miRTarBase - #MIRT305086


—
pre-miRNA Information
pre-miRNA hsa-mir-4662b   
Genomic Coordinates chr8: 124821978 - 124822058
Description Homo sapiens miR-4662b stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4662b
Sequence 50| AAAGAUGGACAAUUGGCUAAAU |71
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1347413245 5 dbSNP
rs577795897 6 dbSNP
rs1051104297 9 dbSNP
rs1020047688 10 dbSNP
rs193002095 13 dbSNP
rs889705107 22 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SRPRB   
Synonyms APMCF1
Description SRP receptor beta subunit
Transcript NM_021203   
Expression
Putative miRNA Targets on SRPRB
3'UTR of SRPRB
(miRNA target sites are highlighted)		 
>SRPRB|NM_021203|3'UTR
   1 GAGGCAGCTCTAAAGCACAAGACCTGGATGTGTGACACACAGTTTTGGAAAAAGGTCTGTGGTAGTCTGGAGTTGATGAG
  81 GAAGGGGTACAAGATGTGGTTAGAAACATTTCTTTGTTCTGGAAACAAAGTACTGTTGAAACCAGCTTGGAATTTTTTTT
 161 TTTTTTTTTTTTAAGTTCAGTTCTCCCTTATGGCTGCCTTTCAAACAAGTACCTTTTATCTGATGCCTGTATCTTCCCTT
 241 TGTTAAGGTGTAACTTGATGTAGGGTCAAGGTTTTTGTGACAACAGGCAGACTCCACACAGAGAGGATATGATGAGAATA
 321 TGGCCATCACCTGAAAAGTTTTCTTATCTTCTGTGCTTTTGGTCCCTGGAAACAAATCCGCCTATGTATGAAGCTAGTTG
 401 ATTTCCAGTTGCACTATTTCCAGTTGCCTCTGAAGTTCACAGGCAATACATTGTCTAGTCCTTTGCGAATTTCTCTGATT
 481 TGTGGGCACAGTTATGAAGTTTCCCCACATGTGAAGACAGGTACAAAATAGCAGAGCCAAGCAGACAGTGGGTCTATTCT
 561 TCATTAGCTCAGTGACTTGTCCACACTCGTCTTAGCACTTACGTTTCAAAAGCTTGTCACAAACCCTTGGAGTCATTCCC
 641 AGATAATAGAACTGGAAATGATAAATCCCCTAATGCCAAGGGTCTAGTGTGTTCTTAGTGGTTATACTGGGAAGTGTGTG
 721 GAGATTTAGGTGCTGCTCTGCTGCTCTGGATGGCTGAAGGCTCCTGGGCCATCTTCATGTGCTGCTTGAAGAGCTCCTAT
 801 TTTGTACTCCTGGCTAGAATGCTGTGGAACAAATACAAAGTGAAAAAAGTTCTCTGTAGATTTCTGAAGTGCATATTCAT
 881 TGATGCCAAGAAAAAAAAAAAGTTGCCTTTTTGAAGTGATGTTTTTTGCTGTCTTCTTAAACACAAGGCTTTTTTGAATG
 961 ATTAGTATATTTCATGGTAAAGAAAACAGCCTGTCTGGCTCAAAGCAATTAAATAGAATGTAATGGTGAGTACAAATGAG
1041 TGCACATGTCAGGACTCAGGTCTAACTCCTTGTCTCCTGAGCCTAAAGATTGCAACATACACAAGAACACACTCCTATTC
1121 CTACCCCACACACTCAGGGACAAGCCCAACTAAAGCTTACAAGGAGACCAGGGTGGCTCTGTCCAGGGGAGAAGCCAGTT
1201 ATGGAACAGTGCATTGAGAGCCATGGTAGGAGAGGCCCACAGTTCTCTGGAGCATGCAGCAGGGGCACCCCACCTGGCCT
1281 TGAGGATCAGGGGGAGTCAAAGGATAAAGCATGGGGCTGATGACGTCTGAGGGAGTGTGATCCTCCATGTATGGCCTCTG
1361 CCTGCTGTCTCACATGTCCCTTCTGGTGGTCACTTGGGCTCTAGGAGTATACGTCACCTCAGACCATCTGGCAGAAATAC
1441 TCCAGGCTCCTACCCCAAAGCACATGTCAGCCTTGCTGCTGGAGCACGAAGACAATGTAAATGAAACATGAAATGGAGGA
1521 GTTGTGAGACCCTGACCCTGAGTCCTTACTTGAAAGCTGCTGCTGGTGTTCTGAGTGTCTTTTGGACTCTTATTTCTTGC
1601 CCTTTTCCTTATTAGGCAAGCAGTAACTTAGGAAGTAGGTAAGAGCAATAAATGTGACATGTTATGTCATCATAGTAGGA
1681 GCTCATGGGAATAAAAGTCAGTGGCTTGATGCTTCTGTTAGAGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1761 AAAAAAAAAAAAAAAAAAA
