNP
rs1347381729 200 dbSNP
rs976805254 202 dbSNP
rs1331812198 204 dbSNP
rs1295455504 209 dbSNP
rs1398748816 212 dbSNP
rs1342958726 217 dbSNP
rs1321723394 220 dbSNP
rs1299142832 221 dbSNP
rs954215554 223 dbSNP
rs886047527 224 dbSNP
rs1466097285 227 dbSNP
rs1372044756 234 dbSNP
rs1168424970 236 dbSNP
rs1478735870 237 dbSNP
rs866620872 244 dbSNP
rs3814559 249 dbSNP
rs1484576503 251 dbSNP
rs987382582 259 dbSNP
rs978451462 260 dbSNP
rs924860200 271 dbSNP
rs1345779879 272 dbSNP
rs573539034 276 dbSNP
rs1406164367 277 dbSNP
rs1278107541 278 dbSNP
rs924243261 279 dbSNP
rs956507967 280 dbSNP
rs1339014632 281 dbSNP
rs1279401180 295 dbSNP
rs1414534099 302 dbSNP
rs534811855 315 dbSNP
rs553215910 318 dbSNP
rs751783581 323 dbSNP
rs948442775 327 dbSNP
rs1396302776 331 dbSNP
rs1395357032 332 dbSNP
rs1328643789 335 dbSNP
rs1466739996 337 dbSNP
rs1424180814 339 dbSNP
rs1056782536 343 dbSNP
rs1471686629 348 dbSNP
rs1044205568 355 dbSNP
rs1188023430 359 dbSNP
rs1443175605 360 dbSNP
rs928374884 361 dbSNP
rs1259259027 366 dbSNP
rs1459187853 366 dbSNP
rs3814560 368 dbSNP
rs1354665402 374 dbSNP
rs1286273066 391 dbSNP
rs1048032685 392 dbSNP
rs1246031695 410 dbSNP
rs886341283 411 dbSNP
rs181508408 414 dbSNP
rs146227758 416 dbSNP
rs576010113 422 dbSNP
rs898543435 428 dbSNP
rs1005850376 430 dbSNP
rs1015610209 433 dbSNP
rs996807279 442 dbSNP
rs897137084 444 dbSNP
rs1200134098 451 dbSNP
rs1028375984 453 dbSNP
rs543383765 454 dbSNP
rs955656858 480 dbSNP
rs868729836 482 dbSNP
rs1008372787 493 dbSNP
rs866039229 497 dbSNP
rs1032280455 498 dbSNP
rs148426983 501 dbSNP
rs985683577 502 dbSNP
rs1441583529 503 dbSNP
rs1238916489 512 dbSNP
rs1463003630 519 dbSNP
rs1450353662 523 dbSNP
rs1022844290 529 dbSNP
rs1210754398 533 dbSNP
rs1350482370 537 dbSNP
rs34700264 537 dbSNP
rs990434658 538 dbSNP
rs1241925383 555 dbSNP
rs968337613 557 dbSNP
rs528706792 558 dbSNP
rs1433680959 564 dbSNP
rs750798365 567 dbSNP
rs1324188175 572 dbSNP
rs1399887072 581 dbSNP
rs1358430650 582 dbSNP
rs547156381 583 dbSNP
rs979771365 586 dbSNP
rs934350276 599 dbSNP
rs1393043084 610 dbSNP
rs186937199 619 dbSNP
rs533021025 621 dbSNP
rs1297581932 624 dbSNP
rs938446724 627 dbSNP
rs1200280581 636 dbSNP
rs1047546007 645 dbSNP
rs572888599 646 dbSNP
rs550967604 648 dbSNP
rs1340219305 649 dbSNP
rs1243703499 661 dbSNP
rs1282056101 671 dbSNP
rs1353889681 672 dbSNP
rs1277493372 677 dbSNP
rs886047528 679 dbSNP
rs556909401 680 dbSNP
rs1037542639 683 dbSNP
rs1487281376 691 dbSNP
rs1255496485 696 dbSNP
rs4244329 697 dbSNP
rs749767485 698 dbSNP
rs1262247966 701 dbSNP
rs1338359304 704 dbSNP
rs1299770067 707 dbSNP
rs1400392098 708 dbSNP
rs1441615865 712 dbSNP
rs768105360 713 dbSNP
rs1185066535 714 dbSNP
rs1370419295 715 dbSNP
rs1445420570 716 dbSNP
rs1050208653 719 dbSNP
rs998219338 720 dbSNP
rs1477753814 723 dbSNP
rs1261657812 728 dbSNP
rs41317020 729 dbSNP
rs891192197 731 dbSNP
rs74809305 734 dbSNP
rs1289966343 737 dbSNP
rs1022474586 761 dbSNP
rs747823079 762 dbSNP
rs1402018062 763 dbSNP
rs1031830177 764 dbSNP
rs1207631186 765 dbSNP
rs113586403 766 dbSNP
rs1278649768 767 dbSNP
