pre-miRNA Information
pre-miRNA hsa-mir-4436b-1   
Genomic Coordinates chr2: 110086433 - 110086523
Description Homo sapiens miR-4436b-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-4436b-2   
Genomic Coordinates chr2: 110284853 - 110284943
Description Homo sapiens miR-4436b-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4436b-3p
Sequence 60| CAGGGCAGGAAGAAGUGGACAA |81
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs760150076 9 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol ZMAT4   
Synonyms -
Description zinc finger matrin-type 4
Transcript NM_001135731   
Other Transcripts NM_024645   
Expression
Putative miRNA Targets on ZMAT4
3'UTR of ZMAT4
(miRNA target sites are highlighted)
>ZMAT4|NM_001135731|3'UTR
   1 TGAAAGCATCAATCAAGACATAAGAACAAAACATTAGCATTTCTCTGCCGTGGAGAATTGCTTATCAACCACCAGAGGAG
  81 GCTTCTTTCTTGAACAATAAACATTTCTTATAAGGATTCACAGATTCACATACGACTGATCTTGATTTTTGGAAATGAAT
 161 GAGGTTTCTTTTTTCTTTTTCCTTTTTTTAATTTTGGGGTAAGTTATGATATTTGGATGGATTTTTAAATTCTTTCCTGA
 241 TAACATATTTAGCACATGTTCTAAATTATAATCCTATAGCAAACAGTTGGAGCATTATTCAAACTGAAAGTGGAAAAATT
 321 TAAATTTCCAATTTATTCTAGATTTCCTCAGAGCATAATTATTCTGTTAAATCCTCAATGAGTGTGATGTAAACCACCTC
 401 TATCCAGAAATATACATTCTTTTCTCATCATGTTGGACACAGTTGAGGGTGACATGCACAGAACTGGAACAGATCACTAT
 481 TAGTGGAAAATACCAAATGGACAAATAAATACCAGTCGTTTTCTCCGTTCTCCAAGCACAGGAGCCAGGTTTACCATCTG
 561 AACAATGAAGACGAAGGGAGTAAATAAAGGAAGAATTCTCATCTTTTTTCCTGATCATTCAAAGAACAGTTTCTCAAGGT
 641 TAAGCCAAGTCCTCCTTGCAAGTTGCCAAATAATAGCTTAGGAAAAGAATTAGTCTGCCTGCATGATGATCTTCTTAGGC
 721 AAAAACGTCTTCACAGCCCTTGACCTTGGTGAATTTTTTTCCCCAAAAGCATCCAAAAGAAGAATTATAAACCCCAGAAT
 801 GAGATGGAAATAAACAAGTATTTTTTTTTATGATGTTTGGCCTGAACTGTGGGCTTTAATTGGGGGATACTGATCGTTTG
 881 GAAAGAAGTGAGAAAATTCTGAAGAAATGGCGGCCTTGGGCTAGGCGGGGTCCCCTATTTCTTCTGTTTCTCACTGAAGT
 961 CCTACTGCTGAGCCAAGACTCAGTCACTCTGGAAAGAGCATGACCGATAAAGAAAACAGTTCCTTTCTGATGGGGAGCGT
1041 CTGAGTGCAGATCATGAGGCTCTTTCTCTAGGTTTAATTCTTTTCCATGGTGACCGGACTTGGTGTCTTGTAGCCTGGTT
1121 ACGAAGTGGGACGTTGAGCTTCTACTGACGATGCCCTGCATGGACCAGCTGGGATCTGGCTGGGGCTGCCCTGTGTCCCT
1201 AACGACCATAGGCAATCCATCTTCTTGTGTCAGCAATTTCTGGACACCCACTGTTTTCCACCAAGAGCTGAGGTGGCAAC
1281 AACTCAGTGAGCAATAAACAAAATGACACAGAAATGCACAGTGTTGTTATGAAGGAGCCTGTTTACCTGTGTTCAAAATC
1361 TGGCACCATTCCCTTGAGCAGGGCCCGCTCAGGAGGGACCAGGTCTGCCAGTTTCTGTGCCTGCAGAGAGACGAAGCCCC
1441 ACGAGCCACACCCTACTCTACAAGAGGAAAGGGGGTTGGATGGGAAGAATCTATTTTGCTGTTTTGGAAAGCACACAGCC
1521 GACCTACAAACCTCCTGTGATGGTGTTTCTTCGGATGTGTAAAATAAGGCTTTATTTGTCAATTCCGCTGTAAAATAAGC
1601 ATTGTCCGAGTAAAAACAGCAGCAACAACAAAAAAAAAAAAAAAAA
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' aacaggugaagaagGACGGGAc 5'
                        ||||||| 
Target 5' ggatctggctggggCTGCCCTg 3'
1172 - 1193 140.00 -16.10
2
miRNA  3' aacaggUGAAGAAG-GACGGGAc 5'
                || ||||| | ||||| 
