miRTarBase - #MIRT541208


—
pre-miRNA Information
pre-miRNA hsa-mir-16-2   
Genomic Coordinates chr3: 160404745 - 160404825
Description Homo sapiens miR-16-2 stem-loop
Comment This entry represents a second putative hairpin precursor sequence for miR-16, located on chromosome 3 (see also MIR:MI0000070). The sequence was previously named mir-16-3 here and in references .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-16-2-3p
Sequence 53| CCAAUAUUACUGUGCUGCUUUA |74
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30477465 2 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs746992239 2 dbSNP
rs775368833 4 dbSNP
rs373202341 10 dbSNP
rs768780684 13 dbSNP
rs1341798864 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol HOXA10   
Synonyms HOX1, HOX1.8, HOX1H, PL
Description homeobox A10
Transcript NM_018951   
Expression
Putative miRNA Targets on HOXA10
3'UTR of HOXA10
(miRNA target sites are highlighted)		 
>HOXA10|NM_018951|3'UTR
   1 TGAATCTCCAGGCGACGCGGTTTTTTCACTTCCCGAGCGCTGGTCCCCTCCCTCTGTCTTCAGGCTCTGCCCAGGAACTC
  81 GCACCTGTGCTGGAGCCCTGTTCCTCCCTCCCACACTCGCCATCTCCTGGGCCGTTACATCTGTGCAGGGCTGGTTTGTT
 161 CTGACTTTTTGTTTCTTTGTGTTTGCTTGGTGCTGGTTTATTTGTTGTTTTCTGGGGGAAAAAGCCATATCATGCTAAAA
 241 TTCTATAGAGATAGATATTGTCCTAAGTGTCAAGTCCTGACTGGGCTGGGTTTGCTGTCTTGGGGTCCCACTGCTCGAAA
 321 TGGCCCCTGTCTTCGGCCGAGCTGGTTTCCTGCCCAGCCTGGGGCAAACCTAGCCGGAAGGCCGAGGTCCCATTGTTGGC
 401 GCTGAGGTGTCTGGCCTGAGGTCAATGGTGCAAAGGAGCCGCCACCGGGCATGTCTGCCTGGAGTGCTGTGCTGTGTTTA
 481 ATCAGGGGATACAGGCCCCTGGGTTTCTTTTTTCTTTCTTCCTTTCTTCCTTGGCCAAGAGAAGGGCTTACAGGCATGGA
 561 CATGCAGGTTGGCAAACGGGCTTGACTTTGGCTGATTTAAAAAGTGAGAAAGAAAGTAAAAAAGGTTAATTTTTCCTTCC
 641 TCTGTAAGATATCCCAGCTTTAAAAAGAAAAAAAAAGAATTACCAAGAGAAGGGGACTTCTCTTCCAGTTTCTGTAAGGT
 721 CTTACATTGCCTGACTAAAATGTTTCATTTACCTCTAAATTTCCATATCCTTCTGGCTGTAGATAAATAATGTAGTTTTG
 801 TTTATGCATTTGGAATTAGTGGATTTTTTTGTCATTAAAATTGTTACCACTGGTAACATGTGACAAGCACACCACAATTC
 881 TCCCTATCTTGTGAAGTTGTTTTTTTAAATCGCCTTGAACAAAAAGTTTTTTTTTTGTTTGTTTTTGCTTTCTGAAATTC
 961 ACAGAAGCCTAGGAGGACTGGGGTAAGCGGAATAAACTAGAGAAGGGAGACATTGTTTGGATTTCCTTTATACTGTGAAG
1041 TTACATGCATAAAAGGGTCAAACCTGTAGATGCAGAAAAAGAAAAAAACTATAAATACAAATCTGTATAAATGTCTATTA
1121 TTATGAAGAATTGCCAATCTTGTTTTAAGCAAATGCATTCTATCGTTATTATAAATGTTAGTTCTAGCTCTATTTACTTC
1201 TAATCTTAAATCAGAATAAATTAATATTGTATTGCTGCTGTGCGTGGAAAAAGACGATGTTTATGTTCTTATAGAATAAA
1281 AGCTGTGGAATGAAGCTTTTTAATTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1361 AAAAAAAAAAAAAAAAAAAAAAAAA
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' auUUCGUC--GUGUCAUUAUAACc 5'
            || |||  :| | |||||||| 
Target 5' taAATCAGAATAAATTAATATTGt 3'
 1207 - 1230 162.00 -6.50
2 
miRNA  3' auuUCGUCGUGUCAUUAUAACc 5'
             || || |:|  :|||||| 
Target 5' tatAG-AG-ATA--GATATTGt 3'
 244 - 261 129.00 -5.40
3 
miRNA  3' auUUCGUCGUGUCA---UUAUAACc 5'
            |:||  |: :||   | |:||| 
Target 5' gaAGGC--CGAGGTCCCATTGTTGg 3'
