miRTarBase - #MIRT457105


—
pre-miRNA Information
pre-miRNA hsa-mir-3616   
Genomic Coordinates chr20: 47166967 - 47167058
Description Homo sapiens miR-3616 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3616-3p
Sequence 60| CGAGGGCAUUUCAUGAUGCAGGC |82
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 3 20 + 47167028 29233923 MiREDiBase
A-to-I 20 20 + 47167045 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1241656567 2 dbSNP
rs1336777739 8 dbSNP
rs1288261512 13 dbSNP
rs750749182 21 dbSNP
rs751652021 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol DCX   
Synonyms DBCN, DC, LISX, SCLH, XLIS
Description doublecortin
Transcript NM_000555   
Other Transcripts NM_178151 , NM_178152 , NM_178153   
Expression
Putative miRNA Targets on DCX
3'UTR of DCX
(miRNA target sites are highlighted)		 
>DCX|NM_000555|3'UTR
   1 AGGAGGGGAGAGTGCTCAGAGTCCAGAGTACAAATCCAAGCCTATCATTGTAGTAGGGTACTTCTGCTCAAGTGTCCAAC
  81 AGGGCTATTGGTGCTTTCAAGTTTTTATTTTGTTGTTGTTGTTATTTTGAAAAACACATTGTAATATGTTGGGTTTATTT
 161 TCCTGTGATTTCTCCTCTGGGCCACTGATCCACAGTTACCAATTATGAGAGATAGATTGATAACCATCCTTTGGGGCAGC
 241 ATTCCAGGGATGCAAAATGTGCTAGTCCATGACCTTTCAATGGAAAGCTTAGGTGCCTGCGTTATATTTGCCCTGTCTAA
 321 TTTTGCCCATACAGTCTTCCTTCTGTAGAGGGCTGTTTACATATACAGCACTTAAAATGTTTGTGTGGGAAAAAAAAAAC
 401 TCATTGGCAGATCCAAGAATGACAAACACAAGTGCCCCTTTTCTCTGGATCTCAAGAATGGTGGAGGACCCTGGAAGGAC
 481 AGCAAGGCAGCTCCCCAGCCTCACTCTTCACTCCTGATTGAGGCCCGGGTTTGTTGTCCAGCACCAATTCTGGCTGTCAA
 561 TGGGGAGAAATAAACCAACAACTTATAATTGTGACACCAGATGCTTAGGATCCTGGTGCTGGGTTAGCTAAGAGAATAGA
 641 CAGAATTGGAAAATACTGCAGACATTTCCGAAGAGTTTATAAAGCACAGTGAATTCCTGGTCAATCTCTCCACTGAGGCA
 721 ATTTGGAATCAATAAGCAATTGATAATAGTTTGGAGTAAGGGACTTCATATACCTGATTCCTCTAGAAGGCTGTCTAACA
 801 TACCACATGATTACATGAACTGTATGGTATCCATCTATCTCTGTTCTATTGAATGCCTTGTTAACAGCCAACACTGAAAA
 881 CACTGTGAGAATTTGTTTTCAGGTCTGACACCTTTCAGTCTCTTTTTATAGCAAGAAATCAATATCCTTTTTATAAAAAT
 961 TCATGTCTGTATTTCAGGAGCAAACTCTTCAGGCTCCTTTTTTATAAACTGGTGATTTTTCTTTTGTCTAAAAAACACAT
1041 GAAGAAAATTTACCAAAAAAAAAAAAAAAAGCAGAAGAATAATGTAGTTTAGAAATTATGCTGTCACTGCCAAACAGTAA
1121 CCTCCAGGAGAAAACAAGATGAATAGCAGAGGCCAATTCAATAGAATCAGTTTTTTGATAGCTTTTTAACAGTTATGCTT
1201 GCATTAATAATTTCAATGTGGACCAGACATTCTAATTATATTTTAAATGAAATGTTACAGCATATTTTAAGCAACTCTTT
1281 TTATCTATAATCCTAATATTTCATACTGAAGACACAGAAATCTTTCACTTGTCTTTAACATTAGAAAGGATTTCTCTTTA
1361 CTAAGGACTGATCATTTGAAATAGTTTTCAGTCTTTTGAGATACAGGTTTATAACACTGCTTTTTTTTTTCTGTAATCAT
1441 AGCCCATAATGGCAAAGACAACTAAATTTAAGTGAAGGTCATGCATGCCAATTCTGTGTTTGCTTTTAGCAGATATGAAG
1521 ATTTCCTTATTTCTTTGTAATTGTGCAGATATTTTGAAAGGCACAGCATTCGAAGCCAAGCTGCTGTTTGGCTACTGAAT
1601 GGCTTGCAGTTGTTCCTCCACTCTAAATGGAATGAGCTTGCTGTGTGTGTGTGTGGTGGTGGTGGGAGGGGGTGGTGCAT
1681 GTGTGTGTGTGTGTGTGCATCTGCAGCTGCTTCAAAATTAGGAAATACTACAGGACACCCCTGTAATGGATTGGTGGCAA
1761 CTGGGTGGCACTGCTGATGTGCACTGTGTAGGGGGGAACCCAGTGGTGGTGGGGTAGCTCAGATGCCCCTAGACAAGCTT
1841 CAGATGTCTGTAGCTACCAGAAACATTTTCGGTTCAGGAAAAGTGAGATGATGGTAGTACTGGTTTCTGGTGAAATTGAA
1921 GAACCCCAAATGATGAGGATCTCTTTTTGCCCCCTCTCCTTTTTTTGTAGACCCATTCAAAACCATTAATAAGCCCATTT
2001 TACTAAGCCCCTATTTCTTTCTAGAAGCTCAGGGTTTTCTTAGTGCCTCCCAGAACATTTTGTAGTTAATTGGGAAAAAG
2081 TGATACTTGGATTAGGGGGTGTGGGCATAAAGAATGGTGGGAGGCCTGATTTTAAACTTCAGGCCAGAACCCCCAATGAC
2161 TCCACCCATAGTCTCACTTTAGGTCTCATTTAGTCCATCACCTTTATTTTAAGTTGAGGAAGTGGAGGCTGGTAAAGAGC
2241 AGGACCAGAGGAAGAATCCAGATTTCCTTATGCTTGGGCCTCACACTAGCTCTCTGAGTATTTCCTTGATTGCGGTATAT