Target 5' gcaaaaACGTCTTCACAGCCCTt 3'
719 - 741 132.00 -13.00
3
miRNA  3' aacagGUGAAGAAGGACGGGAc 5'
               ||:||||  ||||| | 
Target 5' attagCATTTCT--CTGCCGTg 3'
33 - 52 129.00 -17.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30474690 2 COSMIC
COSN29468701 10 COSMIC
COSN30158844 10 COSMIC
COSN30479255 14 COSMIC
COSN30526776 33 COSMIC
COSN31580417 43 COSMIC
COSN14343256 49 COSMIC
COSN31510611 50 COSMIC
COSN8518938 69 COSMIC
COSN30488600 85 COSMIC
COSN31542229 85 COSMIC
COSN31574353 107 COSMIC
COSN30187924 122 COSMIC
COSN17178150 133 COSMIC
COSN31506651 136 COSMIC
COSN31532911 136 COSMIC
COSN31533543 145 COSMIC
COSN31583575 168 COSMIC
COSN31601812 172 COSMIC
COSN30158255 175 COSMIC
COSN30158256 181 COSMIC
COSN31600252 182 COSMIC
COSN30167547 236 COSMIC
COSN6695528 246 COSMIC
COSN5681586 313 COSMIC
COSN5235499 496 COSMIC
COSN31610053 529 COSMIC
COSN31517922 598 COSMIC
COSN31519605 633 COSMIC
COSN23697453 671 COSMIC
COSN8518937 699 COSMIC
COSN17288501 743 COSMIC
COSN31520171 760 COSMIC
COSN31590007 793 COSMIC
COSN20105409 820 COSMIC
COSN25634260 911 COSMIC
COSN31535640 1150 COSMIC
COSN25122565 1189 COSMIC
COSN31489798 1191 COSMIC
COSN26601391 1218 COSMIC
COSN31515926 1240 COSMIC
COSN8518936 1249 COSMIC
COSN31516232 1415 COSMIC
COSN28767943 1424 COSMIC
COSN31487820 1442 COSMIC
COSN28686224 1456 COSMIC
COSN28707656 1498 COSMIC
COSN28794600 1498 COSMIC
COSN5681585 1502 COSMIC
COSN30543074 1507 COSMIC
COSN31482362 1619 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs768913532 5 dbSNP
rs1398488394 6 dbSNP
rs1331169399 7 dbSNP
rs376838736 8 dbSNP
rs747190369 12 dbSNP
rs780255632 14 dbSNP
rs372262834 17 dbSNP
rs1161514878 19 dbSNP
rs1038649299 20 dbSNP
rs368817026 24 dbSNP
rs779172783 27 dbSNP
rs1456655012 31 dbSNP
rs376360770 32 dbSNP
rs1051615126 33 dbSNP
rs1197820486 37 dbSNP
rs372127993 49 dbSNP
rs367883917 50 dbSNP
rs1359491988 51 dbSNP
rs1331019206 58 dbSNP
rs538784959 60 dbSNP
rs1289114080 64 dbSNP
rs1041300927 68 dbSNP
rs1200406021 69 dbSNP
rs1204252245 71 dbSNP
rs1248911665 77 dbSNP
rs1472063516 79 dbSNP
rs1007125983 80 dbSNP
rs1342603487 82 dbSNP
rs1413679057 92 dbSNP
rs890055793 93 dbSNP
rs1043214347 107 dbSNP
rs1390673438 114 dbSNP
rs947541310 116 dbSNP
rs573564905 125 dbSNP
rs1368862286 131 dbSNP
rs559741020 133 dbSNP
rs938661159 134 dbSNP
rs1242386292 141 dbSNP
rs1283337325 143 dbSNP
rs1356987693 143 dbSNP
rs549758314 151 dbSNP
rs1284232574 158 dbSNP
rs536540642 165 dbSNP
rs1449537753 174 dbSNP
rs988049001 181 dbSNP
rs1333667192 184 dbSNP
rs1253559646 188 dbSNP
rs1440288536 189 dbSNP
rs1185881738 190 dbSNP
rs1368188890 191 dbSNP
rs1166079621 196 dbSNP
rs928627964 196 dbSNP
rs1388831603 197 dbSNP
rs1430869405 198 dbSNP
rs1308674934 201 dbSNP
rs567456193 206 dbSNP
rs1394453762 208 dbSNP