 377 - 399 100.00 -8.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30543498 16 COSMIC
COSN31507740 34 COSMIC
COSN16127709 54 COSMIC
COSN30185062 54 COSMIC
COSN30137737 71 COSMIC
COSN31501410 97 COSMIC
COSN30461537 106 COSMIC
COSN30474195 107 COSMIC
COSN30507600 166 COSMIC
COSN30147660 167 COSMIC
COSN31487954 244 COSMIC
COSN22720472 248 COSMIC
COSN24302012 262 COSMIC
COSN24302010 263 COSMIC
COSN9984113 336 COSMIC
COSN32057146 446 COSMIC
COSN28740719 450 COSMIC
COSN4933004 497 COSMIC
COSN15661511 561 COSMIC
COSN20907053 635 COSMIC
COSN17881026 769 COSMIC
COSN30176303 888 COSMIC
COSN20104005 926 COSMIC
COSN31568187 984 COSMIC
COSN15660977 988 COSMIC
COSN26647984 1002 COSMIC
COSN8516351 1020 COSMIC
COSN2217783 1049 COSMIC
COSN28250395 1076 COSMIC
COSN20104001 1088 COSMIC
COSN31567904 1100 COSMIC
COSN28250394 1143 COSMIC
COSN31567611 1165 COSMIC
COSN31484294 1292 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1236808468 1 dbSNP
rs17471576 2 dbSNP
rs1198164114 4 dbSNP
rs747738780 8 dbSNP
rs1040256044 9 dbSNP
rs778399036 13 dbSNP
rs1013895177 16 dbSNP
rs1010581533 17 dbSNP
rs1212295614 19 dbSNP
rs891602770 24 dbSNP
rs1334805309 28 dbSNP
rs1274096679 29 dbSNP
rs1216743348 30 dbSNP
rs1360092701 31 dbSNP
rs1054719781 32 dbSNP
rs754550354 33 dbSNP
rs753333177 34 dbSNP
rs1323977871 37 dbSNP
rs779907501 38 dbSNP
rs756048291 39 dbSNP
rs1464129466 40 dbSNP
rs531741488 41 dbSNP
rs767297069 45 dbSNP
rs373365520 46 dbSNP
rs369862511 47 dbSNP
rs764395158 50 dbSNP
rs1204942596 51 dbSNP
rs1218610370 52 dbSNP
rs1053188019 56 dbSNP
rs1254294865 57 dbSNP
rs763170850 60 dbSNP
rs775677789 61 dbSNP
rs1345193602 63 dbSNP
rs73290334 67 dbSNP
rs760038836 69 dbSNP
rs776872085 72 dbSNP
rs771260155 73 dbSNP
rs747368667 81 dbSNP
rs1235208933 82 dbSNP
rs778595414 84 dbSNP
rs761592694 85 dbSNP
rs768275709 86 dbSNP
rs748838771 87 dbSNP
rs1366814171 93 dbSNP
rs756030359 94 dbSNP
rs1444309434 96 dbSNP
rs904269122 97 dbSNP
rs750320011 100 dbSNP
rs1196780341 104 dbSNP
rs780858123 116 dbSNP
rs757188346 118 dbSNP
rs751374742 120 dbSNP
rs1259050236 121 dbSNP
rs764446537 123 dbSNP
rs1432156870 125 dbSNP
rs763225004 127 dbSNP
rs1476313226 130 dbSNP
rs1179399754 132 dbSNP
rs1168296967 133 dbSNP
rs752738940 134 dbSNP
rs759800102 137 dbSNP
rs765302128 139 dbSNP
rs549494563 143 dbSNP
rs1278506837 148 dbSNP
rs771416128 150 dbSNP
rs761076915 154 dbSNP
rs949689370 157 dbSNP
rs916916222 161 dbSNP
rs527399102 165 dbSNP
rs560654095 170 dbSNP
rs987361889 171 dbSNP
rs773536601 173 dbSNP
rs184878327 177 dbSNP
rs1415215748 178 dbSNP
rs1376894847 179 dbSNP
rs764182627 180 dbSNP
rs777112623 183 dbSNP
rs533428262 187 dbSNP
rs779445442 190 dbSNP
rs1417800441 193 dbSNP
rs1411940938 208 dbSNP
rs769284720 215 dbSNP
rs961521027 216 dbSNP
rs1215263363 218 dbSNP
rs564802186 219 dbSNP
rs910036060 221 dbSNP
rs1200019785 223 dbSNP
rs1193808586 224 dbSNP