2321 GTACTACTAGAAAATACCAAATGGATATATTTTCTTTAGGATAACCTTTGAACCAACAATCTTCAATAACAATAGTACAT
2401 CTTCCATCTTACTTTTAATCGAGTATAAGGAAATGTTTCTTTATGGCCATTTTGGAGGGAGCAGGGGATGAGGCTTGGCA
2481 TAGTCCAAAATTTAAGTCTCCAATAATTAATTGCATTTTAAATTGGCCCACTTTCAAGGCAATTTTTTTTGTGTGTCTGT
2561 AACTGAGCTCCTCCACCCCTGTCATTCACTTCCAATTTTACCCAATCCAATTTTAGCACTCAAGTTCCATTGTGTTAATT
2641 TCTGCACGGTCAACAAACATCAAGTCAGCAAGCATTTGCCACCACTCCCTATACTTCTCCCTCCTTCTTACACACACACA
2721 CACACACACACACACAATCCATCTCTTGCTTGTTCCTACCTCCTGATTTTTCTTCCCTACAGAAATAGAAATAGGGACAA
2801 AGAAGGGGAAAATGTATATATTGGGGCTGGGCTGAACAACTAACTTCATAAGTAGTATTAACTAGGGGTAAATTGAGAGA
2881 AAAGCTCCTTTTCTCTTCACTGTTTTGGAAAGGATAGCCATTAGCATGACTGCTTTGTGTCCTTATGGACTTTAGTATTA
2961 GCCTAGATTGAATTATAGCGTTTTCTAGCTGGAAGGAACCTTAAGATCACATCATCTACTCCTCTACTCCAAATTTCTCA
3041 TTCTTCAGGCCAGGAAACCGAGACACAGAGGTAAAGTAATTTCCCCAAGGTCACACAGCTGGCTGGGGCAGGATTGGGTT
3121 TACAACCCACATCTCCTGGCTCTTATTCCAGGGCCTTTTCCCACTAAGTAGTATTGCCTTCCATTAGGCTCCTGAGAGTT
3201 ATTTCTCAGGGTCATGTTGCATCTTGGAGCCACATGCTGCTGCCCTGATCTCAGTGGGAAATCCACCCAGCAACCTAATA
3281 CAGCCCCTTTTCCCTGCATTCACCTGGTTCCCATCCACATGGGTTGCAGATGTCCTTGAAGAGAGTGAGGCATTGAGGGC
3361 CAATAGGAGCAATGGGGTCCCTGGCCTTGTCCATCTGATTCAGGAGATCACTGCTCCATCGTGAGGAGCCCTCTGAATAG
3441 CCCCCCACTGAATGCTTGCCTTGCCCAAATGGAATGGAGGAAGATTGATTTTCTCCATCAGTTCACCTTGTGTCATCTCA
3521 TAATGGTTGGTCTTTCCAGGCTGAGGGAAATGTTTCTTGTTTCCAGAGTAGAAAAAGAAAGAGTGGAACAATAGCTTTGT
3601 TCATCCTAACTTTCTGAGATGGCTTTTCAACATTTTAAAAAAACTAGTGTGGCTACCATTCACTGGCAATGATTTCTTTT
3681 AGAATATGGGAGTAAGATGAGCTAGAGAAAATAACCTGGTCTCACTGTGGTTGCCCTCATCCACAATGTCCCCAAAGCCA
3761 TCCTGCTCTGATGAGGACAATTTCCAGGTATAAGCAAGGGGCTTTGTGACAAAAATGTACCCTGGCTGATGTTAAACATT
3841 GGCTCCTGTGTTTGCACCAAAATAGCAAGCTGTGTGCTCTATACACTCTTCCCATCGTCTTGTGTACACTGCTCCTGTGG
3921 CCTTCCACAGCAGAAACCAGGGCAAAAGGGTCCAAACACATGGTTTTCCTTGCTGCAAGGCTCTTCCTGGGAACTAAGGG
4001 GGTATTTATTAGTTCAGTTCTAAGAGACCTCCTTCTGGGCTTACCCCACTCCTCAGGTACTTCTCTCTCCTTCCTCCTTC
4081 TCCTCCACAGTCACAAGTAACCAAGGAACCTGAAAGTGGATGTGTAGCTATTTGAAGAAGGCAAGGAACCCTGAGATTCT
4161 TCTTTGAATCCTCTAGTCCAAGTCTTAGACCAGTGATTGGTGCTTACCTTGAACAAAATTTTGTCTGTGTTCCTAATCCC
4241 TTCAATACTCTGGGTACAATGCTCCCAATCACCCTGCACATTTGATTCTAAATGGCTTTTATTTTTTAAAAATCCATATC
4321 CCTAGGACAAGAGAACAGGATGCCTATATCCCCAAAATGAGCTCCAGGACACTGATGGGAATGATCCCAAAGATCACCCC
4401 ACCTCAGAAACGTCTGTGCCAAGAGACTTCCCCAGATAGAAACACTGGGACAGTGGTTTGAACGACTTCTTTTATGGTTG
4481 TCCAGTTTGCTATGGAAATAAAAGGCATTGATTTTTTAAAAAGATGATTGGAACCTGTCTTTGGCCACATAGGGCCACTT
4561 GGATCCATTTCCAGGCCTTACTCATATATTGCCTTCACTGAAGGGCTTTGGCTTTAAGTCCCAGACTGGTCTCCCAAGTG
4641 AACCATAAGTGTTTTGGAGCTCATCTGGGGTGAGGCATGAGAATGTTGCCCCATCTATCCCTTCAGGAAAAGGTGCCTTC
4721 CCTCCCTTTCTCCTAAAGCCTGGTCCCCAGAAATTGTTTTTGTCTCCAAAAGTCTAGTATGGTCTTTATACACCCAGACT
4801 CTTAGTGTTGCGTCCTGCCTTGTTTCCTTGTTAAGGATCTATGCAGACCTCCCGCTTTGGCTTAGCTAGCGTGACATTGG
4881 CTATCATTTGACAAGACTAACTTTTTTTTTTTTTTTTTTTTGACTGAGTCTCCCTCTGTCACCTAGGCTGGAGTGCAGTG
4961 GCACAATCTTGGCTCGCTGCAACCTTCACCCTTCACCTCCCAGGTCGAAGCGATTCTCCTGCCTCAGTCTCCCGAGTAGC
5041 TGGGATTACAGGCGTGCGCCACCAAATCTGGCTATTTTTTTATTATTATTATTTTTAGTAGAGATGGGGTTTCACCATGT
5121 TGGCCAGACTGGTCTTGAACTCTTGGCCTCAAATTATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGA
5201 GCCACCATGCCCAGCTGACAAGACTAATTTTTTATCCCTTGGTTTATTGGCTTCAACATCTTCTGGAATCAGAGGTGATT
5281 TTTTCTTACCTTGGATGCCTGAGACTAGGGGAGTATAGAATTCCAATTGGTAATTAAGGCATCTTTCTGCTCCTGATCAG
