miRTarBase - #MIRT448382


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pre-miRNA Information
pre-miRNA hsa-mir-4251   
Genomic Coordinates chr1: 3127975 - 3128035
Description Homo sapiens miR-4251 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4251
Sequence 35| CCUGAGAAAAGGGCCAA |51
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs529666453 6 dbSNP
rs761641851 13 dbSNP
rs1417009298 15 dbSNP
rs915117785 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TP53INP1   
Synonyms SIP, TP53DINP1, TP53INP1A, TP53INP1B, Teap, p53DINP1
Description tumor protein p53 inducible nuclear protein 1
Transcript NM_001135733   
Other Transcripts NM_033285   
Expression
Putative miRNA Targets on TP53INP1
3'UTR of TP53INP1
(miRNA target sites are highlighted)		 
>TP53INP1|NM_001135733|3'UTR
   1 GACTCACGGGCACAGAAGTGGAAGCTCAAAATGAAATGGGGCAGCATATTCATTGTTATGTTGCAGCTCTTGCTGCTCAT
  81 ACAACTTTTCTGGAACAACCCAAGAGCTTTCGCCCTTCCCAGTGGATAAAAGAACACAGTGAAAGACAGCCTCTTAACAG
 161 AAATAGCCTTCGTCGCCAAAATCTTACCAGGGATTGCCACCCTCGGCAAGTCAAGCACAATGGCTGGGTTGTTCATCAGC
 241 CCTGCCCGCGTCAGTACAATTACTAATAGTTTCAAGTTTTGTTGGTTGGTTTCTCTTGGTTTGTGCTTACATGTATGGAT
 321 GTGTGTATATGTACAGTGAAAATGTTGTCTCTTTACAACCAATTGATAACCAATCACATAGTTTTATCAGTGTATTTAGA
 401 CACTATCTTGAAAATCAGATTTATATGCTGTGTATCACATAATGCCTTGCCTTTAACATTTACTTTTTTTGTACACTTTT
 481 TCAGATTATTTCTGGAAACATATCAATATAATTACAGTGTTTGGGGGTGTCTTTAAATATATTAGGTTATACATTAGTCA
 561 GCATTTTAAAGACATTTCTTCCCAAGTACGAGAATAGGCATCTTTCATTTTCATTTTATTTTGTATTACTTAATCTTTTA
 641 AGCAAGCAAAAATTTATTCTCAGGGTCAGCTGTACACTTTATTGACCAGTACTTGATAATCTCTCTGTATATGATGAATA
 721 CATTTTTACACACTAACATTAGCATTAACAGGTGATAGTTGCCATGGATATAATGGAATTATGGCTGGACTTTCTTTTGA
 801 AAGAAAACTTGATGTATTCTGTGTGTATGGTTTTTCCCCAGATTAGTCATACAGTTCATTTGGAATTCAGGTACATTAAG
 881 CTTTAGTGAAGAGTGCATGCAGTAATTCCAATGTGACTGCATGACGTGGTACAGACATTACAGGTGTTGTAGACAGAGGC
 961 ACTTGTCTCGTGCAGAGGGATTAAATTAGACCTGTGAGATTATATTTGGAAAAATTCATGTCTGTAACTAACCCATTAGT
1041 GCAGTATTTAATTTGTTACTATTCCTTCCCGCCAATTCTGTCCACTCCTCACCTCGCATCAGCTATAAATTTGGAAGTAC
1121 TTGTCCAGGCACTCAAGTGACTTCATATTTCTCTCTGCCCATGGGAAAAGAGATAGGCTTTATATTTCCACAGAGTGAAA
1201 AATCCTCTGTCATGGAGCCTGTCCTGCCAAGTGGCAAGAGTGTGGGGACTGTCTGGTGATGATGTCTTTCATGGCATCTG
1281 AGTGAAGAGTGACAGGTTGGCTCAACTTTTTTCTTTTTTTTTTTTTAATTGCCTTGTATTGTAAGTATTCTTCCCTGCAG
1361 TCCAAGTGACTTTTCATTTTTTGTTTTAACTTCAGGCAAAATCTTTAACCACTCTGGCCTCTGTTTCCCCCACCAACGGG
1441 GAGCAGTGACATTTACCTCCCTCACAGAGTCACTGTGAGGATTCTATACTGATTTGAAGTGGAGCTGTTCAGAACTGAAC
1521 CTTGTAGGAAATTCCAAGGGCCTTTCTACTGAATCTGGTGATGGGGTGGGGCCGTGGCACTTTCTCTGCCACAGCTGTTC
1601 TTCACAGTGTTGGTGCTAATGAGGCCAGGGTGCAGGGTTCGATTCACACGTAGGCCAGTTAACTTAGAGAAAATCTATTT
1681 CCTTACCTCTAGCCAGTCACTTCCTTTTTCCGCAGTTGTGATGGGTTTTGCTGAGCCATCCACTCTGACTGATTTCCTCT
1761 GAAGTAAACATATTTACAATCCAAAGCAATTCTACTGACAGAAGTGTTGCCTTCATAATCAAACAGCTTGTTTTTCCATC
1841 TCCTCTGCAACCCTAATTAAATGAGTACAGGTCTACAAAATGTTTTCAAGGAGAAAAGCAGCATATCCTTAAGTGAAGTA
1921 TTATATTTTTCAATAACCCTGTAGTGGCTTGATGCAGGGAACCCTGGGGGACTTTCAGCGAAGAGCTGTGCTCTTTTCTG
2001 ACTAGATTAGAGCGTTTGGAGTGGAAGACGTCAAATGTGTAGTGAGATGGAGGTTTTACATTGTTCTTCTACTGGCTGTG
2081 ATGAAGTGCCAGAATGTCTCTTTAGAACAAGAGTTAGATTCCCCCTTTCTCCTTATTGCCCCTTCCGTTTTGACTTCCCC
2161 TTTATTTATTTGTTGTCTAATTAGGGGCCAAGTCTGTAAAGTTTTGTCAAAGTGAGTTAGAAGTTGTTTTCTCTTACTAT
2241 TTGTGTTTACCAGAGTTGGGAGATAAGATAGTTTCCATGAAGGTGTGTATGTTTTATACGATGTTTGTTATAGGGCCATG
2321 CATTGGTAACTTGAAAATAGACCAGCTTAATGTCTTCAGGATGTAAAACTCTGAATACACGGCGTCTCTTTTTCATACAT
2401 TGCATGTAAGTTGTTAGTACCTCACAAGCTACAGAAGTTCAGCCATGAGATTTTGTTTGGCAACATGAACAGATTTGTGT
2481 ATAACTGCAATGGCCTTTTTTTCCAGATTTCCTTATTGACTTTTTGTTTGCCTTACCTGGGGCTAGTTTTTTATGCTTTG
2561 TACCTAGAAAACAAAAAATTACATTCGTTGGGCTTTTTTTCAAGGTTGGGATTACCACACCACCTGGAATATCATACTGT
2641 GGTTTCTGCCTAAAATTGGCACATGTAAGTATTGAAGAAAATGGTTATATAATTCAGTTGAAACTCTTGGTTATTAGATG
2721 TTAGGCATCTCCTGTATGTAAGACACAAGGCCAACCACAACACAGAACGATGTTGACCTGTTAAGTATTCTCTGAAACAT
2801 GGCCAAAATGCATTTTATGAGCTTTTTTTTTTGCTATTGTAAATATTAGTGGTTTACAATGCGCTTTAGACATATTTCTT
2881 TAAAATGCAAGCAGTGAGAAATAAGACCTCTCTGAATTAGTAGCTCTAAACTGTTAACATAGAATGTTACTTGGAAAAAG
2961 TCTGGAATATGTGGTGTACACAAGCAGTGCTTCGTGAATGAGTTTCTTAGCTTTTATAGTGCGCCATGTTTCTCAAAGTT
3041 TGTTTTTGTTGACAAAACATTTTATAATATATATCTTATGTTTATTTTTTTTCTCAACTAATTGTGTACTGCACTGTAAG