rs1486334469 224 dbSNP
rs984260476 227 dbSNP
rs984325488 228 dbSNP
rs1262521734 230 dbSNP
rs970169494 233 dbSNP
rs1213798881 235 dbSNP
rs1175231119 244 dbSNP
rs781235329 248 dbSNP
rs757225018 254 dbSNP
rs1395958169 255 dbSNP
rs1363216752 256 dbSNP
rs1419261364 264 dbSNP
rs954110250 270 dbSNP
rs1387223584 279 dbSNP
rs1233659473 285 dbSNP
rs1023072550 287 dbSNP
rs766126385 291 dbSNP
rs1395047091 299 dbSNP
rs1362250957 305 dbSNP
rs1290091797 307 dbSNP
rs1323448455 313 dbSNP
rs1014539517 315 dbSNP
rs539086286 316 dbSNP
rs896050904 317 dbSNP
rs1236996122 321 dbSNP
rs1388541719 322 dbSNP
rs544635763 325 dbSNP
rs1463479135 328 dbSNP
rs1237862573 329 dbSNP
rs548609072 329 dbSNP
rs758706160 335 dbSNP
rs1187313791 337 dbSNP
rs1464519164 337 dbSNP
rs1429317954 338 dbSNP
rs1258506303 339 dbSNP
rs1264175690 339 dbSNP
rs1205698601 341 dbSNP
rs41315938 354 dbSNP
rs752896480 355 dbSNP
rs1464550119 358 dbSNP
rs1448659797 364 dbSNP
rs1273900267 365 dbSNP
rs1214172500 375 dbSNP
rs998888759 376 dbSNP
rs1185113330 378 dbSNP
rs765373188 379 dbSNP
rs1042799233 384 dbSNP
rs943200399 385 dbSNP
rs1243854157 387 dbSNP
rs891735543 388 dbSNP
rs1326619182 389 dbSNP
rs1297357001 392 dbSNP
rs755143342 395 dbSNP
rs1363742111 396 dbSNP
rs1365654381 397 dbSNP
rs753840630 400 dbSNP
rs1443691364 401 dbSNP
rs1389273443 402 dbSNP
rs1163010053 409 dbSNP
rs1435442977 412 dbSNP
rs575988684 415 dbSNP
rs1481875907 418 dbSNP
rs1462881362 421 dbSNP
rs766911997 425 dbSNP
rs999945112 428 dbSNP
rs1327063408 436 dbSNP
rs1168527836 439 dbSNP
rs1449090700 440 dbSNP
rs555770661 441 dbSNP
rs1195599047 443 dbSNP
rs1469746417 446 dbSNP
rs1265230217 447 dbSNP
rs1044094504 448 dbSNP
rs949819964 449 dbSNP
rs1209017282 451 dbSNP
rs1339898326 463 dbSNP
rs1317413887 466 dbSNP
rs1252859442 467 dbSNP
rs1332609182 468 dbSNP
rs916902294 468 dbSNP
rs1341051458 475 dbSNP
rs143844631 476 dbSNP
rs1332231190 480 dbSNP
rs1393238266 481 dbSNP
rs940280732 482 dbSNP
rs573420935 487 dbSNP
rs553523598 488 dbSNP
rs910168062 492 dbSNP
rs1329855325 494 dbSNP
rs972759225 495 dbSNP
rs533994608 496 dbSNP
rs984376484 500 dbSNP
rs939980602 502 dbSNP
rs571412010 503 dbSNP
rs1398998062 511 dbSNP
rs1306592652 512 dbSNP
rs1429291188 522 dbSNP
rs775462762 526 dbSNP
rs1164607786 527 dbSNP
rs1375083842 530 dbSNP
rs1395969466 530 dbSNP
rs1175563219 533 dbSNP
rs148077971 535 dbSNP
rs970105335 538 dbSNP
rs541876384 540 dbSNP
rs762520636 544 dbSNP
rs1438357956 545 dbSNP
rs965870588 553 dbSNP
rs1306807154 554 dbSNP
rs1023125170 556 dbSNP
rs1482507823 565 dbSNP
rs1280686138 566 dbSNP
rs1235839369 568 dbSNP
rs993404335 572 dbSNP
rs775284134 577 dbSNP
rs745555888 578 dbSNP
rs1338068909 586 dbSNP
rs1032306349 587 dbSNP
rs1409642004 588 dbSNP
rs1376285328 592 dbSNP
rs1315077680 594 dbSNP
rs1294459788 600 dbSNP
rs1412993577 604 dbSNP
rs1188690232 605 dbSNP
rs1423586179 606 dbSNP
rs998546133 608 dbSNP
rs537795954 611 dbSNP