5361 AAGGGCAGGTTAGTTGGGAGAGGTCAGATGGCACAACAGAAGTCACCTTGTAAGTAAGGCAAAGACTTGAAGGCATTAGC
5441 GTTTCTCATTACTAGGTCAATAACCTGAGGGAATCAATGGCTTTTTGCCGCTCTACCTCTTGTGTATCTCTTTGACTTTT
5521 CTTTCTCTGTCTAGTTTCCTCTGTTCTCAGTTTATATTCTATGTTATCAGTCTCTCTTTCCACAGTACAAACATCCATCC
5601 TTTCTCCTGTGCAATTCTGTCTCTCCCTCTTATTATCTTTATTTGTACTTTTTCCTTCCTCCCTGTCTAGGCATTGGGCA
5681 TGTGCCTCTTCTTAGCCTGTGATTTTGCCTTGGGACTGATGATAAATTATTTCCAGATTCAATCAGCCCTGGTCCTACCC
5761 CAGTCCAATCAGAAGTATGTTGGTGGGAATCAACCTGATCCTGGCCCTTTCTTCTTCTCCATTTTCATTCGTAATCCCCC
5841 TCAGCAGATCTTTACAAGCAGTTTCCTTATAGCTCATGTATCTTTAGGTCTTTGCCTTCCAAGCACTGTACAGAATACTT
5921 TGTGGTTCCTTTTTAGTCTGACATTTTGTGGAGCAGTGAAGCGTGCTCAGAGACATAATCAGCTGAAGAGAAAAAATCCA
6001 CCCATGGATTTATATCAGCTAAATACTAATAATTGATTTTGTTTGATGTGCCCATAATTTTTAAAGCTGCAATATAATAT
6081 AATGAGGGACCACAGGTAATTTCTCCTGTCATTTGTTTTGGCTGGATGGGGGTGGGGGAGTAATTGCTTAAAGTTTTACC
6161 ATTACACATTAAACTCTCTATAATAATCTTGTTTGGGGCTTGCTAACTGTTGAGCTGTTTTAACTAAACTGGTAGGCAAT
6241 CGGAGTTGATTTAAATGAAAAGATAATTTAACAAATCTATACTATAAAAAGAGACATTTGCTTAATTGACATGTATTTTT
6321 TCCTTCTGAGTCACCTAAACATTTACTCTTGACACCAACTGTTCATGATACTGAATAGACAGTCCATATAAGAGAAATTA
6401 GTGGACCTAAAGAAGCCAGATTGTAGGTGTTAATTTATTAAACAGAGTGCAAAGCCCTTGGAAATGTCACTGCTTGGCAA
6481 TACCATATGGAATGCCAAAATTTACAATGACTTTTCTTTATAAGTTATCCAAAAGGGATTTGAACAAGTAAGAGGTTATG
6561 CCAAAATGTCTCCAATGTATGGTCCTGTAATATATTGCAGCTTGAAGCCAATGATCCCTTATGACTTGTATACAACTAAT
6641 GCATGTTTTATTGAATTTTGCATTTCCCACGTGTGGTAAGTTCTTTAAAATGTTTTTGATCACCTTTTTGTGCCATTAAA
6721 CTTGTACAGAAAATGTTTTTATGGCCATTTTCAAAGGGAGAAAGTTTAAAATGGAAACAGCCCACCCTTTCTGCCCTATA
6801 GCTGTAGTTAGAATTGAGTACCTGTAGCAAAACAGCTGTAATTGGTGGTTGTAGTGTTAGAGGTGTTAGCTTGCTAGTGA
6881 CTAGCTTTGGAGAGTAAATGCATGGTATTGTACATCACATTTCTTAACTCGTTTTAACCTCTGAAAAGAATATATTCTTC
6961 TTTGTAGTCCTTCTTCCCACCCCCTTGCCCTCTCCCTCTCCCTGCTCCCAGTTGTCTTACAGTTGTAAATATCTGATTTG
7041 AGGCCCAATAACTCTTGCCAAGTAAAGTCAGCAAACAACAAACAAACCAAAATGTGGGGAAAAGGCATTTCTCAACCATC
7121 TCTCAGCAGTTATTGATCATTTCTTAAGGAACAGCATTGTGATCAAAGACTCAACTTTACGTAAAAATCAGTGGTAAATT
7201 GGGGTTGTATTTGGCCATTTGATTACATTTCAGGATTGAATAGTTTTCAGAATCACATGTAATCCAAAGACAGTAGGTAG
7281 TGATGTCCCTTATCCCTGCAGCTGTTTTAAGATAGAGACCTCAGAAGACTCTGCTTGACCGATGACCAATAATTATTTGA
7361 AAAAAAAAGAAAAAATGAGAGAAATAAAACAGATATTTAAGAACTTTAGCCACCTATTTAGAATAGTTATAGCCAGAAAA
7441 AAAAACAAGGGCATGAGTTCAAATGCATTACTATCAGTGTCCTAGGCAATACCTAACCTACTCTGAAATTGTGATTCAAA
7521 AGCAGTATTTCAAGAGGCATTCTCCTTTTTTGGTTTGCTGACCCCACTTGGACTGGTAGGTTTGGTGAGGCCCCCATAAA
7601 CCAGCTGGAGCAGACCCTTTTCATCTCCTGTGCCTGTAACACCCCTCTTCCCCCACCCCCTCCGCAATTCAATGAGGGCT
7681 TTCTTGGGTCAGAGGACTTCAAGGTTGTCTAGAGAAGTTTGCCATGTGTGTAAGGTGCTGTGAACTGTGAGTGCTGAAGA
7761 TTCGCAGCATTCAATACCAGGCAGCCAAAGAGCTGCTCTTGCAATTATTTTGGCTCTCAAGCTCTGTTCTTCATCGCATT
7841 CTCATTTCTGTGTACATTTGCAAGATGTGTGTAATGTCATTTTCCAAAAATAAAATTTGATTTCAATAAAAAAAAAAAAA
7921 AAAAAAAAAAAAAAA
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' cgGACGUAGUACUUUACGGGAGc 5'
            || ||||:|||:: |||||| 
Target 5' tgCTCCATCGTGAGGAGCCCTCt 3'
 3412 - 3434 153.00 -25.00
2 
miRNA  3' cgGA-CGUAGU-AC-UUUACGGGAGc 5'
            || |: ||| || :: ||||||| 
Target 5' acCTGGTCTCACTGTGGTTGCCCTCa 3'
 3714 - 3739 153.00 -21.20
3 
miRNA  3' cgGACGUAGUACUUUACGGGAgc 5'
            ||||:|:|| |  ||||||  
Target 5' gcCTGCGTTAT-ATTTGCCCTgt 3'
 295 - 316 148.00 -23.60