rs1034730092 209 dbSNP
rs1333272138 222 dbSNP
rs764534145 232 dbSNP
rs1247885450 245 dbSNP
rs1295365086 246 dbSNP
rs1341318865 253 dbSNP
rs980083487 257 dbSNP
rs761287833 264 dbSNP
rs1165123929 265 dbSNP
rs1199587663 277 dbSNP
rs114751099 280 dbSNP
rs1023817904 281 dbSNP
rs1185780149 286 dbSNP
rs774013803 293 dbSNP
rs1232591503 295 dbSNP
rs1272397276 300 dbSNP
rs1013064398 312 dbSNP
rs1449344374 328 dbSNP
rs527302080 329 dbSNP
rs898686043 331 dbSNP
rs80291665 338 dbSNP
rs1025802617 339 dbSNP
rs1172276507 341 dbSNP
rs1403157737 347 dbSNP
rs1454402938 349 dbSNP
rs1318236776 353 dbSNP
rs1364385144 364 dbSNP
rs1483267219 371 dbSNP
rs745935497 378 dbSNP
rs887361659 397 dbSNP
rs1321089722 401 dbSNP
rs1051072767 402 dbSNP
rs145974613 403 dbSNP
rs965522069 405 dbSNP
rs111322524 412 dbSNP
rs1019263222 413 dbSNP
rs1229588903 417 dbSNP
rs531462075 418 dbSNP
rs1187688614 421 dbSNP
rs1347913152 422 dbSNP
rs1431563422 428 dbSNP
rs1198215614 430 dbSNP
rs1378445822 437 dbSNP
rs1471043118 438 dbSNP
rs921336867 445 dbSNP
rs1156685369 447 dbSNP
rs1039786920 451 dbSNP
rs563902269 453 dbSNP
rs1290609131 455 dbSNP
rs915110947 461 dbSNP
rs1385765128 464 dbSNP
rs988014889 470 dbSNP
rs956609989 481 dbSNP
rs1226120472 490 dbSNP
rs1352753431 499 dbSNP
rs927878621 502 dbSNP
rs762671733 504 dbSNP
rs1328981037 509 dbSNP
rs1216930887 510 dbSNP
rs981771041 517 dbSNP
rs140243018 523 dbSNP
rs768833601 523 dbSNP
rs1326104826 524 dbSNP
rs749489489 525 dbSNP
rs777582613 526 dbSNP
rs1180364530 536 dbSNP
rs1411479487 540 dbSNP
rs1044333745 541 dbSNP
rs1160967577 546 dbSNP
rs1411256860 547 dbSNP
rs1348075469 552 dbSNP
rs1023368780 554 dbSNP
rs1160209208 555 dbSNP
rs973177385 557 dbSNP
rs1366971905 558 dbSNP
rs948760867 563 dbSNP
rs1473672221 564 dbSNP
rs962862353 572 dbSNP
rs1017076052 573 dbSNP
rs1197069057 578 dbSNP
rs1224721240 587 dbSNP
rs1309528741 593 dbSNP
rs1488025166 597 dbSNP
rs1320444156 603 dbSNP
rs1004797846 611 dbSNP
rs1330210916 616 dbSNP
rs1247283806 622 dbSNP
rs1223585909 624 dbSNP
rs887340739 641 dbSNP
rs1444805798 645 dbSNP
rs1251399489 649 dbSNP
rs1481055280 657 dbSNP
rs1178743094 659 dbSNP
rs916489622 666 dbSNP
rs1266897854 668 dbSNP
rs1423026055 669 dbSNP
rs1164203463 683 dbSNP
rs984031502 687 dbSNP
rs4737147 693 dbSNP
rs530373787 696 dbSNP
rs561446086 698 dbSNP
rs1306834210 702 dbSNP
rs1330839547 703 dbSNP
rs1280960113 708 dbSNP
rs998179605 710 dbSNP
rs1368668592 715 dbSNP
rs374911648 720 dbSNP
rs899860588 725 dbSNP
rs1039755908 727 dbSNP
rs1362168150 737 dbSNP
rs540993512 744 dbSNP
rs965124262 745 dbSNP
rs748176093 753 dbSNP
rs1429176774 755 dbSNP
rs1235933035 761 dbSNP
rs769470206 761 dbSNP
rs747630945 764 dbSNP
rs1447532875 765 dbSNP
rs572093859 768 dbSNP
rs1052184828 769 dbSNP
rs1458868642 772 dbSNP