rs1210845145 612 dbSNP
rs1401536249 613 dbSNP
rs1032855690 616 dbSNP
rs769321783 618 dbSNP
rs1470460191 622 dbSNP
rs1414146909 624 dbSNP
rs1179746560 625 dbSNP
rs1311872206 628 dbSNP
rs773693027 629 dbSNP
rs1007343827 630 dbSNP
rs745419504 631 dbSNP
rs1212496899 636 dbSNP
rs775960962 639 dbSNP
rs1277229804 641 dbSNP
rs569252324 642 dbSNP
rs1212722631 643 dbSNP
rs1353426739 643 dbSNP
rs1266852965 646 dbSNP
rs1228150136 648 dbSNP
rs1356435558 649 dbSNP
rs1351245886 650 dbSNP
rs1295504256 651 dbSNP
rs143721613 652 dbSNP
rs1278487275 654 dbSNP
rs1446030392 658 dbSNP
rs1340149760 667 dbSNP
rs1319032487 671 dbSNP
rs1051643004 672 dbSNP
rs1390732498 675 dbSNP
rs1211694054 676 dbSNP
rs771667354 677 dbSNP
rs773021308 677 dbSNP
rs1156791093 678 dbSNP
rs1188767364 681 dbSNP
rs1368663707 684 dbSNP
rs1420725271 685 dbSNP
rs1456649064 687 dbSNP
rs1454122791 691 dbSNP
rs1418250689 692 dbSNP
rs997717349 695 dbSNP
rs1022774885 696 dbSNP
rs746881966 697 dbSNP
rs1471591276 698 dbSNP
rs770477352 699 dbSNP
rs748543251 702 dbSNP
rs1036699794 714 dbSNP
rs1245679043 719 dbSNP
rs1428600719 722 dbSNP
rs939645897 730 dbSNP
rs747882283 731 dbSNP
rs888129149 734 dbSNP
rs571081671 737 dbSNP
rs1355909336 741 dbSNP
rs17427826 742 dbSNP
rs1271052657 746 dbSNP
rs1433176735 749 dbSNP
rs1363044683 752 dbSNP
rs148950169 765 dbSNP
rs372423243 766 dbSNP
rs781663521 768 dbSNP
rs1166605759 773 dbSNP
rs1403460345 774 dbSNP
rs1243227373 779 dbSNP
rs766398346 780 dbSNP
rs1168075672 782 dbSNP
rs116681061 786 dbSNP
rs1245624228 791 dbSNP
rs1255268470 792 dbSNP
rs1187441449 795 dbSNP
rs1455359585 796 dbSNP
rs1469280741 800 dbSNP
rs750865808 803 dbSNP
rs1219812493 805 dbSNP
rs1451340019 806 dbSNP
rs948847344 807 dbSNP
rs915956841 809 dbSNP
rs1216512191 812 dbSNP
rs546828943 813 dbSNP
rs768011970 816 dbSNP
rs1398475854 819 dbSNP
rs1160606022 823 dbSNP
rs1296933281 824 dbSNP
rs1235166235 825 dbSNP
rs1345720901 828 dbSNP
rs1371630964 829 dbSNP
rs1295279821 830 dbSNP
rs370539354 831 dbSNP
rs532933177 831 dbSNP
rs1441975688 833 dbSNP
rs1434227969 835 dbSNP
rs1349020670 838 dbSNP
rs1329331174 840 dbSNP
rs533580346 841 dbSNP
rs1371402626 843 dbSNP
rs1225542548 849 dbSNP
rs1284974195 854 dbSNP
rs1387983143 858 dbSNP
rs1167412752 863 dbSNP
rs958249378 867 dbSNP
rs1212361688 870 dbSNP
rs1454381180 872 dbSNP
rs1426685096 873 dbSNP
rs1189920806 877 dbSNP
rs1478008318 882 dbSNP
rs1233766951 884 dbSNP
rs1181475716 886 dbSNP
rs1207795334 888 dbSNP
rs1231986368 894 dbSNP
rs1482176936 896 dbSNP
rs1274269419 897 dbSNP
rs1211668421 899 dbSNP
rs1348487884 900 dbSNP
rs1313963245 904 dbSNP
rs1276548818 905 dbSNP
rs1299287779 906 dbSNP
rs1217365647 909 dbSNP
rs1366847637 911 dbSNP
rs1157702531 912 dbSNP
rs1032322796 916 dbSNP
rs528609608 920 dbSNP
rs145991830 921 dbSNP
rs960456063 925 dbSNP
rs1014545810 926 dbSNP
rs1015728047 926 dbSNP
rs1003980797 927 dbSNP
rs1271254386 927 dbSNP