3121 GTGAAAATTAGCCATCCATTATTTATCTTCTGTGGCAATGCATTTATATGGTTGATTGGGTGGGGAATTTTTTGCAGAAA
3201 GATGCAAAGTGATTGGGTTTTCGACTTCCTATCGCAGGGAGCTTTTAAGAAATATTAATTTCCTATACATTTTTCCAATC
3281 CCCATGCAAACTGTTCCTGTTTACATACCTTCTCTGTTGTATCAGTACTTTGAGTGAGAAGACAGTTTATTTAAAACTTG
3361 AGCAGGCTGTTCAGCATTGTTTCTGCTTCTGAAATCTGTATAGTACACTGGTTTGTAATCATTATGTCTTCATTGAAATC
3441 CTTGCTACTTCTCTTCCTCCTCAATGAAATACATTATATATTATCTTTATGTACTCTTAAGAAAAACGAGCAAGGAAGAG
3521 TATCTTCATTATTCTCATTTTCTCTGAGTTGGAAACAAAAACATGAAGGACTCCAACTAGAAGACAGATATTTACATTTA
3601 AATAGATTAGTGGGAAAACTTTAAGAGTTTCCACATATTAGTTTTCATTTTTTGAGTCAAGAGACTGCTCCTTGTACTGG
3681 GAGACACTAGTAGTATATGTTTGTAATGTTACTTTAAAATTATCTTTTTATTTTATAAGGCCCATAAATACTGGTTAAAC
3761 TCTGTTAAAAGTGGGCCTTCTATCTTGGATGGTTTCACTGCCATCAGCCATGCTGATATATTAGAAATGGCATCCCTATC
3841 TACTTACTTTAATGCTTAAAATTATACATAAAATGCTTTATTTAGAAAACCTACATGATACAGTGGTGTCAGCCTTGCCA
3921 TGTATCAGTTTCACTTGAAATTTGAGACCAATTAAATTTCAACTGTTTAGGGTGGAGAAAGAGGTACTGGAAAACATGCA
4001 GATGAGGATATCTTTTATGTGCAACAGTATCCTTTGCATGGGAGGAGAGTTACTCTTGAAAGGCAGGCAGCTTAAGTGGA
4081 CAATGTTTTGTATATAGTTGAGAATTTTACGACACTTTTAAAAATTGTGTAATTGTTAAATGTCCAGTTTTGCTCTGTTT
4161 TGCCTGAAGTTTTAGTATTTGTTTTCTAGGTGGACCTCTGAAAACCAAACCAGTACCTGGGGAGGTTAGATGTGTGTTTC
4241 AGGCTTGGAGTGTATGAGTGGTTTTGCTTGTATTTTCCTCCAGAGATTTTGAACTTTAATAATTGCGTGTGTTTTTTTTT
4321 TTTTTAAGTGGCTTTGTTTTTTTTTCTCAAGTAAAATTGTGAACATATTTCCTTTATAGGGGCAGGGCATGAGTTAGGGA
4401 GACTGAAGAGTATTGTAGACTGTACATGTGCCTTCTTAATGTGTTTCTCGACACATTTTTTTTCAGTAACTTGAAAATTC
4481 AAAAGGGACATTTGGTTAGGTTACTGTACATCAATCTATGCATAAATGGCAGCTTGTTTTCTTGAGCCACGGTCTAAATT
4561 TTGTTTTTATAGAAATTTTTTATACTGATTGGTTCATAGATGGTCAGTTTTGTACACAGACTGAACAATACAGCACTTTG
4641 CCAAAAATGAGTGTAGCATTGTTTAAACATTGTGTGTTAACACCTGTTCTTTGTAATTGGGTTGTGGTGCATTTTGCACT
4721 ACCTGGAGTTACAGTTTTCAATCTGTCAGTAAATAAAGTGTCCTTTAACTTCAAAAAAAAAAAAAAA
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' aaccgGGAAAAGAGUCc 5'
               ::| ||||||| 
Target 5' aaaaaTTTATTCTCAGg 3'
 648 - 664 144.00 -11.80
2 
miRNA  3' aaccgGGAAAAGAGUCc 5'
               ::||||:|||| 
Target 5' acacaTTTTTTTTCAGt 3'
 4451 - 4467 136.00 -8.10
3 
miRNA  3' aacCGGGA-AAAGAGUcc 5'
             ||| | |||||||  
Target 5' tgcGCCATGTTTCTCAaa 3'
 3020 - 3037 134.00 -10.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18723034 107 COSMIC
COSN27937174 127 COSMIC
COSN15792388 297 COSMIC
COSN27649873 477 COSMIC
COSN19324461 497 COSMIC
COSN14929010 785 COSMIC
COSN22311337 1053 COSMIC
COSN20730456 1214 COSMIC
COSN24302668 1303 COSMIC
COSN30606751 1314 COSMIC
COSN29884715 1337 COSMIC
COSM9185554 1362 COSMIC
COSM233633 1374 COSMIC
COSM4979391 1392 COSMIC
COSM5760491 1429 COSMIC
COSM6449790 1441 COSMIC
COSM7088964 1442 COSMIC
COSM5503390 1455 COSMIC
COSM7598231 1457 COSMIC
COSM7628555 1458 COSMIC
COSM3432642 1473 COSMIC
COSM3902225 1489 COSMIC
COSM2791923 1490 COSMIC
COSM1292752 1505 COSMIC
COSM6869260 1512 COSMIC
COSM7559409 1512 COSMIC
COSM371553 1513 COSMIC
COSM6806636 1516 COSMIC
COSM9590980 1528 COSMIC
COSM295195 1533 COSMIC
COSM247953 1538 COSMIC
COSM6806634 1546 COSMIC
COSM5656224 1553 COSMIC
COSM5409985 1563 COSMIC
COSM6193746 1564 COSMIC
COSM1458741 1565 COSMIC
COSM8807761 1580 COSMIC
COSM6273927 1587 COSMIC
COSM8276053 1589 COSMIC
COSM7000603 1590 COSMIC
COSM6806637 1591 COSMIC
COSM1230128 1602 COSMIC
COSN30125718 1609 COSMIC
COSN30158186 1631 COSMIC
COSN31586154 1634 COSMIC
COSN31505465 1637 COSMIC
COSN31563795 1666 COSMIC
COSN20076443 1668 COSMIC
COSN30166915 1675 COSMIC
COSN31547895 1681 COSMIC
COSN31500742 1692 COSMIC
COSN30179923 1701 COSMIC
COSN31601696 1716 COSMIC
COSN31602453 1737 COSMIC
COSN28778037 1748 COSMIC
COSN31547540 1894 COSMIC
COSN31481921 2002 COSMIC
COSN31555310 2057 COSMIC
COSN28817393 2070 COSMIC
COSN16958318 2310 COSMIC
COSN27656820 2310 COSMIC
COSN9689126 2313 COSMIC
COSN27383328 2655 COSMIC
COSN22648507 2706 COSMIC
COSN14459083 2930 COSMIC
COSN31550547 3133 COSMIC
COSN28691259 3441 COSMIC
COSN26562590 3464 COSMIC
COSN26596057 3487 COSMIC
COSN17008749 3504 COSMIC
COSN25280559 3513 COSMIC
COSN32057822 3514 COSMIC
COSN30542663 3525 COSMIC
COSN5692693 3678 COSMIC
COSN32057821 3716 COSMIC
COSN20105719 3837 COSMIC
COSN9689125 3872 COSMIC
COSN20091839 3906 COSMIC