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1222815354 12 dbSNP
rs1354744501 17 dbSNP
rs372810866 19 dbSNP
rs369073759 23 dbSNP
rs374697232 26 dbSNP
rs1478731311 31 dbSNP
rs765611981 36 dbSNP
rs752386303 38 dbSNP
rs772280172 40 dbSNP
rs189964472 48 dbSNP
rs1424414465 69 dbSNP
rs1430277373 82 dbSNP
rs780264779 83 dbSNP
rs968163760 88 dbSNP
rs1368522662 108 dbSNP
rs1298590461 115 dbSNP
rs1328502324 117 dbSNP
rs755012417 124 dbSNP
rs1438710319 126 dbSNP
rs1273101349 130 dbSNP
rs746033465 136 dbSNP
rs1368834202 138 dbSNP
rs780872657 140 dbSNP
rs1229837926 148 dbSNP
rs1277389930 152 dbSNP
rs757038705 182 dbSNP
rs1387445892 185 dbSNP
rs1204810528 186 dbSNP
rs750822866 189 dbSNP
rs1016465806 194 dbSNP
rs1196162803 199 dbSNP
rs751282213 200 dbSNP
rs1449513173 204 dbSNP
rs956569756 213 dbSNP
rs905480541 217 dbSNP
rs1428889461 230 dbSNP
rs1163559245 240 dbSNP
rs953302108 244 dbSNP
rs1044451232 254 dbSNP
rs1321793323 259 dbSNP
rs1012587069 261 dbSNP
rs1435884117 263 dbSNP
rs768041873 264 dbSNP
rs1166663503 272 dbSNP
rs111957035 273 dbSNP
rs758322095 283 dbSNP
rs1266356199 295 dbSNP
rs1358885288 299 dbSNP
rs1207746250 300 dbSNP
rs934469880 301 dbSNP
rs924427674 302 dbSNP
rs1288699877 304 dbSNP
rs1042898294 329 dbSNP
rs947298348 351 dbSNP
rs1244455393 352 dbSNP
rs1036475701 368 dbSNP
rs185895343 374 dbSNP
rs896025981 379 dbSNP
rs1161737282 390 dbSNP
rs1451708410 390 dbSNP
rs1393942314 400 dbSNP
rs1457838333 400 dbSNP
rs764664288 407 dbSNP
rs954739098 410 dbSNP
rs1382208272 412 dbSNP
rs1203007780 427 dbSNP
rs1344033735 434 dbSNP
rs1275135137 449 dbSNP
rs1342709740 460 dbSNP
rs759198260 463 dbSNP
rs753479047 465 dbSNP
rs937543454 467 dbSNP
rs767800510 470 dbSNP
rs1265747018 474 dbSNP
rs1485240276 478 dbSNP
rs1276860109 480 dbSNP
rs1437195642 494 dbSNP
rs962150957 498 dbSNP
rs183467301 500 dbSNP
rs1046944 506 dbSNP
rs1335255838 516 dbSNP
rs946418137 527 dbSNP
rs1417450175 529 dbSNP
rs1046945 537 dbSNP
rs1200178786 546 dbSNP
rs1473011667 546 dbSNP
rs1161622196 547 dbSNP
rs1006435869 548 dbSNP
rs774556643 553 dbSNP
rs1046946 556 dbSNP
rs1453146851 558 dbSNP
rs1023898306 560 dbSNP
rs1012968703 578 dbSNP
rs1412303377 591 dbSNP
rs1046947 594 dbSNP
rs1371529246 595 dbSNP
rs1394658581 597 dbSNP
rs1312613674 608 dbSNP
rs1350753843 610 dbSNP
rs1229894607 612 dbSNP
rs762564357 614 dbSNP
rs1046948 615 dbSNP
rs1046950 616 dbSNP
rs775215086 622 dbSNP
rs935155947 626 dbSNP
rs1433274389 633 dbSNP
rs998547535 649 dbSNP
rs902974981 656 dbSNP
rs769344597 658 dbSNP
rs769600860 664 dbSNP
rs953271143 669 dbSNP
rs763548918 670 dbSNP
rs1184699013 677 dbSNP
rs1249878748 679 dbSNP
rs775714462 680 dbSNP
rs1362781643 692 dbSNP
rs1046951 697 dbSNP
rs1176800002 704 dbSNP
rs1379913903 706 dbSNP
rs1464942689 710 dbSNP
rs1179885012 739 dbSNP
rs1371631529 750 dbSNP
rs745609369 750 dbSNP
rs1484022703 763 dbSNP
rs1305812775 764 dbSNP
rs191555505 770 dbSNP
rs187654364 771 dbSNP
rs1209837664 772 dbSNP
rs1302697852 780 dbSNP
rs933258082 785 dbSNP
rs923285746 790 dbSNP
rs1275261672 798 dbSNP
rs1344123663 804 dbSNP
rs1202695738 806 dbSNP
rs1249840902 821 dbSNP
rs1480407677 828 dbSNP
rs1280925803 831 dbSNP
rs972095014 833 dbSNP
rs868455849 841 dbSNP
rs1350043921 844 dbSNP
rs1452652131 848 dbSNP
rs1193621037 854 dbSNP
rs963434580 856 dbSNP
rs1432021410 879 dbSNP
rs1167051681 882 dbSNP
rs1353580038 903 dbSNP