rs1434956109 928 dbSNP
rs888090739 929 dbSNP
rs200308341 933 dbSNP
rs202072231 934 dbSNP
rs749029384 935 dbSNP
rs1419941449 937 dbSNP
rs1473051069 937 dbSNP
rs34311813 937 dbSNP
rs77547662 937 dbSNP
rs1240499606 941 dbSNP
rs978100088 941 dbSNP
rs1173745054 947 dbSNP
rs1491547723 948 dbSNP
rs531145557 948 dbSNP
rs1491401985 949 dbSNP
rs1184774994 954 dbSNP
rs1471846769 955 dbSNP
rs1245382504 961 dbSNP
rs764970570 963 dbSNP
rs759058440 966 dbSNP
rs1484377503 967 dbSNP
rs1254276539 973 dbSNP
rs1209558324 976 dbSNP
rs1356682133 980 dbSNP
rs1227311435 982 dbSNP
rs576389557 988 dbSNP
rs1341901652 989 dbSNP
rs1216017710 990 dbSNP
rs1465474373 997 dbSNP
rs747352583 1001 dbSNP
rs1485119374 1002 dbSNP
rs1208133941 1007 dbSNP
rs1230167054 1009 dbSNP
rs192011351 1011 dbSNP
rs375339151 1012 dbSNP
rs1192380084 1014 dbSNP
rs914085333 1020 dbSNP
rs746511841 1021 dbSNP
rs1300531756 1024 dbSNP
rs1476278316 1025 dbSNP
rs1465163695 1026 dbSNP
rs1030459076 1031 dbSNP
rs1433038482 1033 dbSNP
rs1161927013 1035 dbSNP
rs1314894374 1037 dbSNP
rs1456115116 1039 dbSNP
rs773340621 1045 dbSNP
rs997370301 1046 dbSNP
rs771881117 1050 dbSNP
rs748016457 1055 dbSNP
rs988606947 1056 dbSNP
rs368795776 1059 dbSNP
rs1181341211 1060 dbSNP
rs1486201268 1063 dbSNP
rs778532761 1066 dbSNP
rs1036187478 1068 dbSNP
rs1231589050 1069 dbSNP
rs1327020844 1070 dbSNP
rs1006130523 1071 dbSNP
rs1245301722 1072 dbSNP
rs1323145032 1075 dbSNP
rs1345094782 1077 dbSNP
rs768947024 1081 dbSNP
rs925272825 1084 dbSNP
rs1395108356 1086 dbSNP
rs79213620 1088 dbSNP
rs1188997921 1089 dbSNP
rs397977560 1089 dbSNP
rs36075045 1090 dbSNP
rs1048387945 1091 dbSNP
rs1322011249 1092 dbSNP
rs1433468367 1097 dbSNP
rs780114284 1099 dbSNP
rs1166097878 1103 dbSNP
rs980771620 1105 dbSNP
rs1453156954 1113 dbSNP
rs1156857538 1117 dbSNP
rs1170807322 1120 dbSNP
rs1458211917 1124 dbSNP
rs778006123 1125 dbSNP
rs1367099977 1126 dbSNP
rs969943291 1131 dbSNP
rs948689379 1132 dbSNP
rs916011268 1133 dbSNP
rs1438333427 1137 dbSNP
rs1022800895 1138 dbSNP
rs756256153 1150 dbSNP
rs1450481121 1154 dbSNP
rs1463461251 1155 dbSNP
rs992768732 1158 dbSNP
rs1057457111 1162 dbSNP
rs187492587 1165 dbSNP
rs1263464089 1172 dbSNP
rs1243565120 1174 dbSNP
rs1209241227 1175 dbSNP
rs1272386776 1177 dbSNP
rs780419644 1180 dbSNP
rs1342462323 1181 dbSNP
rs1299151852 1182 dbSNP
rs1225599198 1184 dbSNP
rs1195199156 1188 dbSNP
rs1268319331 1190 dbSNP
rs1365084355 1200 dbSNP
rs1324717994 1218 dbSNP
rs960115887 1223 dbSNP
rs1389038793 1226 dbSNP
rs1015446625 1231 dbSNP
rs1365578657 1241 dbSNP
rs1388972903 1242 dbSNP
rs938762897 1243 dbSNP
rs1430615907 1246 dbSNP
rs1372681397 1253 dbSNP
rs952470267 1256 dbSNP
rs1391030122 1260 dbSNP
rs1390438832 1263 dbSNP
rs1449004953 1268 dbSNP
rs1441725842 1269 dbSNP
rs1278120360 1274 dbSNP
rs1230259443 1275 dbSNP
rs924801765 1288 dbSNP
rs1342695699 1291 dbSNP