COSN20105713 4163 COSMIC
COSN6370834 4231 COSMIC
COSN21451307 4237 COSMIC
COSN6370833 4280 COSMIC
COSN19547964 4385 COSMIC
COSN43138 4441 COSMIC
COSN2299790 4509 COSMIC
COSN23253340 4575 COSMIC
COSN2299789 4625 COSMIC
COSN2299788 5164 COSMIC
COSN17902413 5577 COSMIC
COSN20105707 5653 COSMIC
COSN9461156 5656 COSMIC
COSN28585180 5673 COSMIC
COSN28784126 5687 COSMIC
COSN31563654 5756 COSMIC
COSN31597352 5796 COSMIC
COSN31547124 5915 COSMIC
COSN20920123 5969 COSMIC
COSN31524007 5971 COSMIC
COSN17037890 6026 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs372202256 5 dbSNP
rs547387114 7 dbSNP
rs761769608 8 dbSNP
rs765389649 8 dbSNP
rs1358134369 9 dbSNP
rs776515512 11 dbSNP
rs768768820 14 dbSNP
rs1348642829 15 dbSNP
rs759754798 15 dbSNP
rs1377241740 19 dbSNP
rs1327747428 20 dbSNP
rs978162109 28 dbSNP
rs112270989 29 dbSNP
rs764025923 29 dbSNP
rs1392526312 30 dbSNP
rs376328320 31 dbSNP
rs1423885714 36 dbSNP
rs1327309391 40 dbSNP
rs1022581299 41 dbSNP
rs1383273275 42 dbSNP
rs1233412253 45 dbSNP
rs1161808388 46 dbSNP
rs769926486 47 dbSNP
rs780386673 47 dbSNP
rs372004389 48 dbSNP
rs746055999 49 dbSNP
rs1181276564 50 dbSNP
rs956902677 52 dbSNP
rs760770345 53 dbSNP
rs1480413096 58 dbSNP
rs1231426022 74 dbSNP
rs183276653 81 dbSNP
rs1464638674 101 dbSNP
rs543441818 102 dbSNP
rs1012693649 103 dbSNP
rs1462499944 103 dbSNP
rs539761545 105 dbSNP
rs1031193684 111 dbSNP
rs570658727 115 dbSNP
rs1416406467 127 dbSNP
rs1476447314 128 dbSNP
rs1166510118 131 dbSNP
rs373317343 132 dbSNP
rs1394495643 133 dbSNP
rs1003687583 137 dbSNP
rs1321397267 142 dbSNP
rs1308488817 152 dbSNP
rs142215779 153 dbSNP
rs1372103956 156 dbSNP
rs554594874 163 dbSNP
rs1045874466 164 dbSNP
rs1353507355 167 dbSNP
rs1235016651 174 dbSNP
rs1012625123 175 dbSNP
rs1328651756 176 dbSNP
rs894139513 184 dbSNP
rs1407301573 185 dbSNP
rs541134548 186 dbSNP
rs1048683625 188 dbSNP
rs1336553096 189 dbSNP
rs550723222 190 dbSNP
rs3021403 191 dbSNP
rs1486945183 194 dbSNP
rs1189193130 195 dbSNP
rs919144136 198 dbSNP
rs536868435 208 dbSNP
rs748356516 209 dbSNP
rs944523461 209 dbSNP
rs1220068124 210 dbSNP
rs1400876553 222 dbSNP
rs2945556 227 dbSNP
rs1159873796 231 dbSNP
rs1373318900 232 dbSNP
rs1416380264 237 dbSNP
rs1418606495 237 dbSNP
rs1405996256 241 dbSNP
rs1183825253 247 dbSNP
rs886285875 249 dbSNP
rs1243511392 251 dbSNP
rs527728924 253 dbSNP
rs1218803445 277 dbSNP
rs1351716498 277 dbSNP
rs997268346 278 dbSNP
rs3019172 281 dbSNP
rs3019171 283 dbSNP
rs953454877 285 dbSNP
rs1212034935 288 dbSNP
rs762711435 299 dbSNP
rs943059033 302 dbSNP
rs1234074496 303 dbSNP
rs956957938 304 dbSNP
rs376176022 307 dbSNP
rs1315827507 310 dbSNP
rs1392876631 312 dbSNP
rs1436400854 324 dbSNP
rs538483369 326 dbSNP
rs1304327531 327 dbSNP
rs1354602407 334 dbSNP
rs781569969 335 dbSNP
rs1408106985 336 dbSNP
rs889942360 337 dbSNP
rs1247710667 339 dbSNP
rs1330985732 343 dbSNP
rs1336368771 345 dbSNP
rs1383136820 348 dbSNP
rs911460184 364 dbSNP
rs1314760019 365 dbSNP
rs1450954679 369 dbSNP
rs1053986869 375 dbSNP
rs1338049970 376 dbSNP
rs1289985246 379 dbSNP
rs547911882 385 dbSNP
rs1274516165 386 dbSNP
rs1437974735 387 dbSNP
rs1343507038 388 dbSNP
rs1167080499 390 dbSNP
rs924122031 406 dbSNP
rs1384888833 407 dbSNP
rs1194064377 410 dbSNP
rs1182703490 422 dbSNP
rs1442562267 425 dbSNP
rs1460420828 427 dbSNP
rs1169640657 430 dbSNP
rs1397115035 431 dbSNP
rs1461021165 434 dbSNP
rs978109685 434 dbSNP
rs1396984115 444 dbSNP
rs1023769206 447 dbSNP
rs556470200 461 dbSNP
rs2467676 462 dbSNP
rs1258411853 463 dbSNP
rs1224126400 470 dbSNP
rs1230053037 472 dbSNP
rs567264220 473 dbSNP
rs1356237037 474 dbSNP
rs58251489 475 dbSNP
rs58486395 476 dbSNP
rs146282014 477 dbSNP
rs1491035650 477 dbSNP
rs201770242 477 dbSNP
rs1393122525 479 dbSNP
rs201029092 479 dbSNP
rs141760825 481 dbSNP
rs199966589 481 dbSNP
rs1475614740 483 dbSNP
rs201910691 483 dbSNP
rs917635722 485 dbSNP
rs994449810 487 dbSNP
rs1159517327 499 dbSNP
rs1362304772 499 dbSNP
rs1375163027 499 dbSNP
rs1455507269 499 dbSNP
rs557721378 499 dbSNP
rs75775560 499 dbSNP
rs1359658404 500 dbSNP
rs1491146696 500 dbSNP
rs1286487894 504 dbSNP
rs571392745 506 dbSNP
rs552787151 507 dbSNP
rs897770077 507 dbSNP
rs1244170889 508 dbSNP
rs1485930259 514 dbSNP