rs1336485379 768 dbSNP
rs112725217 769 dbSNP
rs1384586557 777 dbSNP
rs548911456 779 dbSNP
rs1219003844 785 dbSNP
rs1031249636 790 dbSNP
rs1195653139 797 dbSNP
rs1302453211 801 dbSNP
rs1307961146 803 dbSNP
rs960943485 805 dbSNP
rs1350855447 807 dbSNP
rs1361140072 812 dbSNP
rs761813161 823 dbSNP
rs1241168541 827 dbSNP
rs1465178764 829 dbSNP
rs1422091583 834 dbSNP
rs992457284 838 dbSNP
rs567526495 841 dbSNP
rs771762635 843 dbSNP
rs1021850177 844 dbSNP
rs970309087 848 dbSNP
rs1180497943 850 dbSNP
rs979766925 850 dbSNP
rs1035795332 852 dbSNP
rs959811421 857 dbSNP
rs1237703319 863 dbSNP
rs1197397395 864 dbSNP
rs1456113889 868 dbSNP
rs1199237418 869 dbSNP
rs772943843 869 dbSNP
rs1482847871 873 dbSNP
rs907622147 876 dbSNP
rs980237859 878 dbSNP
rs941834644 881 dbSNP
rs909616458 882 dbSNP
rs534547830 895 dbSNP
rs918544605 897 dbSNP
rs1398246754 899 dbSNP
rs921828986 902 dbSNP
rs1178222542 903 dbSNP
rs760576805 908 dbSNP
rs1333923895 910 dbSNP
rs1236507463 923 dbSNP
rs34517775 925 dbSNP
rs933854304 926 dbSNP
rs1051101730 927 dbSNP
rs931924799 928 dbSNP
rs1414056233 931 dbSNP
rs1437245459 935 dbSNP
rs1159853220 936 dbSNP
rs1198753493 944 dbSNP
rs886047529 946 dbSNP
rs1049736667 951 dbSNP
rs553098035 955 dbSNP
rs891153416 956 dbSNP
rs571672290 957 dbSNP
rs1407272369 961 dbSNP
rs1053572330 965 dbSNP
rs1392039997 968 dbSNP
rs1367449327 972 dbSNP
rs1453001433 978 dbSNP
rs3750611 984 dbSNP
rs1459768122 986 dbSNP
rs1044221638 989 dbSNP
rs1157654755 994 dbSNP
rs151301091 1008 dbSNP
rs1021819061 1009 dbSNP
rs1178647700 1018 dbSNP
rs1381813803 1018 dbSNP
rs765782466 1018 dbSNP
rs999689940 1019 dbSNP
rs1192890661 1020 dbSNP
rs1311553176 1021 dbSNP
rs1488670015 1023 dbSNP
rs1262137201 1024 dbSNP
rs745681473 1024 dbSNP
rs1264812444 1043 dbSNP
rs139340617 1046 dbSNP
rs1002228925 1052 dbSNP
rs1198319705 1054 dbSNP
rs1035361472 1068 dbSNP
rs1389084009 1072 dbSNP
rs543023183 1075 dbSNP
rs1362048432 1076 dbSNP
rs1158851964 1081 dbSNP
rs555336739 1085 dbSNP
rs1014598937 1093 dbSNP
rs963117445 1100 dbSNP
rs1459208556 1102 dbSNP
rs1433658249 1110 dbSNP
rs1177885717 1112 dbSNP
rs771827389 1116 dbSNP
rs970154146 1119 dbSNP
rs1489183475 1132 dbSNP
rs1266703108 1145 dbSNP
rs371748674 1149 dbSNP
rs1482956898 1150 dbSNP
rs573448961 1151 dbSNP
rs773083796 1153 dbSNP
rs909659694 1156 dbSNP
rs931909426 1168 dbSNP
rs987833906 1171 dbSNP
rs1278138117 1190 dbSNP
rs911815366 1191 dbSNP
rs540494473 1196 dbSNP
rs1217176515 1198 dbSNP
rs944000708 1214 dbSNP
rs1318541937 1215 dbSNP
rs535693765 1224 dbSNP
rs373113574 1225 dbSNP
rs886047530 1225 dbSNP
rs1397710922 1238 dbSNP
rs972561930 1239 dbSNP
rs759504043 1240 dbSNP
rs1463152539 1241 dbSNP
rs764142826 1246 dbSNP
rs1053136451 1248 dbSNP
rs891861329 1253 dbSNP
rs867912536 1254 dbSNP
rs1366245240 1255 dbSNP
rs1478664672 1257 dbSNP
rs1373484973 1265 dbSNP
rs918387078 1271 dbSNP
rs1423429000 1278 dbSNP
rs886047531 1284 dbSNP
rs1254345266 1285 dbSNP
rs1202193277 1286 dbSNP
rs1461881730 1288 dbSNP
rs947474375 1289 dbSNP
rs553053506 1291 dbSNP
rs1385072456 1293 dbSNP
