pre-miRNA Information
pre-miRNA hsa-mir-216a   
Genomic Coordinates chr2: 55988950 - 55989059
Description Homo sapiens miR-216a stem-loop
Comment This human miRNA was predicted by computational methods using conservation with mouse and Fugu rubripes sequences .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-216a-5p
Sequence 19| UAAUCUCAGCUGGCAACUGUGA |40
Evidence Experimental
Experiments Cloned
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 15 2 - 55989027 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs757094946 2 dbSNP
rs746980700 8 dbSNP
rs1249388997 12 dbSNP
rs1188616124 15 dbSNP
rs1490501989 19 dbSNP
rs1465789697 20 dbSNP
rs370221981 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
BA0G4V miR-216a Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Tissue .
BA0G4V miR-216a Safety Biomarker (SAF) Clinical/Experimental Data Expression Increase Plasma MiRNA qPCR analyses
Gene Information
Gene Symbol SYNPO2L   
Synonyms -
Description synaptopodin 2 like
Transcript NM_001114133   
Other Transcripts NM_024875   
Expression
Putative miRNA Targets on SYNPO2L
3'UTR of SYNPO2L
(miRNA target sites are highlighted)
>SYNPO2L|NM_001114133|3'UTR
   1 ACAGGCACAGGTCCCAGGACCAAGGAGAGGTGGAACATCCAGTTCCTAAAGTTGCTTCTCCTACCCTATCCCATCCCCTG
  81 TCACGCATCTGGAAGCTAAATTGCCTCCTGCCAGAGATGGTTTCCAAGTTGATGTCCCCTTCCCCCACCTTCCTCCTCAC
 161 TCTCTACCTCCCTGCCGCTTTCCAACCAAGTATGTCTGCTTTGGTATCTTTGCCTCTCTTTGTCTCTGCATTTCCTTTCC
 241 TGGATCTCTGTCTTTATTTCCAGGCTTCTCCACCCATATTCCTCCACAGATCTCTCTTCCTTGACATTTGTGCTTTTCTC
 321 CCTGGGCCTCATTTTAATGTTCAGTGAGAAGTAAACAGAGCAGAAGTGACCACTGGGACTTCAGGCAAGAAGCTCACCAC
 401 CAGGCACACAGCAAAGGGACTGAACTGACCCCTGTTTGCACTAAGCCACCCCCACCCCCCACTCTGCTTTCCCAAGCTTG
 481 ACTGGCATATACCTAGGCCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCTCTTCCGTCTAAGGCATGAA
 561 TAAGAGGGGAGGTCAAAATAAAGACCCAATCTGAGGCCGGGCACGGTGGCTCACGCCGGTAATCCCAGCACTTTGGGAGG
 641 CCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATTTCCACTAAAAATAC
 721 AAAAAATTAGCTGGGCGTGGTGGCGAGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCT
 801 GGAAGGCGGAGCTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGGGCGACGGAGCGAGACTCTGTCTCAAAAC
 881 AAACAAACAAACAAAAGACCCAATCTGAGTCTTATCGTTGTACTGATAGAAGGGTCAGATATCCCCACATGGAGTTGAGT
 961 GGGAGAAAGAGATTCACTAGAGAATAACTCCTTAGAGACCAATGTCTGTAGCAGGTGTACAGCATCTTGTGAAAGTTATG
1041 GAGCATGAAAAGACTGAAGGGCCAGGACAGTTTGCATGGGCTGAGTTATACCAGCTAGACCAGGAATAGAACAAAGAATT
1121 CTATACCTCAGGATTTCAAAAAGTTAGCAACTTGAGAGGCCAGTGCTGAGCAACCCAGTACCCAGGAAATGAAAAAAAGA
1201 AAGAAAATTCCCTCCGAGAATGAACAAATCATTGGCTTCATTGCCTCATGAGCTTGAGAGAAAGGAGAAGAGAGCCAGAG
1281 TGTGGCAAGTGAGGCCAAAATCAGAAGCATGGCAGAAATGAGTGTAAGTGATTGAGCCACAGACAGAAGTGTGGCGAGGG
1361 ACAATGCCATATTGGGAGAAGGTAAAGTTGAGTAACAAGAAACCAACCGTGTGTGAGAGGGGGATTGGAAAAAAATTTGA
1441 GGGAGAAGAATGTTAGAATGGAAGGGAATGATGGTGGAAGGGAGGTGTGAGGGTGTGTGCTGAGTGTTGAAAGAACGGTT
1521 GGTGTCTGTGTGATTTTCCTTGAGTCTGTTCTTCAGTGTGTCTTCTGCAGCTTGCCATGACTGCCTGGGAAAGAGTAGGG