rs1176723107 519 dbSNP
rs1248428540 520 dbSNP
rs1421124531 524 dbSNP
rs1036233931 531 dbSNP
rs1394702918 539 dbSNP
rs751151425 547 dbSNP
rs1328572008 553 dbSNP
rs534930834 556 dbSNP
rs1433298942 562 dbSNP
rs532780681 572 dbSNP
rs959653435 576 dbSNP
rs1382147401 577 dbSNP
rs1016153611 582 dbSNP
rs1360545803 583 dbSNP
rs1304998511 585 dbSNP
rs563822215 592 dbSNP
rs544096471 593 dbSNP
rs1006150544 597 dbSNP
rs866710992 598 dbSNP
rs1365135328 607 dbSNP
rs67638412 609 dbSNP
rs71569103 609 dbSNP
rs932078281 614 dbSNP
rs1422445102 615 dbSNP
rs1026148111 619 dbSNP
rs1369747269 623 dbSNP
rs564988853 625 dbSNP
rs915301028 629 dbSNP
rs1282146652 637 dbSNP
rs551897529 644 dbSNP
rs1170953995 652 dbSNP
rs1249533411 669 dbSNP
rs529999585 683 dbSNP
rs1452755138 685 dbSNP
rs201654101 685 dbSNP
rs1195925627 687 dbSNP
rs564644373 691 dbSNP
rs1490374528 692 dbSNP
rs1428453996 695 dbSNP
rs1169026427 696 dbSNP
rs1267655307 698 dbSNP
rs762794270 700 dbSNP
rs901580844 708 dbSNP
rs970963872 710 dbSNP
rs1368113137 722 dbSNP
rs1213771758 732 dbSNP
rs1227202163 739 dbSNP
rs560959798 740 dbSNP
rs192048857 748 dbSNP
rs79118914 750 dbSNP
rs958726409 763 dbSNP
rs1467311979 764 dbSNP
rs1215722039 766 dbSNP
rs558669451 768 dbSNP
rs1485783394 775 dbSNP
rs994500720 792 dbSNP
rs897487412 798 dbSNP
rs1014510285 806 dbSNP
rs535323496 811 dbSNP
rs890356037 811 dbSNP
rs1397541170 818 dbSNP
rs892808672 823 dbSNP
rs544875447 825 dbSNP
rs1429834264 836 dbSNP
rs936929299 841 dbSNP
rs1053872265 849 dbSNP
rs186016622 851 dbSNP
rs1292760933 855 dbSNP
rs935355475 860 dbSNP
rs924228307 861 dbSNP
rs1461314510 883 dbSNP
rs576190249 885 dbSNP
rs1290910494 890 dbSNP
rs1214131317 899 dbSNP
rs1244130548 902 dbSNP
rs1488912496 908 dbSNP
rs1421320879 911 dbSNP
rs1256022616 921 dbSNP
rs1042518651 929 dbSNP
rs1178509410 940 dbSNP
rs1480763796 945 dbSNP
rs1427976287 949 dbSNP
rs949604147 961 dbSNP
rs757779476 962 dbSNP
rs1399712028 965 dbSNP
rs949680340 967 dbSNP
rs917982196 969 dbSNP
rs1346682596 973 dbSNP
rs1439160347 975 dbSNP
rs991325250 977 dbSNP
rs556143972 988 dbSNP
rs536563409 990 dbSNP
rs1400364546 991 dbSNP
rs1195537931 992 dbSNP
rs959367234 994 dbSNP
rs749966192 997 dbSNP
rs1284805288 999 dbSNP
rs1350235950 1000 dbSNP
rs916823683 1010 dbSNP
rs1286595314 1025 dbSNP
rs754254310 1025 dbSNP
rs765216704 1026 dbSNP
rs1210580108 1036 dbSNP
rs146472525 1039 dbSNP
rs1027394551 1049 dbSNP
rs544754679 1050 dbSNP
rs950607096 1054 dbSNP
rs1469318037 1059 dbSNP
rs1281427607 1060 dbSNP
rs181033339 1070 dbSNP
rs761871377 1075 dbSNP
rs1026265240 1076 dbSNP
rs533805643 1087 dbSNP
rs571354778 1088 dbSNP
rs764697227 1092 dbSNP
rs1373581586 1101 dbSNP
rs1017327493 1103 dbSNP
rs1334943220 1106 dbSNP
rs1335309763 1119 dbSNP
rs1440109476 1131 dbSNP
rs1028893253 1137 dbSNP
rs114691680 1140 dbSNP
rs893636991 1151 dbSNP
rs1053586369 1153 dbSNP
rs369585949 1167 dbSNP
rs532548467 1171 dbSNP
rs998504758 1191 dbSNP
rs1436786860 1192 dbSNP
rs1470890413 1193 dbSNP
rs1201785060 1194 dbSNP
rs1239671417 1196 dbSNP
rs1439873566 1203 dbSNP
rs1363957640 1210 dbSNP
rs949392978 1215 dbSNP
rs2945555 1217 dbSNP
rs778459251 1218 dbSNP
rs1042634444 1221 dbSNP
rs1417006147 1222 dbSNP
rs773190417 1227 dbSNP
rs1173158329 1228 dbSNP
rs949548808 1229 dbSNP
rs1395649385 1238 dbSNP
rs1245342314 1248 dbSNP
rs1204765851 1251 dbSNP
rs1401338054 1258 dbSNP
rs1440366271 1266 dbSNP
rs752825883 1269 dbSNP
rs1261841161 1270 dbSNP
rs1234418757 1273 dbSNP
rs562140556 1278 dbSNP
rs1351502266 1284 dbSNP
rs1337995091 1286 dbSNP
rs1055175911 1290 dbSNP
rs570238273 1320 dbSNP
rs1457945117 1322 dbSNP
rs1269851239 1323 dbSNP
rs1223922283 1324 dbSNP
rs372668524 1335 dbSNP
rs1290188188 1336 dbSNP
rs138854584 1343 dbSNP
rs1350756149 1346 dbSNP
rs771092479 1349 dbSNP
rs747078472 1350 dbSNP
rs774341350 1351 dbSNP
rs1278589681 1355 dbSNP
rs369163386 1357 dbSNP
rs1332645423 1360 dbSNP
rs778413054 1361 dbSNP
rs550171438 1367 dbSNP
rs145208833 1368 dbSNP
rs1299959638 1370 dbSNP
rs1460977762 1374 dbSNP
rs765854775 1379 dbSNP
rs1385688250 1380 dbSNP
rs758008415 1385 dbSNP
rs201253664 1387 dbSNP
rs764976916 1395 dbSNP
rs761569527 1399 dbSNP
rs954403435 1399 dbSNP
rs1325232459 1400 dbSNP
rs1405013947 1401 dbSNP