rs776607268 906 dbSNP
rs1458136817 911 dbSNP
rs770877895 939 dbSNP
rs1388036875 942 dbSNP
rs1439508669 944 dbSNP
rs962120771 952 dbSNP
rs1367190700 964 dbSNP
rs4469647 967 dbSNP
rs1225943807 969 dbSNP
rs1294526622 974 dbSNP
rs1322080860 978 dbSNP
rs182044105 980 dbSNP
rs984923327 981 dbSNP
rs1351591353 993 dbSNP
rs969598567 994 dbSNP
rs1293249517 1012 dbSNP
rs1446188732 1021 dbSNP
rs893189450 1021 dbSNP
rs1361273629 1029 dbSNP
rs1039911444 1036 dbSNP
rs1414721881 1038 dbSNP
rs1383587347 1041 dbSNP
rs1156254208 1042 dbSNP
rs370887855 1044 dbSNP
rs1419298473 1046 dbSNP
rs1424756886 1047 dbSNP
rs1412530180 1049 dbSNP
rs1187148689 1050 dbSNP
rs1471677864 1051 dbSNP
rs1239058676 1052 dbSNP
rs1211052720 1053 dbSNP
rs1446692099 1054 dbSNP
rs1390777680 1055 dbSNP
rs1432874140 1055 dbSNP
rs1288187188 1062 dbSNP
rs1266498789 1069 dbSNP
rs1229761084 1071 dbSNP
rs1234200583 1071 dbSNP
rs1332901065 1071 dbSNP
rs1379691917 1071 dbSNP
rs34693940 1071 dbSNP
rs375343458 1071 dbSNP
rs1210627765 1072 dbSNP
rs1329939521 1073 dbSNP
rs1242034774 1074 dbSNP
rs1483793238 1074 dbSNP
rs1024285216 1075 dbSNP
rs992404407 1077 dbSNP
rs1474648897 1079 dbSNP
rs199990129 1080 dbSNP
rs1413586125 1087 dbSNP
rs1398437874 1106 dbSNP
rs746975317 1114 dbSNP
rs1158306434 1115 dbSNP
rs1005004367 1121 dbSNP
rs1449991529 1124 dbSNP
rs1381756121 1140 dbSNP
rs746884210 1141 dbSNP
rs1354555784 1144 dbSNP
rs1414434240 1145 dbSNP
rs1285206287 1146 dbSNP
rs189576806 1155 dbSNP
rs758340223 1161 dbSNP
rs1035822330 1163 dbSNP
rs1222091026 1171 dbSNP
rs1284191573 1177 dbSNP
rs1363957881 1189 dbSNP
rs1318127226 1191 dbSNP
rs1458303714 1197 dbSNP
rs1485532614 1205 dbSNP
rs1035310378 1216 dbSNP
rs1182538985 1218 dbSNP
rs1253451570 1225 dbSNP
rs752576172 1228 dbSNP
rs1001723520 1249 dbSNP
rs1157441211 1254 dbSNP
rs1388802194 1260 dbSNP
rs906081531 1261 dbSNP
rs1043345201 1277 dbSNP
rs1374692417 1291 dbSNP
rs185209490 1293 dbSNP
rs754468429 1303 dbSNP
rs1474979593 1306 dbSNP
rs1246348349 1308 dbSNP
rs902899674 1350 dbSNP
rs1190770270 1354 dbSNP
rs1021335210 1365 dbSNP
rs1278984606 1371 dbSNP
rs1368374242 1375 dbSNP
rs754944182 1394 dbSNP
rs1221475869 1404 dbSNP
rs753252019 1411 dbSNP
rs1347623481 1414 dbSNP
rs1206226937 1415 dbSNP
rs1276369621 1420 dbSNP
rs893513809 1430 dbSNP
rs1052536570 1431 dbSNP
rs1246824479 1431 dbSNP
rs935039937 1433 dbSNP
rs766100843 1435 dbSNP
rs1191730483 1439 dbSNP
rs911658696 1444 dbSNP
rs1449853763 1458 dbSNP
rs1170205851 1461 dbSNP
rs1398935879 1462 dbSNP
rs987234872 1465 dbSNP
rs760230275 1476 dbSNP
rs1350610791 1496 dbSNP
rs888971411 1498 dbSNP
rs1050716587 1503 dbSNP
rs933246747 1509 dbSNP
rs901802751 1510 dbSNP
rs752037006 1532 dbSNP
rs1036327149 1571 dbSNP
rs940680163 1572 dbSNP
rs973382924 1575 dbSNP
rs1194938131 1580 dbSNP
rs1452845174 1581 dbSNP
rs1211206475 1585 dbSNP
rs1252333058 1587 dbSNP
rs963700621 1600 dbSNP
rs1190414693 1617 dbSNP
rs1371171243 1619 dbSNP
rs1474959374 1627 dbSNP
rs1167619409 1643 dbSNP
rs1414716791 1645 dbSNP
rs1463105859 1646 dbSNP
rs1291259099 1649 dbSNP
rs1014893410 1656 dbSNP
rs764485155 1656 dbSNP
rs983454621 1656 dbSNP
rs909268242 1658 dbSNP
rs1325109855 1666 dbSNP
rs1340983198 1666 dbSNP
rs1035791317 1669 dbSNP
rs1001692470 1670 dbSNP
rs984892234 1672 dbSNP
rs1336443230 1679 dbSNP
rs1230948131 1681 dbSNP
rs763565538 1681 dbSNP