rs933907974 1308 dbSNP
rs1047537 1309 dbSNP
rs942723991 1309 dbSNP
rs532898128 1310 dbSNP
rs147739377 1311 dbSNP
rs1036319947 1312 dbSNP
rs1398972964 1313 dbSNP
rs1329199859 1318 dbSNP
rs563039225 1320 dbSNP
rs886047532 1341 dbSNP
rs896082430 1342 dbSNP
rs1397170017 1344 dbSNP
rs1309510289 1348 dbSNP
rs1205459645 1350 dbSNP
rs999531622 1360 dbSNP
rs1004931572 1368 dbSNP
rs530449578 1369 dbSNP
rs1185699757 1373 dbSNP
rs1445286509 1379 dbSNP
rs13389 1380 dbSNP
rs756513824 1386 dbSNP
rs1176885170 1390 dbSNP
rs1224740864 1391 dbSNP
rs12766601 1395 dbSNP
rs994579577 1400 dbSNP
rs1209600983 1412 dbSNP
rs567464767 1412 dbSNP
rs953293763 1422 dbSNP
rs545227757 1430 dbSNP
rs1448365400 1433 dbSNP
rs1336222315 1434 dbSNP
rs987329001 1440 dbSNP
rs1403356703 1443 dbSNP
rs562845793 1450 dbSNP
rs886047533 1451 dbSNP
rs905438021 1454 dbSNP
rs1425489252 1461 dbSNP
rs1379922984 1463 dbSNP
rs1156866029 1471 dbSNP
rs528359630 1473 dbSNP
rs546479337 1474 dbSNP
rs913263333 1479 dbSNP
rs1450216809 1481 dbSNP
rs571378786 1494 dbSNP
rs962782855 1495 dbSNP
rs947451589 1514 dbSNP
rs1043124811 1517 dbSNP
rs41290466 1518 dbSNP
rs937477269 1521 dbSNP
rs1241670798 1528 dbSNP
rs1057318994 1532 dbSNP
rs371813619 1535 dbSNP
rs1455950138 1545 dbSNP
rs986618708 1548 dbSNP
rs1332788311 1551 dbSNP
rs1304364779 1555 dbSNP
rs1005164144 1558 dbSNP
rs1366150442 1561 dbSNP
rs911162422 1563 dbSNP
rs1276125762 1564 dbSNP
rs1363779561 1570 dbSNP
rs1035977839 1577 dbSNP
rs979850427 1587 dbSNP
rs1172091478 1591 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' ugcaaauuuaaaguGGGGAAGa 5'
                        ::||||| 
Target 5' -------------cUUCCUUCc 3'
 		1 - 9
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 ENST00000393677.4 | 3UTR | CUUCCUUCCUCACUCUCUCCAGC
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
Click to see details
Click to see details
133 hsa-miR-3179 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT102087 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT110061 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 6
MIRT112198 BTG2 BTG anti-proliferation factor 2 2 2
MIRT117668 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT146657 MINK1 misshapen like kinase 1 2 2
MIRT175505 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT180535 TXNIP thioredoxin interacting protein 2 2
MIRT190624 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190650 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT366902 NONO non-POU domain containing octamer binding 2 2
MIRT443554 ZFP3 ZFP3 zinc finger protein 2 2
MIRT445953 MLLT11 MLLT11, transcription factor 7 cofactor 2 2
MIRT446042 HMCN1 hemicentin 1 2 2
MIRT447968 MSH6 mutS homolog 6 2 2
MIRT448634 ONECUT1 one cut homeobox 1 2 2
MIRT449316 MRO maestro 2 2
MIRT451380 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451547 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451807 CDCA3 cell division cycle associated 3 2 4
MIRT451916 ILK integrin linked kinase 2 2
MIRT451938 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452189 KIAA1456 KIAA1456 2 2