rs1480305476 1401 dbSNP
rs776605526 1421 dbSNP
rs764011815 1425 dbSNP
rs996117662 1429 dbSNP
rs1282898277 1430 dbSNP
rs760551466 1436 dbSNP
rs1346745814 1440 dbSNP
rs775456475 1452 dbSNP
rs772155217 1453 dbSNP
rs1343338732 1459 dbSNP
rs148827655 1462 dbSNP
rs771481093 1463 dbSNP
rs749667821 1466 dbSNP
rs189831461 1467 dbSNP
rs1399000235 1469 dbSNP
rs1408645657 1474 dbSNP
rs748615146 1476 dbSNP
rs144109211 1481 dbSNP
rs750089584 1482 dbSNP
rs768515431 1491 dbSNP
rs1476052610 1492 dbSNP
rs757108010 1499 dbSNP
rs909329055 1501 dbSNP
rs138400077 1508 dbSNP
rs1443640130 1509 dbSNP
rs527728622 1512 dbSNP
rs185282859 1513 dbSNP
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rs200978262 1525 dbSNP
rs754479287 1527 dbSNP
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rs1309907291 1553 dbSNP
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rs1244986186 1557 dbSNP
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rs1173056121 1569 dbSNP
rs1410868570 1570 dbSNP
rs1419512721 1572 dbSNP
rs372267324 1575 dbSNP
rs1017860192 1576 dbSNP
rs986022964 1580 dbSNP
rs1182631413 1583 dbSNP
rs771535529 1587 dbSNP
rs745376357 1588 dbSNP
rs756928155 1589 dbSNP
rs753451554 1590 dbSNP
rs777588834 1591 dbSNP
rs1229899317 1592 dbSNP
rs755884231 1593 dbSNP
rs771192696 1597 dbSNP
rs1159575409 1599 dbSNP
rs1315876324 1600 dbSNP
rs1245316801 1602 dbSNP
rs752634816 1604 dbSNP
rs1300115144 1609 dbSNP
rs907658551 1611 dbSNP
rs1213343812 1613 dbSNP
rs370100507 1615 dbSNP
rs902867314 1617 dbSNP
rs759326688 1622 dbSNP
rs1427067388 1626 dbSNP
rs1386369307 1633 dbSNP
rs749272729 1634 dbSNP
rs1442225315 1636 dbSNP
rs766516843 1637 dbSNP
rs1177354759 1639 dbSNP
rs376470637 1644 dbSNP
rs896773303 1645 dbSNP
rs2924479 1649 dbSNP
rs376161483 1652 dbSNP
rs117962027 1654 dbSNP
rs887845205 1656 dbSNP
rs1242081142 1661 dbSNP
rs1282276898 1662 dbSNP
rs1309664087 1668 dbSNP
rs553286088 1669 dbSNP
rs542484737 1671 dbSNP
rs1257684210 1675 dbSNP
rs1483642634 1676 dbSNP
rs1049191975 1678 dbSNP
rs1195280687 1684 dbSNP
rs1248708968 1684 dbSNP
rs929263296 1697 dbSNP
rs919268980 1700 dbSNP
rs957968524 1703 dbSNP
rs975988188 1707 dbSNP
rs1316980919 1708 dbSNP
rs944619518 1710 dbSNP
rs1366989739 1711 dbSNP
rs1163834087 1713 dbSNP
rs1466151006 1716 dbSNP
rs1423681262 1721 dbSNP
rs1297062220 1727 dbSNP
rs1412064574 1737 dbSNP
rs1397716392 1738 dbSNP
rs1385225326 1739 dbSNP
rs770249128 1742 dbSNP
rs1370052714 1745 dbSNP
rs1032240280 1748 dbSNP
rs1170057769 1757 dbSNP
rs910505909 1760 dbSNP
rs986349169 1765 dbSNP
rs1312651897 1766 dbSNP
rs531375044 1769 dbSNP
rs1476012197 1782 dbSNP
rs1256160065 1786 dbSNP
rs1459266460 1787 dbSNP
rs977956706 1789 dbSNP
rs1252604398 1795 dbSNP
rs957217664 1803 dbSNP
rs1191532025 1808 dbSNP
rs1490863619 1816 dbSNP
rs966525599 1828 dbSNP
rs1025194903 1841 dbSNP
rs1013673654 1844 dbSNP
rs1269783455 1845 dbSNP
rs895198326 1848 dbSNP
rs925674559 1849 dbSNP
rs977146501 1854 dbSNP
rs1420761369 1867 dbSNP
rs1033699963 1868 dbSNP
rs995454456 1872 dbSNP
rs1320202449 1873 dbSNP
rs1393250630 1879 dbSNP
rs1434054505 1893 dbSNP
rs966976736 1896 dbSNP
rs1368217477 1898 dbSNP
rs1381518859 1916 dbSNP
rs1287440131 1922 dbSNP
rs1219298266 1924 dbSNP
rs573966900 1930 dbSNP
rs1037245238 1931 dbSNP
rs1433939122 1934 dbSNP
rs1339948696 1936 dbSNP
rs1247589413 1940 dbSNP
rs1485835911 1948 dbSNP
rs940229901 1959 dbSNP
rs1478544375 1966 dbSNP
rs891303577 1966 dbSNP
rs1216180107 1980 dbSNP
rs1416755229 1984 dbSNP
rs1024388372 1988 dbSNP
rs1403171867 1992 dbSNP
rs1346846735 1994 dbSNP
rs1303293905 1998 dbSNP
rs375670576 2016 dbSNP
rs1452777365 2021 dbSNP
rs961233470 2023 dbSNP
rs1342274284 2036 dbSNP
rs181236331 2037 dbSNP
rs1292709931 2039 dbSNP
rs1377254249 2047 dbSNP
rs1230184605 2048 dbSNP
rs1290844345 2050 dbSNP
rs1331251218 2053 dbSNP
rs1410904854 2054 dbSNP
rs896849 2070 dbSNP
rs1169165246 2071 dbSNP
rs921663419 2072 dbSNP
rs1481742316 2074 dbSNP
rs1430055465 2076 dbSNP
rs1198850855 2077 dbSNP
rs879330832 2084 dbSNP
rs1471514305 2085 dbSNP
rs1487609196 2093 dbSNP
rs887958466 2095 dbSNP
rs974427627 2100 dbSNP
rs936317196 2107 dbSNP
rs577713493 2111 dbSNP
rs1156565297 2112 dbSNP
rs1362414397 2117 dbSNP