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' uaaaUCGGUUAACAGGUAGAAa 5'
              :||:  | | ||||||| 
Target 5' tgaaGGCTCCTGGGCCATCTTc 3'
 755 - 776 150.00 -10.50
2 
miRNA  3' uaaAU-CGGUUAA--CAGGUAGAaa 5'
             || |:||  |  | ||||||  
Target 5' gtaTACGTCACCTCAGACCATCTgg 3'
 1407 - 1431 129.00 -7.90
3 
miRNA  3' uaAAUCG-GUU----AACA------GGUAGAAa 5'
            ||||| ||:    ||||      :|:|||| 
Target 5' caTTAGCTCAGTGACTTGTCCACACTCGTCTTa 3'
 562 - 594 124.00 -12.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31593371 24 COSMIC
COSN29480070 43 COSMIC
COSN30170434 76 COSMIC
COSN20068951 173 COSMIC
COSN6750717 295 COSMIC
COSN30045396 880 COSMIC
COSN1267913 1188 COSMIC
COSN22544574 1196 COSMIC
COSN31962151 1217 COSMIC
COSN5520775 1300 COSMIC
COSN23281221 1633 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1254345171 1 dbSNP
rs1374210008 4 dbSNP
rs572085941 6 dbSNP
rs1416082570 10 dbSNP
rs1188578564 12 dbSNP
rs1313017504 13 dbSNP
rs1002716248 16 dbSNP
rs1325429193 20 dbSNP
rs1224792825 21 dbSNP
rs758542213 25 dbSNP
rs375046814 26 dbSNP
rs773503347 27 dbSNP
rs767505659 32 dbSNP
rs1278094723 33 dbSNP
rs552889137 35 dbSNP
rs750386326 40 dbSNP
rs756043624 43 dbSNP
rs201523489 49 dbSNP
rs774642123 50 dbSNP
rs1358199461 60 dbSNP
rs1234079429 61 dbSNP
rs893679506 62 dbSNP
rs1278398296 63 dbSNP
rs114364343 64 dbSNP
rs1398643233 78 dbSNP
rs1368018475 86 dbSNP
rs1020763103 94 dbSNP
rs1424420721 96 dbSNP
rs141040173 98 dbSNP
rs1172779067 99 dbSNP
rs1429377177 102 dbSNP
rs370180689 104 dbSNP
rs975138147 111 dbSNP
rs576103900 129 dbSNP
rs1191621108 131 dbSNP
rs1008786771 132 dbSNP
rs1017708079 143 dbSNP
rs964392495 150 dbSNP
rs1491230152 152 dbSNP
rs78640095 152 dbSNP
rs1284471674 153 dbSNP
rs1307739168 153 dbSNP
rs1346923698 153 dbSNP
rs1491487146 153 dbSNP
rs550674096 153 dbSNP
rs75496501 153 dbSNP
rs879025214 153 dbSNP
rs954958539 153 dbSNP
rs78963965 155 dbSNP
rs1436206863 160 dbSNP
rs1179566324 161 dbSNP
rs1388991354 163 dbSNP
rs1300295176 166 dbSNP
rs1462640850 171 dbSNP
rs1168537084 173 dbSNP
rs973589236 173 dbSNP
rs1234568012 174 dbSNP
rs1440026494 175 dbSNP
rs978264714 176 dbSNP
rs1392808920 178 dbSNP
rs1200032039 181 dbSNP
rs1455320211 183 dbSNP
rs1172860960 184 dbSNP
rs1395138544 185 dbSNP
rs1407754698 186 dbSNP
rs924077940 189 dbSNP
rs936927993 191 dbSNP
rs920336708 197 dbSNP
rs952920960 202 dbSNP
rs1331435171 203 dbSNP
rs982915723 204 dbSNP
rs545105920 208 dbSNP
rs1196438713 209 dbSNP
rs565111503 215 dbSNP
rs115480128 221 dbSNP
rs749760354 236 dbSNP
rs949681908 244 dbSNP
rs1309528624 246 dbSNP
rs1392334567 252 dbSNP