MIRT452498 HMGXB3 HMG-box containing 3 2 2
MIRT452548 ZNF467 zinc finger protein 467 2 2
MIRT453844 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT454515 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT455363 KDM5C lysine demethylase 5C 2 2
MIRT455455 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455628 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 10
MIRT455639 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 10
MIRT455690 GLO1 glyoxalase I 2 2
MIRT456300 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT456784 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT456819 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457566 ZNF34 zinc finger protein 34 2 2
MIRT457604 IDS iduronate 2-sulfatase 2 2
MIRT458236 NXPH3 neurexophilin 3 2 2
MIRT458313 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458350 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458670 GPR35 G protein-coupled receptor 35 2 2
MIRT459675 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT461126 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461918 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462301 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463520 ZBTB7B zinc finger and BTB domain containing 7B 2 2
MIRT464378 URM1 ubiquitin related modifier 1 2 2
MIRT464614 UBE4B ubiquitination factor E4B 2 2
MIRT464711 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465520 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465974 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466058 TMEM189 transmembrane protein 189 2 2
MIRT466548 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT466647 TAGLN2 transgelin 2 2 2
MIRT467357 SP2 Sp2 transcription factor 2 2
MIRT468744 SDC2 syndecan 2 2 2
MIRT470244 PRRC2A proline rich coiled-coil 2A 2 2
MIRT471426 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT471732 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472190 NHP2L1 small nuclear ribonucleoprotein 13 2 2
MIRT472450 NAV2 neuron navigator 2 2 6
MIRT474563 KLHDC3 kelch domain containing 3 2 2
MIRT474936 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475165 IP6K1 inositol hexakisphosphate kinase 1 2 2
MIRT475399 ICMT isoprenylcysteine carboxyl methyltransferase 2 4
MIRT475426 ICK intestinal cell kinase 2 2
MIRT477090 FAM168A family with sequence similarity 168 member A 2 2
MIRT478458 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT478953 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT480096 CALR calreticulin 2 2
MIRT481924 ANKRD33B ankyrin repeat domain 33B 2 2
MIRT483217 APOA1 apolipoprotein A1 2 6
MIRT483882 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483923 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483942 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484209 SUMO1 small ubiquitin-like modifier 1 2 2
MIRT484512 SYT7 synaptotagmin 7 2 2
MIRT484709 RNF11 ring finger protein 11 2 2
MIRT485356 MYO1C myosin IC 2 4
MIRT485615 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT486584 ZNF619 zinc finger protein 619 2 2