rs369335108 2119 dbSNP
rs925224319 2124 dbSNP
rs1049143415 2129 dbSNP
rs937779171 2130 dbSNP
rs548996941 2135 dbSNP
rs1257261815 2140 dbSNP
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rs375246115 2160 dbSNP
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rs1283337501 2189 dbSNP
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rs1278634406 2299 dbSNP
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rs1333340126 2396 dbSNP
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rs967092013 2405 dbSNP
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rs952154113 2515 dbSNP
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rs62523079 2695 dbSNP
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rs747301984 3000 dbSNP
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rs983777530 3210 dbSNP
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rs1234566313 3310 dbSNP
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rs1380557908 4000 dbSNP
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rs1334382732 4836 dbSNP
rs1011778264 4838 dbSNP
rs1477196907 4840 dbSNP
rs1244742847 4844 dbSNP
rs1408010541 4844 dbSNP
rs892079758 4845 dbSNP
rs1180320988 4846 dbSNP
rs1334108444 4847 dbSNP
rs1241215420 4855 dbSNP
rs1289254164 4861 dbSNP
rs572116815 4875 dbSNP
rs1458120059 4885 dbSNP
rs1265456565 4887 dbSNP
rs965355186 4887 dbSNP
rs1018187733 4890 dbSNP
rs1195776639 4892 dbSNP
rs766655340 4905 dbSNP
rs985332971 4912 dbSNP
rs1053681872 4915 dbSNP
rs750631597 4922 dbSNP
rs907257209 4926 dbSNP
rs1044512312 4928 dbSNP
rs187442746 4932 dbSNP
rs1479938438 4934 dbSNP
rs919927722 4949 dbSNP
rs1278782048 4950 dbSNP
rs1466342228 4960 dbSNP
rs1297561829 4964 dbSNP
rs1394201599 4964 dbSNP
rs1393220832 4972 dbSNP
rs1218252648 4978 dbSNP
rs968545251 4979 dbSNP
rs1221990664 4989 dbSNP
rs1285400253 4992 dbSNP
rs1038418466 5000 dbSNP
rs939925010 5005 dbSNP
rs1021427502 5018 dbSNP
rs1227094685 5020 dbSNP
rs1250132005 5033 dbSNP
rs1481871730 5034 dbSNP
rs1206479869 5039 dbSNP
rs1251988539 5040 dbSNP
rs1490034776 5042 dbSNP
rs1196899989 5043 dbSNP
rs1430913336 5044 dbSNP
rs908485530 5045 dbSNP
rs1433590112 5048 dbSNP
rs1169401787 5051 dbSNP
rs1371283519 5063 dbSNP
rs1281592278 5065 dbSNP
rs987021133 5066 dbSNP
rs1376741769 5068 dbSNP
rs955254588 5076 dbSNP
rs1010336982 5077 dbSNP
rs570572679 5082 dbSNP
rs1368488579 5088 dbSNP
rs550825572 5089 dbSNP
rs920985550 5094 dbSNP
rs1293949248 5104 dbSNP
rs1035722177 5106 dbSNP
rs765510485 5116 dbSNP
rs761814760 5133 dbSNP
rs148966293 5135 dbSNP
rs906164725 5139 dbSNP
rs561681972 5140 dbSNP
rs547774525 5148 dbSNP
rs1410466777 5153 dbSNP
rs1358135917 5156 dbSNP
rs1160173985 5172 dbSNP
rs942253417 5176 dbSNP
rs1248100176 5179 dbSNP
rs776793255 5180 dbSNP
rs975142052 5182 dbSNP
rs1048339444 5184 dbSNP
rs1176684068 5188 dbSNP
rs1430054948 5191 dbSNP
rs1189201354 5193 dbSNP
rs967807941 5193 dbSNP
rs929756751 5195 dbSNP
rs1165484069 5196 dbSNP
rs769003100 5200 dbSNP
rs1237518093 5205 dbSNP
rs1208850443 5215 dbSNP
rs1287300929 5215 dbSNP
rs1310029786 5218 dbSNP
rs528122317 5222 dbSNP
rs956469494 5225 dbSNP
rs1031939926 5232 dbSNP
rs761212014 5239 dbSNP
rs1291478808 5240 dbSNP
rs985375336 5252 dbSNP
rs114164845 5253 dbSNP
rs1021479895 5258 dbSNP
rs1353435032 5262 dbSNP
rs907375719 5269 dbSNP
rs1188886927 5273 dbSNP
rs1242468970 5285 dbSNP
rs1165978959 5290 dbSNP
rs545502501 5292 dbSNP
rs77004104 5303 dbSNP
rs564544593 5309 dbSNP
rs775908309 5313 dbSNP
rs1445929664 5321 dbSNP
rs1002909077 5323 dbSNP
rs1347144505 5331 dbSNP
rs1299025426 5346 dbSNP
rs1038367264 5349 dbSNP
rs940061577 5352 dbSNP
rs970039616 5362 dbSNP
rs1285272311 5367 dbSNP
rs1455119205 5367 dbSNP
rs1379426107 5378 dbSNP
rs577064313 5379 dbSNP
rs1006447855 5381 dbSNP
rs62523078 5383 dbSNP
rs1304416546 5389 dbSNP
rs1330698403 5390 dbSNP
rs1208948628 5394 dbSNP
rs1262343877 5395 dbSNP
rs1425440577 5396 dbSNP
rs888002685 5399 dbSNP
rs1237935930 5404 dbSNP
rs1051036619 5406 dbSNP
rs1175488774 5407 dbSNP
rs544817289 5424 dbSNP
rs1414485014 5436 dbSNP
rs994055740 5438 dbSNP
rs1180716598 5451 dbSNP
rs183574676 5452 dbSNP
rs556133231 5460 dbSNP
rs540860913 5461 dbSNP
rs150194304 5466 dbSNP