rs948161259 1695 dbSNP
rs1259562502 1698 dbSNP
rs746889422 1698 dbSNP
rs1446231532 1703 dbSNP
rs181332040 1713 dbSNP
rs1238287874 1715 dbSNP
rs1294924367 1727 dbSNP
rs992769457 1728 dbSNP
rs1436912578 1731 dbSNP
rs1365256539 1738 dbSNP
rs373605202 1741 dbSNP
rs1417327193 1750 dbSNP
rs1457823983 1751 dbSNP
rs188521278 1756 dbSNP
rs1160810795 1760 dbSNP
rs1022294101 1763 dbSNP
rs1382044582 1768 dbSNP
rs1011794885 1777 dbSNP
rs1433706710 1788 dbSNP
rs759710539 1792 dbSNP
rs1292293129 1797 dbSNP
rs1351509385 1804 dbSNP
rs1165403018 1811 dbSNP
rs1258920422 1813 dbSNP
rs1349801402 1826 dbSNP
rs1200938296 1835 dbSNP
rs369547544 1844 dbSNP
rs1428803813 1861 dbSNP
rs1031213082 1870 dbSNP
rs776565016 1871 dbSNP
rs977019951 1896 dbSNP
rs1186149755 1916 dbSNP
rs771255726 1918 dbSNP
rs61181347 1923 dbSNP
rs967028272 1925 dbSNP
rs1184034343 1929 dbSNP
rs1021304310 1933 dbSNP
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rs1052025474 1958 dbSNP
rs1433237671 1964 dbSNP
rs1170714466 1967 dbSNP
rs137896503 1980 dbSNP
rs1392646309 1982 dbSNP
rs749834465 2000 dbSNP
rs771802792 2005 dbSNP
rs748113029 2008 dbSNP
rs536318687 2009 dbSNP
rs1189506933 2012 dbSNP
rs890189441 2023 dbSNP
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rs1209802098 2032 dbSNP
rs1028825895 2034 dbSNP
rs1247739048 2042 dbSNP
rs997763511 2045 dbSNP
rs1481055377 2080 dbSNP
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rs1200274359 2090 dbSNP
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rs1037947212 2123 dbSNP
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rs945883263 6757 dbSNP
rs1407008841 6766 dbSNP
rs1213083803 6767 dbSNP
rs772599099 6781 dbSNP
rs1259608671 6786 dbSNP
rs878858509 6787 dbSNP
rs1183520649 6788 dbSNP
rs1000675630 6789 dbSNP
rs1241043087 6790 dbSNP
rs1443721489 6791 dbSNP
rs868106050 6795 dbSNP
rs1159038141 6798 dbSNP
rs1456163256 6800 dbSNP
rs922402509 6803 dbSNP
rs766994569 6804 dbSNP
rs964202737 6807 dbSNP
rs1344685087 6812 dbSNP
rs1041285858 6826 dbSNP
rs1305054138 6829 dbSNP
rs1018149829 6832 dbSNP
rs1404397010 6836 dbSNP
rs761394618 6841 dbSNP
rs1008141518 6848 dbSNP
rs1310412401 6856 dbSNP
rs1160244023 6857 dbSNP
rs1423602737 6858 dbSNP
rs1378719818 6860 dbSNP
rs1254979457 6869 dbSNP
rs756999424 6880 dbSNP
rs1312193830 6890 dbSNP
rs773951275 6893 dbSNP
rs763989337 6911 dbSNP
rs1460725790 6916 dbSNP
rs1199078233 6921 dbSNP
rs1243270951 6922 dbSNP
rs1165832721 6931 dbSNP
rs1471311799 6935 dbSNP
rs1175636558 6936 dbSNP
rs1407373614 6938 dbSNP
rs994584972 6942 dbSNP
rs1433799313 6945 dbSNP
rs1179253499 6948 dbSNP
rs1404585354 6951 dbSNP
rs1469719489 6955 dbSNP
rs1332534793 6976 dbSNP
rs768265399 6983 dbSNP
rs1356638812 6984 dbSNP
rs746290222 7001 dbSNP
rs984119682 7032 dbSNP
rs1038878066 7038 dbSNP
rs1367721562 7038 dbSNP
rs762996715 7039 dbSNP
rs1280767894 7052 dbSNP
rs1322792329 7058 dbSNP
rs1219150878 7061 dbSNP
rs1259825354 7075 dbSNP
rs1239422815 7076 dbSNP
rs186728581 7093 dbSNP
rs927450217 7094 dbSNP
rs972851213 7098 dbSNP
rs1045909824 7105 dbSNP
rs1248496619 7130 dbSNP
rs1383591661 7136 dbSNP
rs1488914572 7137 dbSNP
rs771347201 7163 dbSNP
rs1201749512 7164 dbSNP
rs1427278292 7165 dbSNP
rs776559301 7166 dbSNP
rs747493265 7180 dbSNP
rs181200249 7181 dbSNP
rs987789550 7185 dbSNP
rs1422107765 7195 dbSNP
rs959624519 7198 dbSNP