rs1395786459 1292 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 3206.0
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 GSM714647. RNA binding protein: AGO2. Condition:mildMNase ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
CLIP-seq Support 1 for dataset GSM714647
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repB
Location of target site ENST00000283921.4 | 3UTR | AAUAAAUUAAUAUUGUAUUGCUGCUGUGCGUGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
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
GSE28260 Renal cortex and medulla 0.758 1.3e-3 0.692 4.4e-3 13 Click to see details
GSE32688 Pancreatic cancer 0.473 3.1e-3 0.436 6.3e-3 32 Click to see details
GSE15076 Monocyte-derived dendritic cells 0.731 1.3e-2 0.617 3.8e-2 9 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.365 3.6e-2 -0.350 4.3e-2 25 Click to see details
GSE38226 Liver fibrosis 0.344 6.3e-2 0.321 7.8e-2 21 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.333 7.6e-2 0.403 3.9e-2 20 Click to see details
GSE17498 Multiple myeloma -0.218 8.8e-2 -0.038 4.1e-1 40 Click to see details
GSE28544 Breast cancer -0.233 1.4e-1 -0.449 1.4e-2 24 Click to see details
GSE21687 Ependynoma primary tumors 0.109 2.0e-1 0.081 2.6e-1 64 Click to see details
GSE19536 Breast cancer -0.072 2.4e-1 -0.135 9.0e-2 100 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.147 2.4e-1 0.066 3.8e-1 25 Click to see details
GSE19783 ER- ER- breast cancer -0.072 2.6e-1 -0.165 7.3e-2 79 Click to see details
GSE26953 Aortic valvular endothelial cells 0.121 2.9e-1 0.045 4.2e-1 24 Click to see details
GSE42095 Differentiated embryonic stem cells -0.073 3.7e-1 -0.018 4.7e-1 23 Click to see details
GSE19350 CNS germ cell tumors 0.053 4.4e-1 -0.161 3.1e-1 12 Click to see details
GSE21032 Prostate cancer 0.006 4.8e-1 -0.036 3.7e-1 83 Click to see details
GSE19783 ER+ ER+ breast cancer 0.011 4.8e-1 0.156 2.6e-1 20 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
STAD 0.399 0.01 0.428 0.01 31 Click to see details
LIHC -0.221 0.06 -0.204 0.08 49 Click to see details
UCEC -0.337 0.08 -0.256 0.15 19 Click to see details
KICH 0.249 0.12 0.131 0.27 25 Click to see details
BLCA -0.245 0.16 -0.259 0.15 18 Click to see details
CHOL -0.305 0.21 -0.533 0.07 9 Click to see details
LUSC 0.129 0.22 0.142 0.2 38 Click to see details
PCPG -0.77 0.22 -0.500 0.33 3 Click to see details
PAAD 0.365 0.32 0.800 0.1 4 Click to see details
HNSC 0.062 0.35 0.085 0.3 42 Click to see details
ESCA -0.119 0.36 -0.145 0.34 11 Click to see details
PRAD -0.05 0.37 -0.039 0.4 48 Click to see details
CESC -0.319 0.4 -0.500 0.33 3 Click to see details
KIRP -0.047 0.4 -0.063 0.37 32 Click to see details
LUAD 0.065 0.42 0.063 0.42 12 Click to see details
BRCA -0.022 0.42 -0.088 0.21 83 Click to see details
KIRC 0.02 0.44 0.029 0.41 68 Click to see details
KIRC 0.02 0.44 0.029 0.41 68 Click to see details