rs1411138543 789 dbSNP
rs143963462 792 dbSNP
rs1404254811 795 dbSNP
rs1021874264 797 dbSNP
rs935173357 800 dbSNP
rs1385639822 805 dbSNP
rs371404575 809 dbSNP
rs1011804830 812 dbSNP
rs576502997 814 dbSNP
rs1362820790 820 dbSNP
rs1216385416 821 dbSNP
rs1432388364 822 dbSNP
rs556286165 824 dbSNP
rs892054003 828 dbSNP
rs927879506 829 dbSNP
rs1003454768 830 dbSNP
rs1242604601 830 dbSNP
rs140366061 830 dbSNP
rs34653580 830 dbSNP
rs1474411134 832 dbSNP
rs1247322149 833 dbSNP
rs982458583 834 dbSNP
rs1465858672 835 dbSNP
rs1188908846 838 dbSNP
rs535663638 840 dbSNP
rs1044492903 841 dbSNP
rs568298463 842 dbSNP
rs916281933 843 dbSNP
rs887803080 860 dbSNP
rs754878675 863 dbSNP
rs1260872414 865 dbSNP
rs751146197 869 dbSNP
rs139042920 872 dbSNP
rs918508168 873 dbSNP
rs1014697088 876 dbSNP
rs1433023704 879 dbSNP
rs1213146051 881 dbSNP
rs1306741369 890 dbSNP
rs776172607 893 dbSNP
rs1298969023 906 dbSNP
rs1285412639 908 dbSNP
rs758177464 911 dbSNP
rs1029901990 912 dbSNP
rs943909213 913 dbSNP
rs556373327 920 dbSNP
rs912308551 921 dbSNP
rs1480477257 922 dbSNP
rs1201207993 924 dbSNP
rs368856007 927 dbSNP
rs999784343 931 dbSNP
rs1409283997 932 dbSNP
rs998878960 933 dbSNP
rs899843347 934 dbSNP
rs1466711678 936 dbSNP
rs1471840123 937 dbSNP
rs1018190468 945 dbSNP
rs1158316433 954 dbSNP
rs1178031757 958 dbSNP
rs1322138123 962 dbSNP
rs1010868977 964 dbSNP
rs1405603629 974 dbSNP
rs1305226795 978 dbSNP
rs893863011 983 dbSNP
rs750072325 990 dbSNP
rs1279857882 993 dbSNP
rs914209627 994 dbSNP
rs1189062151 997 dbSNP
rs1289046985 1001 dbSNP
rs567522155 1005 dbSNP
rs764589807 1006 dbSNP
rs1224031558 1009 dbSNP
rs1249210365 1010 dbSNP
rs1253404843 1023 dbSNP
rs867835255 1032 dbSNP
rs956275549 1033 dbSNP
rs13277268 1034 dbSNP
rs1364678189 1035 dbSNP
rs1162026030 1038 dbSNP
rs1385120183 1039 dbSNP
rs753035859 1043 dbSNP
rs1425413758 1046 dbSNP
rs1165495176 1047 dbSNP
rs1483395486 1049 dbSNP
rs1003042241 1058 dbSNP
rs1337371550 1059 dbSNP
rs1445514480 1062 dbSNP
rs1257371355 1063 dbSNP
rs1314346588 1066 dbSNP
rs1202935744 1072 dbSNP
rs1360019153 1073 dbSNP
rs1046302593 1077 dbSNP
rs534115911 1080 dbSNP
rs948002868 1086 dbSNP
rs1169796254 1089 dbSNP
rs571239765 1091 dbSNP
rs1380700301 1094 dbSNP
rs375465860 1095 dbSNP
rs1012926424 1097 dbSNP
rs1396659104 1111 dbSNP
rs1381697215 1112 dbSNP
rs887880303 1114 dbSNP
rs1049016744 1116 dbSNP
rs1185504392 1117 dbSNP
rs916510217 1118 dbSNP
rs1037344587 1122 dbSNP
rs1461533849 1123 dbSNP
rs1168762878 1127 dbSNP
rs1398872246 1132 dbSNP
rs1296664438 1133 dbSNP
rs1335786154 1134 dbSNP
rs1407771598 1138 dbSNP
rs779609818 1142 dbSNP
rs1369657140 1144 dbSNP
rs941697307 1146 dbSNP
rs1431505487 1149 dbSNP
rs907609828 1150 dbSNP
rs551443016 1153 dbSNP
rs531425044 1154 dbSNP
rs922802056 1156 dbSNP
rs1202183091 1161 dbSNP