rs1373141118 255 dbSNP
rs1329544756 260 dbSNP
rs541178153 273 dbSNP
rs1471106208 276 dbSNP
rs868608375 278 dbSNP
rs561032659 284 dbSNP
rs753896736 287 dbSNP
rs1175826413 288 dbSNP
rs1465433710 289 dbSNP
rs373446162 292 dbSNP
rs1375866077 295 dbSNP
rs1373395776 300 dbSNP
rs1419441473 303 dbSNP
rs938019763 304 dbSNP
rs1176367114 322 dbSNP
rs1269895404 334 dbSNP
rs1337492649 335 dbSNP
rs1263159472 346 dbSNP
rs1199398031 355 dbSNP
rs1343401798 363 dbSNP
rs755217923 369 dbSNP
rs948435230 380 dbSNP
rs1353407542 386 dbSNP
rs893898214 391 dbSNP
rs1259871562 394 dbSNP
rs1383817909 412 dbSNP
rs1333515278 417 dbSNP
rs1394361608 421 dbSNP
rs1044451056 424 dbSNP
rs1160206207 432 dbSNP
rs1458163938 439 dbSNP
rs1212781846 440 dbSNP
rs1379415767 445 dbSNP
rs1250899251 447 dbSNP
rs1156634199 450 dbSNP
rs1446017884 453 dbSNP
rs368796419 454 dbSNP
rs1199094237 455 dbSNP
rs1372197243 456 dbSNP
rs375910279 461 dbSNP
rs1169173006 464 dbSNP
rs191519747 466 dbSNP
rs1461390428 467 dbSNP
rs1047595125 468 dbSNP
rs533271618 474 dbSNP
rs1397131947 487 dbSNP
rs373523189 492 dbSNP
rs563677516 496 dbSNP
rs1360701982 497 dbSNP
rs1324941857 503 dbSNP
rs1009255203 507 dbSNP
rs184776223 509 dbSNP
rs1334341384 512 dbSNP
rs552267768 515 dbSNP
rs1310634542 519 dbSNP
rs772265022 520 dbSNP
rs994458032 522 dbSNP
rs146872693 530 dbSNP
rs1359834013 535 dbSNP
rs950479114 538 dbSNP
rs534892365 539 dbSNP
rs530100021 540 dbSNP
rs1489328627 552 dbSNP
rs983134848 553 dbSNP
rs900400829 557 dbSNP
rs113943912 566 dbSNP
rs370816120 583 dbSNP
rs1374253173 585 dbSNP
rs59518639 587 dbSNP
rs982806690 589 dbSNP
rs374180284 590 dbSNP
rs1225443498 591 dbSNP
rs1490609815 602 dbSNP
rs555916845 603 dbSNP
rs938222934 604 dbSNP
rs747584720 617 dbSNP
rs576093386 618 dbSNP
rs915218966 621 dbSNP
rs945464101 626 dbSNP
rs989587870 627 dbSNP
rs1042479340 628 dbSNP
rs890316358 639 dbSNP
rs944546936 646 dbSNP
rs1039400621 648 dbSNP
rs1403193601 651 dbSNP
rs900416599 653 dbSNP
rs1398192453 657 dbSNP
rs1171032671 659 dbSNP
rs1477203032 662 dbSNP
rs189505187 687 dbSNP
rs547986155 689 dbSNP
rs1246444632 699 dbSNP
rs1219848065 710 dbSNP
rs1439705496 714 dbSNP
rs1384125202 715 dbSNP
rs1273965907 717 dbSNP
rs1198312816 722 dbSNP
rs1316119337 723 dbSNP
rs1299107916 731 dbSNP
rs1265119487 739 dbSNP
rs1225222847 744 dbSNP
rs1368242974 745 dbSNP
rs1273967775 755 dbSNP
rs1434024661 756 dbSNP
rs1337372575 763 dbSNP
rs1027290532 768 dbSNP
rs886082292 770 dbSNP
rs1004612045 772 dbSNP
rs1354869479 780 dbSNP
rs1464817021 782 dbSNP
rs1397454588 785 dbSNP
rs1177999633 788 dbSNP
rs1413065600 796 dbSNP
rs1024044363 800 dbSNP
rs749579719 808 dbSNP