THCA 0 0.5 0.141 0.14 59 Click to see details
THCA 0 0.5 0.141 0.14 59 Click to see details
75 hsa-miR-16-2-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT004488 RARB retinoic acid receptor beta 3 1
MIRT038707 NUCKS1 nuclear casein kinase and cyclin dependent kinase substrate 1 1 1
MIRT057208 PPIF peptidylprolyl isomerase F 2 4
MIRT058726 RSBN1 round spermatid basic protein 1 2 8
MIRT074502 NFATC2IP nuclear factor of activated T-cells 2 interacting protein 2 4
MIRT081544 ZNF431 zinc finger protein 431 2 4
MIRT096893 ERBB2IP erbb2 interacting protein 2 2
MIRT105124 MYC MYC proto-oncogene, bHLH transcription factor 2 2
MIRT107898 PTAR1 protein prenyltransferase alpha subunit repeat containing 1 2 4
MIRT109432 KLHL15 kelch like family member 15 2 6
MIRT166742 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 6
MIRT171257 YWHAG tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma 2 2
MIRT192760 B2M beta-2-microglobulin 2 2
MIRT194905 RBBP6 RB binding protein 6, ubiquitin ligase 2 8
MIRT215599 SUB1 SUB1 homolog, transcriptional regulator 2 2
MIRT223632 ATP6V1C1 ATPase H+ transporting V1 subunit C1 2 4
MIRT241605 AMOTL1 angiomotin like 1 2 4
MIRT291174 SH3GLB1 SH3 domain containing GRB2 like, endophilin B1 2 2
MIRT444286 ABCG2 ATP binding cassette subfamily G member 2 (Junior blood group) 2 2
MIRT463285 ZFX zinc finger protein, X-linked 2 4
MIRT471759 NUS1 NUS1 dehydrodolichyl diphosphate synthase subunit 2 8
MIRT479611 CDC25A cell division cycle 25A 2 2
MIRT481497 ARL6IP1 ADP ribosylation factor like GTPase 6 interacting protein 1 2 8
MIRT483117 SH3BP5 SH3 domain binding protein 5 2 2
MIRT502279 GRPEL2 GrpE like 2, mitochondrial 2 8
MIRT507838 CCNT1 cyclin T1 2 2
MIRT508179 MTRNR2L6 MT-RNR2-like 6 2 4
MIRT510576 UBE2D3 ubiquitin conjugating enzyme E2 D3 2 6
MIRT517853 RPS4X ribosomal protein S4, X-linked 2 4
MIRT521690 PRKAA1 protein kinase AMP-activated catalytic subunit alpha 1 2 8
MIRT525070 FRK fyn related Src family tyrosine kinase 2 2
MIRT527082 UBE2E3 ubiquitin conjugating enzyme E2 E3 2 2
MIRT529552 EI24 EI24, autophagy associated transmembrane protein 2 2
MIRT530426 SULT1B1 sulfotransferase family 1B member 1 2 2
MIRT533909 TBC1D15 TBC1 domain family member 15 2 2
MIRT536627 IPO7 importin 7 2 2
MIRT537647 ERGIC2 ERGIC and golgi 2 2 4
MIRT538512 CLCN3 chloride voltage-gated channel 3 2 2
MIRT539219 ANP32E acidic nuclear phosphoprotein 32 family member E 2 6
MIRT539348 AGO2 argonaute 2, RISC catalytic component 2 4
MIRT539954 CCT4 chaperonin containing TCP1 subunit 4 2 2
MIRT541208 HOXA10 homeobox A10 2 2
MIRT543216 TMEM117 transmembrane protein 117 2 2
MIRT543399 DROSHA drosha ribonuclease III 2 2
MIRT546648 RPS6KA5 ribosomal protein S6 kinase A5 2 2
MIRT546852 RAB1A RAB1A, member RAS oncogene family 2 2
MIRT549917 MRPS30 mitochondrial ribosomal protein S30 2 2
MIRT552998 USP46 ubiquitin specific peptidase 46 2 2