rs1262836511 1162 dbSNP
rs912426067 1165 dbSNP
rs568863540 1166 dbSNP
rs1186029818 1168 dbSNP
rs1246704886 1176 dbSNP
rs1428039054 1179 dbSNP
rs768517907 1180 dbSNP
rs767936103 1189 dbSNP
rs1257915397 1191 dbSNP
rs1477131541 1192 dbSNP
rs1175454064 1193 dbSNP
rs1406636130 1194 dbSNP
rs760035113 1196 dbSNP
rs1318500148 1201 dbSNP
rs1382316938 1204 dbSNP
rs976950564 1209 dbSNP
rs1482939858 1210 dbSNP
rs1222595346 1212 dbSNP
rs914315639 1222 dbSNP
rs774461674 1224 dbSNP
rs1205936099 1227 dbSNP
rs754215792 1227 dbSNP
rs1259519043 1240 dbSNP
rs747479267 1241 dbSNP
rs955939012 1253 dbSNP
rs189899056 1254 dbSNP
rs1489880231 1259 dbSNP
rs1199048169 1263 dbSNP
rs982129822 1267 dbSNP
rs1354927686 1269 dbSNP
rs775783000 1270 dbSNP
rs1481311259 1271 dbSNP
rs1023065958 1272 dbSNP
rs1363168148 1274 dbSNP
rs1454187671 1278 dbSNP
rs1290553222 1281 dbSNP
rs991620124 1283 dbSNP
rs958055101 1289 dbSNP
rs1303423815 1299 dbSNP
rs1346963803 1301 dbSNP
rs1225761177 1304 dbSNP
rs1323508784 1304 dbSNP
rs1305152228 1308 dbSNP
rs150731781 1309 dbSNP
rs184577511 1314 dbSNP
rs1263008709 1318 dbSNP
rs537122545 1321 dbSNP
rs906362062 1322 dbSNP
rs1269894630 1326 dbSNP
rs541306744 1327 dbSNP
rs1490884385 1328 dbSNP
rs1308450072 1334 dbSNP
rs1249636771 1335 dbSNP
rs749812580 1338 dbSNP
rs538191412 1339 dbSNP
rs952095927 1361 dbSNP
rs1028186904 1377 dbSNP
rs993508861 1379 dbSNP
rs372174933 1386 dbSNP
rs1163616906 1393 dbSNP
rs1367068334 1400 dbSNP
rs1012101266 1402 dbSNP
rs368488699 1403 dbSNP
rs1388563111 1408 dbSNP
rs1037647822 1409 dbSNP
rs528026161 1415 dbSNP
rs1392314254 1417 dbSNP
rs941666177 1419 dbSNP
rs1309819486 1422 dbSNP
rs753133 1424 dbSNP
rs1245352861 1425 dbSNP
rs1047471873 1432 dbSNP
rs1361673126 1434 dbSNP
rs1202763920 1436 dbSNP
rs1250947364 1440 dbSNP
rs998181306 1442 dbSNP
rs1049557893 1443 dbSNP
rs192717823 1446 dbSNP
rs1472036307 1451 dbSNP
rs1443870209 1452 dbSNP
rs1412227627 1457 dbSNP
rs1184863888 1461 dbSNP
rs1386630697 1463 dbSNP
rs1450236581 1465 dbSNP
rs1267278857 1471 dbSNP
rs75983141 1475 dbSNP
rs1462831260 1476 dbSNP
rs1300200431 1477 dbSNP
rs747900605 1479 dbSNP
rs1381229305 1487 dbSNP
rs1489519886 1489 dbSNP
rs1266274174 1498 dbSNP
rs1452631985 1501 dbSNP
rs1227828385 1505 dbSNP
rs1385144201 1508 dbSNP
rs1212849574 1510 dbSNP
rs1272602894 1512 dbSNP
rs534640950 1517 dbSNP
rs781001687 1520 dbSNP
rs1260951067 1526 dbSNP
rs1460703600 1531 dbSNP
rs556401275 1532 dbSNP
rs1244873936 1534 dbSNP
rs1230074276 1539 dbSNP
rs1329066584 1543 dbSNP
rs542770950 1544 dbSNP
rs977295644 1550 dbSNP
rs768504092 1552 dbSNP
rs899873097 1564 dbSNP
rs1392294773 1578 dbSNP
rs1469591719 1587 dbSNP
rs1318014423 1595 dbSNP
rs911455794 1596 dbSNP
rs1456239323 1602 dbSNP
rs981092012 1604 dbSNP
rs1269611532 1606 dbSNP
rs1362929242 1607 dbSNP