rs1190043110 814 dbSNP
rs982305917 821 dbSNP
rs938428254 824 dbSNP
rs1239224675 825 dbSNP
rs1178227457 828 dbSNP
rs1245158456 829 dbSNP
rs1259939078 833 dbSNP
rs1204401349 835 dbSNP
rs1277810536 842 dbSNP
rs1217453494 853 dbSNP
rs1348347214 854 dbSNP
rs548654250 855 dbSNP
rs558687392 859 dbSNP
rs959665200 863 dbSNP
rs1374212020 870 dbSNP
rs941868077 871 dbSNP
rs775188581 873 dbSNP
rs762513319 874 dbSNP
rs1402995263 877 dbSNP
rs989709372 881 dbSNP
rs1158444901 882 dbSNP
rs1485044613 886 dbSNP
rs1185187072 887 dbSNP
rs1258794391 888 dbSNP
rs1387317329 890 dbSNP
rs11371594 891 dbSNP
rs1182719470 891 dbSNP
rs1356247005 891 dbSNP
rs1491084519 891 dbSNP
rs567514893 891 dbSNP
rs1424919632 897 dbSNP
rs1239159471 898 dbSNP
rs768360483 903 dbSNP
rs915271181 912 dbSNP
rs13316662 915 dbSNP
rs966689203 921 dbSNP
rs1228582884 922 dbSNP
rs1421946654 922 dbSNP
rs1159453100 929 dbSNP
rs1375096177 930 dbSNP
rs1300602492 932 dbSNP
rs146187953 932 dbSNP
rs371003848 932 dbSNP
rs1432902341 934 dbSNP
rs1314842406 937 dbSNP
rs375426356 938 dbSNP
rs1297900412 955 dbSNP
rs1418238067 957 dbSNP
rs1396521937 961 dbSNP
rs10512913 965 dbSNP
rs541265797 968 dbSNP
rs999579031 972 dbSNP
rs561133625 978 dbSNP
rs1411655202 985 dbSNP
rs1188370226 987 dbSNP
rs150967866 987 dbSNP
rs1333730994 989 dbSNP
rs1031067794 990 dbSNP
rs1263805251 998 dbSNP
rs371366483 999 dbSNP
rs1038872190 1001 dbSNP
rs1011108135 1005 dbSNP
rs761514863 1009 dbSNP
rs1320769391 1021 dbSNP
rs140549382 1022 dbSNP
rs982745965 1028 dbSNP
rs1340667584 1034 dbSNP
rs1208029780 1040 dbSNP
rs928332028 1042 dbSNP
rs1398738849 1046 dbSNP
rs548821412 1047 dbSNP
rs1195703797 1049 dbSNP
rs1348359966 1049 dbSNP
rs1249097344 1058 dbSNP
rs1441877516 1060 dbSNP
rs1048947482 1067 dbSNP
rs570091741 1075 dbSNP
rs1212329643 1077 dbSNP
rs760659622 1091 dbSNP
rs539379102 1098 dbSNP
rs753946440 1099 dbSNP
rs1269142804 1109 dbSNP
rs553196185 1112 dbSNP
rs1001664181 1113 dbSNP
rs1487916527 1114 dbSNP
rs1452821451 1115 dbSNP
rs1033873448 1118 dbSNP
rs1037550817 1118 dbSNP
rs1317957916 1128 dbSNP
rs772671211 1128 dbSNP
rs1217283759 1132 dbSNP
rs865850053 1137 dbSNP
rs543685539 1141 dbSNP
rs959511675 1146 dbSNP
rs1052088976 1150 dbSNP
rs1365997428 1153 dbSNP
rs890353332 1170 dbSNP
rs563401302 1172 dbSNP
rs893900555 1189 dbSNP
rs1011366987 1195 dbSNP
rs754980491 1196 dbSNP
rs1022548574 1198 dbSNP
rs966738304 1199 dbSNP
rs1176789566 1203 dbSNP
rs1461577257 1211 dbSNP
rs191968481 1214 dbSNP
rs1297512082 1221 dbSNP
rs1180080853 1225 dbSNP
rs374456264 1237 dbSNP
rs1448666059 1246 dbSNP
rs532394775 1256 dbSNP
rs779206658 1260 dbSNP
rs1346588243 1264 dbSNP