rs910906214 5467 dbSNP
rs1049392987 5482 dbSNP
rs921101665 5493 dbSNP
rs1351791985 5494 dbSNP
rs1228668924 5496 dbSNP
rs1282217086 5503 dbSNP
rs1321180308 5508 dbSNP
rs1284284710 5530 dbSNP
rs975248597 5531 dbSNP
rs746299146 5546 dbSNP
rs915014273 5550 dbSNP
rs1306791593 5551 dbSNP
rs143742882 5564 dbSNP
rs529127946 5564 dbSNP
rs1254158349 5565 dbSNP
rs988187447 5573 dbSNP
rs1483406740 5574 dbSNP
rs1312641339 5581 dbSNP
rs956410327 5585 dbSNP
rs1266984522 5586 dbSNP
rs1479229546 5590 dbSNP
rs1342435885 5595 dbSNP
rs72676984 5597 dbSNP
rs770716887 5599 dbSNP
rs1170995641 5600 dbSNP
rs1371919993 5606 dbSNP
rs1409849222 5614 dbSNP
rs1302181532 5619 dbSNP
rs928454082 5621 dbSNP
rs1399595470 5630 dbSNP
rs1003128969 5634 dbSNP
rs1358894403 5638 dbSNP
rs981494770 5646 dbSNP
rs1459265674 5647 dbSNP
rs1350335428 5648 dbSNP
rs970092510 5648 dbSNP
rs35706537 5653 dbSNP
rs11408221 5654 dbSNP
rs72676983 5654 dbSNP
rs768818316 5655 dbSNP
rs971679242 5655 dbSNP
rs1422048037 5656 dbSNP
rs1162323607 5658 dbSNP
rs1387922335 5665 dbSNP
rs748762137 5666 dbSNP
rs1323802448 5667 dbSNP
rs1325697784 5667 dbSNP
rs1406775661 5667 dbSNP
rs34737105 5667 dbSNP
rs372670751 5667 dbSNP
rs780807950 5669 dbSNP
rs956047448 5670 dbSNP
rs1193805727 5672 dbSNP
rs1245130428 5675 dbSNP
rs1358558563 5677 dbSNP
rs79606243 5678 dbSNP
rs1022935238 5680 dbSNP
rs1006166455 5681 dbSNP
rs1445642983 5681 dbSNP
rs539573204 5686 dbSNP
rs1182252223 5687 dbSNP
rs1249212824 5687 dbSNP
rs147801532 5687 dbSNP
rs1260620173 5689 dbSNP
rs1211934102 5690 dbSNP
rs952323247 5700 dbSNP
rs1163492035 5706 dbSNP
rs1383707197 5710 dbSNP
rs777377767 5712 dbSNP
rs1322358740 5713 dbSNP
rs771587683 5720 dbSNP
rs1451912728 5726 dbSNP
rs1265282381 5737 dbSNP
rs558850496 5738 dbSNP
rs1013121143 5744 dbSNP
rs1245529857 5746 dbSNP
rs1279222659 5747 dbSNP
rs146521688 5755 dbSNP
rs192250917 5756 dbSNP
rs1017049747 5759 dbSNP
rs1218112223 5766 dbSNP
rs1004594320 5767 dbSNP
rs755621105 5768 dbSNP
rs1040521031 5769 dbSNP
rs1258799916 5775 dbSNP
rs1443644628 5780 dbSNP
rs1187585393 5787 dbSNP
rs537293246 5791 dbSNP
rs1338631036 5796 dbSNP
rs1471431326 5798 dbSNP
rs887124885 5803 dbSNP
rs1412517174 5805 dbSNP
rs370559737 5805 dbSNP
rs889524530 5807 dbSNP
rs1049445021 5821 dbSNP
rs947031567 5826 dbSNP
rs1348675012 5836 dbSNP
rs1411981805 5842 dbSNP
rs1289202828 5853 dbSNP
rs1323287761 5853 dbSNP
rs1051416379 5857 dbSNP
rs368176895 5858 dbSNP
rs373276397 5868 dbSNP
rs764125207 5868 dbSNP
rs1053452475 5873 dbSNP
rs1195703784 5875 dbSNP
rs1249292215 5880 dbSNP
rs1481780894 5885 dbSNP
rs934555804 5886 dbSNP
rs1459782944 5891 dbSNP
rs7760 5892 dbSNP
rs1480006317 5893 dbSNP
rs754764724 5898 dbSNP
rs981213041 5912 dbSNP
rs1379131258 5915 dbSNP
rs1170715881 5917 dbSNP
rs1167256388 5924 dbSNP
rs1368855365 5930 dbSNP
rs1411672535 5933 dbSNP
rs866186715 5940 dbSNP
rs970146335 5949 dbSNP
rs915979487 5958 dbSNP
rs1464652175 5962 dbSNP
rs1303921009 5963 dbSNP
rs1332041549 5965 dbSNP
rs1227420198 5967 dbSNP
rs1420925517 5974 dbSNP
rs984797285 5979 dbSNP
rs952135748 5983 dbSNP
rs1026282843 5988 dbSNP
rs1274939982 5989 dbSNP
rs548081414 5992 dbSNP
rs1189070774 5993 dbSNP
rs1267068389 5993 dbSNP
rs1269282755 5995 dbSNP
rs1433542380 5996 dbSNP
rs966289433 6000 dbSNP
rs1459440445 6012 dbSNP
rs1259278514 6015 dbSNP
rs1388170874 6022 dbSNP
rs1431736490 6024 dbSNP
rs1198019306 6033 dbSNP
rs528038060 6043 dbSNP
rs1365008659 6052 dbSNP
rs1456616786 6058 dbSNP
rs775581704 6058 dbSNP
rs1391923833 6059 dbSNP
rs188961444 6064 dbSNP
rs1257896291 6066 dbSNP
rs370439320 6069 dbSNP
rs1229761395 6071 dbSNP
rs780539011 6075 dbSNP
rs1320586459 6076 dbSNP
rs914962205 6082 dbSNP
rs1266784752 6086 dbSNP
rs1300289345 6100 dbSNP
rs987915764 6101 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions BC-1
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 GSM796037. RNA binding protein: AGO2. Condition:4-Thiouridine PAR-CLIP data was present in GSM796038. RNA binding protein: AGO2. Condition:4-Thiouridine ...

- Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aaccgGGAAAAGAGUCc 5'
               ::| ||||||| 
Target 5' aaaaaUUUAUUCUCAGg 3'
 		7 - 23
Article - Gottwein E; Corcoran DL; Mukherjee N; et al.
- Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
CLIP-seq Support 1 for dataset GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_033285 | 3UTR | AUUUUAUUUUGUAUUACUUAAUCUUUUAAGCAAGCAAAAAUUUAUUCUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903826
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_NS
Location of target site NM_033285 | 3UTR | AAUCUUUUAAGCAAGCAAAAAUUUAUUCUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903828
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_9124
Location of target site NM_033285 | 3UTR | AAAAAUUUAUUCUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_033285 | 3UTR | AAGCAAAAAUUUAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_033285 | 3UTR | UAAGCAAGCAAAAAUUUAUUCUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_033285 | 3UTR | UAUUACUUAAUCUUUUAAGCAAGCAAAAAUUUAUUCUCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000448464.2 | 3UTR | CAAAAAUUUAUUCUCAGGGUCAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM796037
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-1 / 4-Thiouridine
Location of target site ENST00000448464.2 | 3UTR | GCAAGCAAAAAUUUAUUCUCAGGGUCAGCUGUACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM796038
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-1 / 4-Thiouridine
Location of target site ENST00000448464.2 | 3UTR | GCAAGCAAAAAUUUAUUCUCAGGGUCAGCUGUACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
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
98 hsa-miR-4251 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056156 OTUD1 OTU deubiquitinase 1 2 2
MIRT080004 MYL12B myosin light chain 12B 2 2
MIRT080407 ONECUT2 one cut homeobox 2 2 2
MIRT081901 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT090342 SEC61A1 Sec61 translocon alpha 1 subunit 2 8
MIRT096824 ZSWIM6 zinc finger SWIM-type containing 6 2 4
MIRT140185 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT149716 LDLR low density lipoprotein receptor 2 6
MIRT205293 STK11IP serine/threonine kinase 11 interacting protein 2 2
MIRT213265 REST RE1 silencing transcription factor 2 6
MIRT254069 BACH1 BTB domain and CNC homolog 1 2 2
MIRT256251 ANKRD33B ankyrin repeat domain 33B 2 2
MIRT264966 TMEM136 transmembrane protein 136 2 2
MIRT267496 FEN1 flap structure-specific endonuclease 1 2 2
MIRT285077 MIER1 MIER1 transcriptional regulator 2 2
MIRT296167 NCOA3 nuclear receptor coactivator 3 2 2
MIRT316073 ABRACL ABRA C-terminal like 2 2
MIRT360286 HIST1H3E histone cluster 1 H3 family member e 2 2
MIRT364793 PRRC2B proline rich coiled-coil 2B 2 2
MIRT443277 TSPAN15 tetraspanin 15 2 2
MIRT443453 CLIC5 chloride intracellular channel 5 2 2
MIRT445938 KLHL32 kelch like family member 32 2 2
MIRT448012 HLA-DOA major histocompatibility complex, class II, DO alpha 2 2
MIRT448382 TP53INP1 tumor protein p53 inducible nuclear protein 1 2 4
MIRT448499 RYBP RING1 and YY1 binding protein 2 2
MIRT449896 C11orf34 placenta expressed transcript 1 1 2
MIRT450457 ZDHHC2 zinc finger DHHC-type containing 2 2 2
MIRT450849 HTR2A 5-hydroxytryptamine receptor 2A 2 2
MIRT453774 NUCB1 nucleobindin 1 2 10
MIRT464399 URM1 ubiquitin related modifier 1 2 2
MIRT465008 TUBB2A tubulin beta 2A class IIa 2 8
MIRT465145 TSC22D2 TSC22 domain family member 2 2 2
MIRT467799 SLC2A14 solute carrier family 2 member 14 2 2
MIRT472597 NACC1 nucleus accumbens associated 1 2 2
MIRT477969 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT486586 ZNF619 zinc finger protein 619 2 2
MIRT487739 MICAL2 microtubule associated monooxygenase, calponin and LIM domain containing 2 2 4
MIRT492529 PTMA prothymosin, alpha 2 6
MIRT496845 KCNIP2 potassium voltage-gated channel interacting protein 2 2 2
MIRT499064 CTBP1 C-terminal binding protein 1 2 4
MIRT502046 LAMTOR1 late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 2 6
MIRT503907 ZSCAN25 zinc finger and SCAN domain containing 25 2 2
MIRT506776 KLHL15 kelch like family member 15 2 4
MIRT510003 UCP1 uncoupling protein 1 2 6
MIRT513040 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT513174 MOAP1 modulator of apoptosis 1 2 6
MIRT517592 ZNF579 zinc finger protein 579 2 4
MIRT521825 POLR1D RNA polymerase I subunit D 2 2
MIRT530663 TRIM56 tripartite motif containing 56 2 2
MIRT531718 TARS threonyl-tRNA synthetase 2 2
MIRT535154 PLEKHG5 pleckstrin homology and RhoGEF domain containing G5 2 2
MIRT536385 LEFTY1 left-right determination factor 1 2 2
MIRT543847 APIP APAF1 interacting protein 2 2
MIRT546973 PRKAB2 protein kinase AMP-activated non-catalytic subunit beta 2 2 2
MIRT548667 CSRNP3 cysteine and serine rich nuclear protein 3 2 2
MIRT548799 CLIP4 CAP-Gly domain containing linker protein family member 4 2 4
MIRT549610 TMEM101 transmembrane protein 101 2 2
MIRT549716 NUP37 nucleoporin 37 2 4
MIRT549873 ZNF260 zinc finger protein 260 2 2
MIRT555383 PPP1CC protein phosphatase 1 catalytic subunit gamma 2 2
MIRT566976 LBR lamin B receptor 2 2
MIRT568052 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT570970 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT571174 ZNF85 zinc finger protein 85 2 2
MIRT571364 ZNF45 zinc finger protein 45 2 2
MIRT572309 LSM4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated 2 2
MIRT572493 BTN2A2 butyrophilin subfamily 2 member A2 2 2
MIRT606783 KIAA0040 KIAA0040 2 5
MIRT607952 NFAM1 NFAT activating protein with ITAM motif 1 2 10
MIRT609978 HERPUD2 HERPUD family member 2 2 2
MIRT610069 CD300E CD300e molecule 2 2
MIRT610118 IL17REL interleukin 17 receptor E like 2 2
MIRT610151 PRMT8 protein arginine methyltransferase 8 2 4
MIRT611075 ZNF621 zinc finger protein 621 2 2
MIRT612011 COX17 COX17, cytochrome c oxidase copper chaperone 2 2
MIRT617901 PTCHD3 patched domain containing 3 2 2
MIRT618052 MRVI1 murine retrovirus integration site 1 homolog 2 2
MIRT619526 ZNF74 zinc finger protein 74 2 2
MIRT624276 CRISPLD2 cysteine rich secretory protein LCCL domain containing 2 2 2
MIRT625357 MGLL monoglyceride lipase 2 2
MIRT626756 NDUFA9 NADH:ubiquinone oxidoreductase subunit A9 2 2
MIRT628851 FAM151B family with sequence similarity 151 member B 2 2
MIRT630458 GMPS guanine monophosphate synthase 2 2
MIRT634536 MRPS17 mitochondrial ribosomal protein S17 2 2
MIRT638806 DCTN3 dynactin subunit 3 2 2
MIRT647607 TMTC2 transmembrane and tetratricopeptide repeat containing 2 2 2
MIRT650885 PPP1R15A protein phosphatase 1 regulatory subunit 15A 2 2
MIRT653507 SLC43A2 solute carrier family 43 member 2 2 2
MIRT658608 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 2 2
MIRT666345 SKAP2 src kinase associated phosphoprotein 2 2 2
MIRT693743 ACACA acetyl-CoA carboxylase alpha 2 2
MIRT704049 EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 2 2
MIRT709789 CYBRD1 cytochrome b reductase 1 2 2
MIRT711837 AMOTL2 angiomotin like 2 2 2
MIRT711875 VASP vasodilator stimulated phosphoprotein 2 2
MIRT717349 RAB40A RAB40A, member RAS oncogene family 2 2
MIRT717746 MYLK myosin light chain kinase 2 2
MIRT725398 LRIG2 leucine rich repeats and immunoglobulin like domains 2 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
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4251 Imatinib 5291 NSC743414 approved sensitive High Gastrointestinal Stromal Tumor cell line (882R-NC, 882R-OE, 882R-KD)
hsa-miR-4251 Doxorubicin 31703 NSC123127 approved resistant High Triple-Negative Breast Cancer cell line (MDA-MB-231, MDA-MB-468)
hsa-mir-4251 Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-miR-4251 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4251 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (100 ng/ml)

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