rs1216619345 1608 dbSNP
rs1281602420 1609 dbSNP
rs1322613163 1612 dbSNP
rs575059653 1617 dbSNP
rs1264947792 1619 dbSNP
rs565961749 1621 dbSNP
rs1445149038 1623 dbSNP
rs1214460592 1625 dbSNP
rs1242259722 1628 dbSNP
rs1160845372 1631 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 79698.0
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 GSM714646. RNA binding protein: AGO2. Condition:mildMNase "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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084043. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep2 HITS-CLIP data was present in GSM1084044. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep3 HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb HITS-CLIP data was present in GSM1084072. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_AbnovaAb HITS-CLIP data was present in GSM1084073. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_AbnovaAb HITS-CLIP data was present in GSM1084075. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_SantaCruzAb HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084081. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SantaCruzAb HITS-CLIP data was present in GSM1084083. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SigmaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_024645 | 3UTR | UGGGGCUGCCCUGUGUCCCUAACGACCAUAGGCAAUCCAUCUUCUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_024645 | 3UTR | AUGGACCAGCUGGGAUCUGGCUGGGGCUGCCCUGUGUCCCUAACGACCAUAGGCAAUCCAUCUUCUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_024645 | 3UTR | ACUGACGAUGCCCUGCAUGGACCAGCUGGGAUCUGGCUGGGGCUGCCCUGUGUCCCUAACGACCAUAGGCAAUCCAUCUUCUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_001135731 | 3UTR | CCUGCAUGGACCAGCUGGGAUCUGGCUGGGGCUGCCCUGUGUCCCUAACGACCAUAGGCAAUCCAUCUUCUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_024645 | 3UTR | GUUGAGCUUCUACUGACGAUGCCCUGCAUGGACCAGCUGGGAUCUGGCUGGGGCUGCCCUGUGUCCCUAACGACCAUAGGCAAUCCAUCUUCUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1084043
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep2
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1084044
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep3
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM1084068
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_SigmaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM1084072
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_AbnovaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1084073
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep1_AbnovaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset GSM1084075
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep1_SantaCruzAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM1084081