MIRT555254 PREPL prolyl endopeptidase-like 2 2
MIRT555956 NRIP1 nuclear receptor interacting protein 1 2 2
MIRT557095 HOXA9 homeobox A9 2 2
MIRT561396 TUBB2A tubulin beta 2A class IIa 2 2
MIRT561654 RNF219 ring finger protein 219 2 2
MIRT563101 PABPC4L poly(A) binding protein cytoplasmic 4 like 2 2
MIRT565979 RNF44 ring finger protein 44 2 2
MIRT572396 CCDC14 coiled-coil domain containing 14 2 2
MIRT574400 TM9SF3 transmembrane 9 superfamily member 3 2 2
MIRT607623 VSNL1 visinin like 1 2 2
MIRT610645 CTGF connective tissue growth factor 2 2
MIRT623379 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT624687 AR androgen receptor 2 2
MIRT632089 ALDH1A2 aldehyde dehydrogenase 1 family member A2 2 2
MIRT644216 CBS cystathionine-beta-synthase 2 2
MIRT647841 BID BH3 interacting domain death agonist 2 2
MIRT651649 WASF2 WAS protein family member 2 2 2
MIRT689064 AGMAT agmatinase 2 2
MIRT698150 TNPO1 transportin 1 2 2
MIRT700516 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT704081 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT705970 ACBD5 acyl-CoA binding domain containing 5 2 2
MIRT715694 COMMD3-BMI1 COMMD3-BMI1 readthrough 2 2
MIRT717184 BMI1 BMI1 proto-oncogene, polycomb ring finger 2 2
MIRT724607 AP3B1 adaptor related protein complex 3 beta 1 subunit 2 2
MIRT724854 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT725401 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-16-2 Diethylstilbestrol approved 448537 Microarray mammosphere-derived epithelial cells (MDEC) 19549897 2009 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-16-2-3p Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer cell line (HCT-116)
hsa-miR-16-2-3p Mitoxantrone 4212 NSC279836 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved sensitive Low Osteosarcoma cell line (HOS)
hsa-miR-16-2-3p Doxorubicin 31703 NSC123127 approved sensitive Low Osteosarcoma cell line (HOS)
hsa-miR-16-2-3p Paclitaxel 36314 NSC125973 approved sensitive High Non-Small Cell Lung Cancer cell line (H460)
hsa-miR-16-2-3p Bortezomib 387447 NSC681239 approved resistant Low Multiple Myeloma tissue
hsa-miR-16-2-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (CAL-27) (cytosolic RNA)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (CAL-27) (total RNA)
hsa-miR-16-2-3p Vemurafenib 42611257 NSC761431 approved sensitive cell line (451Lu)
hsa-miR-16-2-3p Doxorubicin 31703 NSC123127 approved sensitive cell line (BAS)
hsa-miR-16-2-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-16-2-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (HCT8)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (IGROV-1)
hsa-miR-16-2-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (MDA-231)
hsa-miR-16-2-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-16-2-3p Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)

Error report submission