rs1350150917 7201 dbSNP
rs1033030364 7203 dbSNP
rs41311719 7238 dbSNP
rs904238707 7249 dbSNP
rs1400554310 7251 dbSNP
rs1279963704 7262 dbSNP
rs149236665 7267 dbSNP
rs1457709876 7269 dbSNP
rs1009910063 7286 dbSNP
rs760673673 7289 dbSNP
rs1290305812 7297 dbSNP
rs1367158335 7310 dbSNP
rs779330639 7320 dbSNP
rs963863173 7323 dbSNP
rs190323213 7340 dbSNP
rs1008069571 7341 dbSNP
rs369895441 7350 dbSNP
rs1195058707 7354 dbSNP
rs942552320 7364 dbSNP
rs1046963 7369 dbSNP
rs1167748521 7369 dbSNP
rs1474693199 7369 dbSNP
rs911128575 7369 dbSNP
rs1048824953 7376 dbSNP
rs1161210029 7392 dbSNP
rs1205712198 7395 dbSNP
rs185034093 7414 dbSNP
rs1025581207 7416 dbSNP
rs202000323 7418 dbSNP
rs931300222 7446 dbSNP
rs1319681374 7450 dbSNP
rs1324670323 7452 dbSNP
rs773508426 7456 dbSNP
rs766206993 7457 dbSNP
rs1429928037 7471 dbSNP
rs1284637368 7484 dbSNP
rs918551081 7495 dbSNP
rs972736873 7500 dbSNP
rs1289798825 7502 dbSNP
rs1358852183 7503 dbSNP
rs1217484433 7539 dbSNP
rs949418256 7543 dbSNP
rs1445831599 7546 dbSNP
rs994159816 7557 dbSNP
rs1238414915 7558 dbSNP
rs1446774408 7579 dbSNP
rs1181404101 7585 dbSNP
rs1297147397 7591 dbSNP
rs898470268 7597 dbSNP
rs16986473 7614 dbSNP
rs1296918093 7617 dbSNP
rs959833459 7632 dbSNP
rs1002014644 7654 dbSNP
rs750326162 7656 dbSNP
rs1314065430 7657 dbSNP
rs138409321 7659 dbSNP
rs1425688347 7660 dbSNP
rs1045836825 7664 dbSNP
rs774892407 7668 dbSNP
rs1167637753 7672 dbSNP
rs1474137849 7674 dbSNP
rs892017314 7676 dbSNP
rs761424758 7691 dbSNP
rs751046197 7714 dbSNP
rs763803716 7715 dbSNP
rs762528445 7726 dbSNP
rs1463024461 7729 dbSNP
rs924934314 7737 dbSNP
rs1242909617 7741 dbSNP
rs979160407 7747 dbSNP
rs146898682 7750 dbSNP
rs1224353314 7751 dbSNP
rs942389672 7760 dbSNP
rs189137837 7763 dbSNP
rs1431403170 7764 dbSNP
rs761120900 7767 dbSNP
rs986605847 7773 dbSNP
rs769017285 7776 dbSNP
rs900903861 7802 dbSNP
rs865982158 7805 dbSNP
rs1341526407 7813 dbSNP
rs1331067776 7828 dbSNP
rs773811899 7829 dbSNP
rs1251912280 7835 dbSNP
rs1232662574 7836 dbSNP
rs1326353350 7850 dbSNP
rs41300894 7854 dbSNP
rs748292322 7866 dbSNP
rs1019812791 7875 dbSNP
rs1481132836 7879 dbSNP
rs962690874 7880 dbSNP
rs1006717872 7905 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' cggacguaguacuuuACGGGAGc 5'
                         ||||||| 
Target 5' ---------cccccuUGCCCUCu 3'
 		1 - 14
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 ENST00000356915.2 | 3UTR | CCCCCUUGCCCUCUCC
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
UCEC -0.711 0.02 -0.433 0.12 9 Click to see details
KIRP -0.441 0.23 -0.100 0.44 5 Click to see details
BRCA 0.324 0.27 0.086 0.44 6 Click to see details
STAD -0.658 0.27 -1.000 0.5 3 Click to see details
THCA 0.047 0.43 -0.064 0.4 17 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
PRAD -0.126 0.46 0.500 0.33 3 Click to see details
65 hsa-miR-3616-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT064769 CCND2 cyclin D2 2 2
MIRT066953 ATXN7L3B ataxin 7 like 3B 2 8
MIRT109451 KLHL15 kelch like family member 15 2 4
MIRT110074 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT253112 BCL2L12 BCL2 like 12 2 2
MIRT444698 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT445748 AGO1 argonaute 1, RISC catalytic component 2 2
MIRT446453 CHST15 carbohydrate sulfotransferase 15 2 2