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SantaCruzAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 15 for dataset GSM1084083
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SigmaAb
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 16 for dataset GSM714646
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repA
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 17 for dataset GSM714647
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repB
Location of target site ENST00000315769.7 | 3UTR | UAAAGUGCUGUGUGUG
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
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
87 hsa-miR-4436b-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT066957 ATXN7L3B ataxin 7 like 3B 2 8
MIRT119284 NABP1 nucleic acid binding protein 1 2 6
MIRT128915 KMT2A lysine methyltransferase 2A 2 2
MIRT150116 MIDN midnolin 2 2
MIRT173040 YTHDF3 YTH N6-methyladenosine RNA binding protein 3 2 2
MIRT253117 BCL2L12 BCL2 like 12 2 2
MIRT256997 RGMB repulsive guidance molecule family member b 2 2
MIRT259746 SNX12 sorting nexin 12 2 2
MIRT267278 TMEM109 transmembrane protein 109 2 2
MIRT441934 C1orf109 chromosome 1 open reading frame 109 2 2
MIRT443625 CPSF2 cleavage and polyadenylation specific factor 2 2 2
MIRT445757 AGO1 argonaute 1, RISC catalytic component 2 2
MIRT447835 CTIF cap binding complex dependent translation initiation factor 2 2
MIRT451230 ZNF444 zinc finger protein 444 2 2
MIRT451966 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT453127 HOXC4 homeobox C4 2 2
MIRT454604 RPL13A ribosomal protein L13a 2 2
MIRT455176 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT455547 GJB1 gap junction protein beta 1 2 2
MIRT458197 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT458356 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458923 DNM2 dynamin 2 2 2
MIRT461013 SYT7 synaptotagmin 7 2 2
MIRT461643 ZSWIM4 zinc finger SWIM-type containing 4 2 2
MIRT461997 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 2 2
MIRT462367 BCL7B BCL tumor suppressor 7B 2 2
MIRT464915 TXNIP thioredoxin interacting protein 2 2
MIRT466311 TIMM22 translocase of inner mitochondrial membrane 22 2 2
MIRT466591 TBC1D2B TBC1 domain family member 2B 2 2
MIRT467045 SRSF1 serine and arginine rich splicing factor 1 2 2
MIRT468750 SDC2 syndecan 2 2 2
MIRT468943 RPS24 ribosomal protein S24 2 2
MIRT469474 REEP5 receptor accessory protein 5 2 2
MIRT469913 PTRF caveolae associated protein 1 2 2
MIRT473325 MEX3A mex-3 RNA binding family member A 2 2
MIRT473643 MARK2 microtubule affinity regulating kinase 2 2 2
MIRT474064 LMNB2 lamin B2 2 2
MIRT474357 KMT2D lysine methyltransferase 2D 2 2
MIRT475394 ICMT isoprenylcysteine carboxyl methyltransferase 2 4