MIRT487013 C2orf82 chromosome 2 open reading frame 82 2 2
MIRT487621 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487801 GPR20 G protein-coupled receptor 20 2 4
MIRT488134 GPR107 G protein-coupled receptor 107 2 2
MIRT488773 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT488854 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT489783 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490102 FN3K fructosamine 3 kinase 2 2
MIRT490389 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490434 MYL9 myosin light chain 9 2 2
MIRT490451 GLUD1 glutamate dehydrogenase 1 2 2
MIRT490880 OSBP oxysterol binding protein 2 2
MIRT491037 ALPK3 alpha kinase 3 2 2
MIRT491250 HCN2 hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 2 2
MIRT491748 SEMA3F semaphorin 3F 2 2
MIRT492235 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492490 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT492505 RANBP10 RAN binding protein 10 2 4
MIRT492773 PDGFB platelet derived growth factor subunit B 2 2
MIRT492922 NFAT5 nuclear factor of activated T-cells 5 2 2
MIRT493459 ITFG3 family with sequence similarity 234 member A 2 2
MIRT493654 HDLBP high density lipoprotein binding protein 2 2
MIRT494011 DUSP9 dual specificity phosphatase 9 2 2
MIRT499412 PLCG2 phospholipase C gamma 2 2 4
MIRT499552 C15orf43 telomere repeat binding bouquet formation protein 2 2 2
MIRT501836 NCOA2 nuclear receptor coactivator 2 2 2
MIRT501950 MAT2A methionine adenosyltransferase 2A 2 10
MIRT504066 KCTD12 potassium channel tetramerization domain containing 12 2 4
MIRT504509 PPP1R9B protein phosphatase 1 regulatory subunit 9B 2 2
MIRT508466 HOXB6 homeobox B6 2 4
MIRT512373 CPM carboxypeptidase M 2 2
MIRT513578 EVX1 even-skipped homeobox 1 2 2
MIRT517763 ZNF366 zinc finger protein 366 2 4
MIRT519773 ZNF354B zinc finger protein 354B 2 8
MIRT523568 GGCX gamma-glutamyl carboxylase 2 4
MIRT532802 CLDN11 claudin 11 2 2
MIRT544299 TSPYL1 TSPY like 1 2 2
MIRT544862 MYH2 myosin heavy chain 2 2 4
MIRT556731 KLHL15 kelch like family member 15 2 4
MIRT564347 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT568924 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT569012 CXorf36 chromosome X open reading frame 36 2 2
MIRT569256 FAM129B family with sequence similarity 129 member B 2 2
MIRT569591 PRELP proline and arginine rich end leucine rich repeat protein 2 2
MIRT569779 SAMD14 sterile alpha motif domain containing 14 2 2
MIRT570034 FAM228A family with sequence similarity 228 member A 2 2
MIRT573803 FRMPD4 FERM and PDZ domain containing 4 2 2
MIRT574190 ZNF264 zinc finger protein 264 2 2
MIRT576153 Hmox1 heme oxygenase 1 2 2
MIRT611311 CA8 carbonic anhydrase 8 2 4
MIRT673429 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT674976 SH3BP2 SH3 domain binding protein 2 2 2
MIRT692712 MEAF6 MYST/Esa1 associated factor 6 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-3179 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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