rs951608516 1269 dbSNP
rs911845809 1271 dbSNP
rs1233216517 1276 dbSNP
rs1310779434 1286 dbSNP
rs983152116 1289 dbSNP
rs1303013800 1290 dbSNP
rs1447737871 1290 dbSNP
rs1376458953 1292 dbSNP
rs1312240455 1294 dbSNP
rs1329323225 1299 dbSNP
rs1203236607 1301 dbSNP
rs1403077077 1303 dbSNP
rs1250086717 1310 dbSNP
rs1014566832 1313 dbSNP
rs1303326787 1315 dbSNP
rs1465510656 1321 dbSNP
rs966164911 1322 dbSNP
rs552106577 1323 dbSNP
rs1439852701 1325 dbSNP
rs975209629 1326 dbSNP
rs1467467510 1328 dbSNP
rs559430965 1336 dbSNP
rs921811546 1344 dbSNP
rs1443615710 1346 dbSNP
rs930464761 1352 dbSNP
rs931837835 1354 dbSNP
rs1193103970 1365 dbSNP
rs752916824 1367 dbSNP
rs911843270 1368 dbSNP
rs566903459 1369 dbSNP
rs145619276 1372 dbSNP
rs184714350 1375 dbSNP
rs1045414437 1379 dbSNP
rs375192067 1385 dbSNP
rs1052389289 1392 dbSNP
rs1395324376 1405 dbSNP
rs906841742 1408 dbSNP
rs1373560237 1410 dbSNP
rs1001317829 1412 dbSNP
rs1055940516 1413 dbSNP
rs778037734 1414 dbSNP
rs946832659 1416 dbSNP
rs1473594848 1422 dbSNP
rs1045584759 1433 dbSNP
rs905256536 1445 dbSNP
rs747355815 1448 dbSNP
rs1218060083 1456 dbSNP
rs1292842455 1463 dbSNP
rs1284363506 1464 dbSNP
rs1231308168 1466 dbSNP
rs1211810654 1468 dbSNP
rs1319455580 1469 dbSNP
rs1022429858 1484 dbSNP
rs1283603817 1485 dbSNP
rs116804188 1488 dbSNP
rs781737418 1489 dbSNP
rs1333116911 1496 dbSNP
rs1224265119 1504 dbSNP
rs1339558593 1514 dbSNP
rs1315992469 1520 dbSNP
rs1406685186 1521 dbSNP
rs1018964678 1523 dbSNP
rs1391014483 1529 dbSNP
rs1162355655 1530 dbSNP
rs1459404244 1537 dbSNP
rs1247466071 1538 dbSNP
rs1194994628 1553 dbSNP
rs1477793247 1564 dbSNP
rs966422679 1568 dbSNP
rs974883709 1573 dbSNP
rs1029025167 1574 dbSNP
rs1452614594 1590 dbSNP
rs189531635 1590 dbSNP
rs1289409245 1603 dbSNP
rs1208334420 1613 dbSNP
rs1320049872 1618 dbSNP
rs952092660 1622 dbSNP
rs1185061143 1623 dbSNP
rs984597618 1635 dbSNP
rs551274362 1655 dbSNP
rs1478214218 1659 dbSNP
rs761065981 1666 dbSNP
rs963345307 1670 dbSNP
rs981750168 1673 dbSNP
rs1438342921 1677 dbSNP
rs1331528665 1686 dbSNP
rs181530992 1688 dbSNP
rs1417108493 1692 dbSNP
rs1322446200 1693 dbSNP
rs1403350577 1697 dbSNP
rs1438311413 1706 dbSNP
rs764579688 1709 dbSNP
rs1401780303 1710 dbSNP
rs1166658698 1712 dbSNP
rs928351611 1714 dbSNP
rs1465500542 1718 dbSNP
rs973079952 1722 dbSNP
rs138339421 1726 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545214. RNA binding protein: AGO3. Condition:Control ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uaaaucgguuaacaGGUAGAAa 5'
                        ||||||| 
Target 5' --------------CCAUCUUc 3'
 		1 - 8