MIRT476335 GLTSCR1L BRD4 interacting chromatin remodeling complex associated protein like 2 2
MIRT478651 CTDNEP1 CTD nuclear envelope phosphatase 1 2 2
MIRT479585 CDC42SE1 CDC42 small effector 1 2 2
MIRT479943 CBX5 chromobox 5 2 2
MIRT482001 AMOTL2 angiomotin like 2 2 2
MIRT482043 AMER1 APC membrane recruitment protein 1 2 2
MIRT483070 EXT2 exostosin glycosyltransferase 2 2 6
MIRT484323 KCNH1 potassium voltage-gated channel subfamily H member 1 2 4
MIRT487528 GXYLT2 glucoside xylosyltransferase 2 2 2
MIRT489636 ALS2CL ALS2 C-terminal like 2 2
MIRT490693 SSTR1 somatostatin receptor 1 2 2
MIRT490871 UPK2 uroplakin 2 2 2
MIRT492582 PPM1L protein phosphatase, Mg2+/Mn2+ dependent 1L 2 2
MIRT492945 NEUROD2 neuronal differentiation 2 2 2
MIRT498675 SOD2 superoxide dismutase 2 2 4
MIRT499349 RAB25 RAB25, member RAS oncogene family 2 2
MIRT502338 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT502976 CCNL1 cyclin L1 2 8
MIRT503706 NUP62 nucleoporin 62 2 2
MIRT505567 SMUG1 single-strand-selective monofunctional uracil-DNA glycosylase 1 2 2
MIRT507808 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT513242 FBXO41 F-box protein 41 2 6
MIRT513586 EVX1 even-skipped homeobox 1 2 2
MIRT525036 FRK fyn related Src family tyrosine kinase 2 2
MIRT531035 TDGF1P3 teratocarcinoma-derived growth factor 1 pseudogene 3 2 2
MIRT531939 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT534912 PUM2 pumilio RNA binding family member 2 2 2
MIRT535717 N4BP1 NEDD4 binding protein 1 2 2
MIRT540498 ZMAT4 zinc finger matrin-type 4 2 4
MIRT541465 AURKA aurora kinase A 2 2
MIRT554328 SH3GLB1 SH3 domain containing GRB2 like, endophilin B1 2 2
MIRT561572 SLC6A9 solute carrier family 6 member 9 2 2
MIRT564715 ZNF322P1 zinc finger protein 322 pseudogene 1 2 2
MIRT576176 Hmox1 heme oxygenase 1 2 2
MIRT629712 XKR4 XK related 4 2 2
MIRT636182 THBD thrombomodulin 2 2
MIRT646315 MPHOSPH8 M-phase phosphoprotein 8 2 2
MIRT649174 IQSEC1 IQ motif and Sec7 domain 1 2 2
MIRT666945 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT684057 FOLR1 folate receptor 1 2 2
MIRT687585 MAU2 MAU2 sister chromatid cohesion factor 2 2
MIRT689953 ZNF185 zinc finger protein 185 with LIM domain 2 2
MIRT704071 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT704327 DCUN1D5 defective in cullin neddylation 1 domain containing 5 2 2
MIRT705406 ATP1B3 ATPase Na+/K+ transporting subunit beta 3 2 2
MIRT710488 CDH5 cadherin 5 2 2
MIRT718241 LCE1A late cornified envelope 1A 2 2
MIRT723182 CDCA4 cell division cycle associated 4 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4436b-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4436b-3p Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)

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