MIRT451956 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452332 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT453115 HOXC4 homeobox C4 2 2
MIRT455167 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT457105 DCX doublecortin 2 2
MIRT458349 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT461635 ZSWIM4 zinc finger SWIM-type containing 4 2 2
MIRT462354 BCL7B BCL tumor suppressor 7B 2 2
MIRT462750 EFNB1 ephrin B1 2 2
MIRT465801 TMEM91 transmembrane protein 91 2 2
MIRT468741 SDC2 syndecan 2 2 2
MIRT468935 RPS24 ribosomal protein S24 2 2
MIRT469166 RNF111 ring finger protein 111 2 2
MIRT469466 REEP5 receptor accessory protein 5 2 2
MIRT469605 RALGAPA2 Ral GTPase activating protein catalytic alpha subunit 2 2 2
MIRT470600 POTEM POTE ankyrin domain family member M 2 2
MIRT470630 POTEG POTE ankyrin domain family member G 2 2
MIRT471061 PIM2 Pim-2 proto-oncogene, serine/threonine kinase 2 2
MIRT473179 MLEC malectin 2 2
MIRT474351 KMT2D lysine methyltransferase 2D 2 2
MIRT477386 ENTPD7 ectonucleoside triphosphate diphosphohydrolase 7 2 2
MIRT477452 ELOVL1 ELOVL fatty acid elongase 1 2 2
MIRT479938 CBX5 chromobox 5 2 2
MIRT481633 ARF1 ADP ribosylation factor 1 2 2
MIRT485404 MIDN midnolin 2 2
MIRT486996 ZFAND2B zinc finger AN1-type containing 2B 2 2
MIRT488315 LDOC1 LDOC1, regulator of NFKB signaling 2 2
MIRT490609 SLC47A1 solute carrier family 47 member 1 2 4
MIRT490686 SSTR1 somatostatin receptor 1 2 2
MIRT490864 UPK2 uroplakin 2 2 2
MIRT492572 PPM1L protein phosphatase, Mg2+/Mn2+ dependent 1L 2 2
MIRT492687 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT492939 NEUROD2 neuronal differentiation 2 2 2
MIRT494944 IFFO2 intermediate filament family orphan 2 2 2
MIRT503137 ATG9A autophagy related 9A 2 6
MIRT507792 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT512248 ARPP19 cAMP regulated phosphoprotein 19 2 4
MIRT512585 ZNF223 zinc finger protein 223 2 2
MIRT531029 TDGF1P3 teratocarcinoma-derived growth factor 1 pseudogene 3 2 2
MIRT532014 NOX5 NADPH oxidase 5 2 2
MIRT534906 PUM2 pumilio RNA binding family member 2 2 2
MIRT555370 PPP1R12A protein phosphatase 1 regulatory subunit 12A 2 2
MIRT559524 ARHGAP12 Rho GTPase activating protein 12 2 4
MIRT560005 ZNF282 zinc finger protein 282 2 2
MIRT561566 SLC6A9 solute carrier family 6 member 9 2 2
MIRT565714 SESN3 sestrin 3 2 2
MIRT568365 AURKA aurora kinase A 2 2
MIRT570343 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT573036 GREM2 gremlin 2, DAN family BMP antagonist 2 2
MIRT629706 XKR4 XK related 4 2 2
MIRT649162 IQSEC1 IQ motif and Sec7 domain 1 2 2
MIRT660691 ANAPC1 anaphase promoting complex subunit 1 2 2
MIRT666940 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT694390 MTA1 metastasis associated 1 2 2
MIRT704066 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT704316 DCUN1D5 defective in cullin neddylation 1 domain containing 5 2 2
MIRT709848 SNX12 sorting nexin 12 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3616 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-3616-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3616-3p Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-3616-3p Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)
hsa-miR-3616-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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