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 58477.0
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uaaaucgguuaacaGGUAGAAa 5'
                        ||||||| 
Target 5' --------------CCAUCUUc 3'
 		1 - 8
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 GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_021203 | 3UTR | GUGUGGAGAUUUAGGUGCUGCUCUGCUGCUCUGGAUGGCUGAAGGCUCCUGGGCCAUCUUCAUGUGCUGCUUGAAGAGCUCCUAUUUUGUACUCCUGGCUAGAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000466490.2 | 3UTR | CCAUCUUCAUGUGCUGCUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000466490.2 | 3UTR | CCAUCUUCAUGUGCUGCUUG
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
74 hsa-miR-4662b Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055639 TRUB1 TruB pseudouridine synthase family member 1 2 4
MIRT056782 ARID5B AT-rich interaction domain 5B 2 2
MIRT060844 CEP350 centrosomal protein 350 2 2
MIRT069982 GEMIN2 gem nuclear organelle associated protein 2 2 2
MIRT071727 CCNK cyclin K 2 2
MIRT105115 MYC MYC proto-oncogene, bHLH transcription factor 2 4
MIRT122207 TNPO1 transportin 1 2 2
MIRT125595 SCD stearoyl-CoA desaturase 2 2
MIRT164186 SCOC short coiled-coil protein 2 2
MIRT175513 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT305086 SRPRB SRP receptor beta subunit 2 4
MIRT305178 SLC25A36 solute carrier family 25 member 36 2 2
MIRT441913 KRT78 keratin 78 2 2
MIRT442485 TBC1D19 TBC1 domain family member 19 2 2
MIRT445024 PPARA peroxisome proliferator activated receptor alpha 2 2
MIRT447763 TTLL7 tubulin tyrosine ligase like 7 2 2
MIRT447927 SCRN1 secernin 1 2 2
MIRT450058 IL17RA interleukin 17 receptor A 2 2
MIRT452799 FAM136A family with sequence similarity 136 member A 2 2
MIRT453410 RHD Rh blood group D antigen 2 4
MIRT453687 CEBPD CCAAT/enhancer binding protein delta 2 2
MIRT455278 DDX39B DExD-box helicase 39B 2 10
MIRT457140 ASPH aspartate beta-hydroxylase 2 2
MIRT462837 BCL3 B-cell CLL/lymphoma 3 2 2
MIRT469805 RAB14 RAB14, member RAS oncogene family 2 2
MIRT471481 PDE7B phosphodiesterase 7B 2 2
MIRT473885 M6PR mannose-6-phosphate receptor, cation dependent 2 6
MIRT474190 LETMD1 LETM1 domain containing 1 2 2
MIRT475892 H3F3C H3 histone family member 3C 2 8
MIRT477569 EIF1AX eukaryotic translation initiation factor 1A, X-linked 2 2
MIRT478765 CS citrate synthase 2 2
MIRT480210 CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 2 2
MIRT490709 FSTL4 follistatin like 4 2 2
MIRT491431 PDZD11 PDZ domain containing 11 2 4
MIRT493383 KIAA1614 KIAA1614 2 4
MIRT493699 H3F3B H3 histone family member 3B 2 4
MIRT500563 XBP1P1 X-box binding protein 1 pseudogene 1 2 8
MIRT502297 GNG12 G protein subunit gamma 12 2 6
MIRT503321 FICD FIC domain containing 2 4
MIRT504119 C9orf170 chromosome 9 open reading frame 170 2 4
MIRT506389 NUCKS1 nuclear casein kinase and cyclin dependent kinase substrate 1 2 4
MIRT515598 FBXL13 F-box and leucine rich repeat protein 13 2 4
MIRT517664 TRIM72 tripartite motif containing 72 2 4
MIRT526185 FBXO32 F-box protein 32 2 2
MIRT527110 ARHGAP15 Rho GTPase activating protein 15 2 2
MIRT527952 GDI2 GDP dissociation inhibitor 2 2 2
MIRT532979 ZNF12 zinc finger protein 12 2 2
MIRT533169 WEE1 WEE1 G2 checkpoint kinase 2 4
MIRT533999 SUZ12 SUZ12 polycomb repressive complex 2 subunit 2 2
MIRT536186 MAOB monoamine oxidase B 2 2
MIRT536652 INIP INTS3 and NABP interacting protein 2 2
MIRT539222 ANP32E acidic nuclear phosphoprotein 32 family member E 2 6
MIRT540562 PPIC peptidylprolyl isomerase C 2 2
MIRT543311 ZNF585B zinc finger protein 585B 2 2
MIRT546632 RTN4 reticulon 4 2 2
MIRT554550 RRN3 RRN3 homolog, RNA polymerase I transcription factor 2 2
MIRT558356 DNAJA2 DnaJ heat shock protein family (Hsp40) member A2 2 2
MIRT561115 CLEC2D C-type lectin domain family 2 member D 2 2
MIRT565475 SPRY1 sprouty RTK signaling antagonist 1 2 2
MIRT565551 SMG1 SMG1, nonsense mediated mRNA decay associated PI3K related kinase 2 2
MIRT566499 PBX2P1 PBX homeobox 2 pseudogene 1 2 2
MIRT570932 ZNF284 zinc finger protein 284 2 2
MIRT573947 ZNF708 zinc finger protein 708 2 2
MIRT611173 ZNF347 zinc finger protein 347 2 2
MIRT643364 TRIM10 tripartite motif containing 10 2 2
MIRT647543 NLRP12 NLR family pyrin domain containing 12 2 2
MIRT656664 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT661960 FAHD1 fumarylacetoacetate hydrolase domain containing 1 2 2
MIRT669283 C19orf44 chromosome 19 open reading frame 44 2 2
MIRT670210 SLC24A4 solute carrier family 24 member 4 2 2
MIRT675813 MED28 mediator complex subunit 28 2 2
MIRT676226 TMEM91 transmembrane protein 91 2 2
MIRT694354 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT696276 TACO1 translational activator of cytochrome c oxidase I 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4662b Apicidin 6918328 sensitive High Hepatocellular Carcinoma cell line (HA22T)
hsa-miR-4662b Vorinostat 5311 NSC701852 approved sensitive High Hepatocellular Carcinoma cell line (HA22T)
hsa-mir-4662b Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-miR-4662b Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4662b Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-4662b Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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