1601 AAATACCCAGAGCCAAAACCTCCTTTCAGTCCCACCCCATCCCTCAAAACCCCAGCTATTGCTTCTTTTCAGCTTCAGGT
1681 CCTGATCTCCAATCTTAGTATGGACTCCCTTCTCACCAAGACCACCACCAGCTACGTTTGCTGTGTAATCTGGAAAGTGA
1761 TAATTTCCTTTGCTTGTTGGGTGTGAGTCACAATACTTTGGTTTGTGCACAAGAATAAATTTATGCCCCATACCTTC
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' agUGUCAACGGUCGACUCUAAu 5'
            :||| ||  |||||||||| 
Target 5' ttGCAG-TG--AGCTGAGATTg 3'
813 - 831 163.00 -18.80
2
miRNA  3' agUGUCAACGGUCG--ACUCUAAu 5'
            ||:|||| :: |  || |||| 
Target 5' gaACGGTTGGTGTCTGTGTGATTt 3'
1513 - 1536 130.00 -14.40
3
miRNA  3' aguGUCAACGGUCGACUCUAAu 5'
             || |||||   |||| || 
Target 5' cttCA-TTGCCTCATGAGCTTg 3'
1236 - 1256 126.00 -11.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30490493 15 COSMIC
COSN30190615 27 COSMIC
COSN31494091 64 COSMIC
COSN30171291 72 COSMIC
COSN30499582 105 COSMIC
COSN31547997 116 COSMIC
COSN31514448 153 COSMIC
COSN31567440 246 COSMIC
COSN26440260 310 COSMIC
COSN20092128 348 COSMIC
COSN25475760 399 COSMIC
COSN24540908 454 COSMIC
COSN20107262 499 COSMIC
COSN20107266 500 COSMIC
COSN28693316 841 COSMIC
COSN28643791 868 COSMIC
COSN28201940 871 COSMIC
COSN5253713 886 COSMIC
COSN31547643 890 COSMIC
COSN26580977 963 COSMIC
COSN25441468 991 COSMIC
COSN5883476 1004 COSMIC
COSN26581459 1031 COSMIC
COSN26668033 1091 COSMIC
COSN31516583 1437 COSMIC
COSN1500339 1479 COSMIC
COSN30544429 1518 COSMIC
COSN31529323 1546 COSMIC
COSN28858030 1589 COSMIC
COSN30123972 1623 COSMIC
COSN1122392 1642 COSMIC
COSN30544036 1656 COSMIC
COSN18713652 1678 COSMIC
COSN30164802 1681 COSMIC
COSN1122390 1741 COSMIC
COSN30129019 1775 COSMIC
COSN26435903 1784 COSMIC
COSN28187135 1809 COSMIC
rs3740293 335 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1216962456 5 dbSNP
rs189798321 8 dbSNP
rs754863833 9 dbSNP
rs1206091329 13 dbSNP
rs200943721 15 dbSNP
rs1189285955 16 dbSNP
rs1324426955 27 dbSNP
rs766117288 29 dbSNP
rs561222652 30 dbSNP
rs746136240 31 dbSNP
rs1360135153 32 dbSNP
rs41280406 33 dbSNP
rs529926811 51 dbSNP
rs765862668 55 dbSNP
rs900507997 60 dbSNP
rs760246909 65 dbSNP
rs942038874 66 dbSNP
rs1357063932 71 dbSNP
rs35459518 79 dbSNP
rs1017325699 80 dbSNP
rs1007655346 84 dbSNP
rs376406191 85 dbSNP
rs1301510095 97 dbSNP
rs867419711 98 dbSNP
rs1333158012 101 dbSNP
rs1207757267 103 dbSNP
rs909312958 108 dbSNP
rs566427671 110 dbSNP
rs1465305079 119 dbSNP
rs1207959667 127 dbSNP
rs890152684 129 dbSNP
rs983488240 132 dbSNP
rs1447682910 138 dbSNP
rs1403769576 139 dbSNP
rs1051854715 146 dbSNP
rs562628569 147 dbSNP
rs1174415644 166 dbSNP
rs143952122 174 dbSNP
rs534999959 177 dbSNP
rs1414561328 178 dbSNP
rs929489959 179 dbSNP
rs558549174 185 dbSNP
rs992374084 186 dbSNP
rs1037878849 190 dbSNP
rs749481949 191 dbSNP
rs1437947160 196 dbSNP
rs1293824282 197 dbSNP
rs959583358 198 dbSNP
rs1482063279 199 dbSNP
rs1289992249 203 dbSNP
rs942144626 204 dbSNP
rs915995421 213 dbSNP
rs1266143993 223 dbSNP
rs1471867868 228 dbSNP
rs1033930629 239 dbSNP
rs767093147 249 dbSNP
rs938750689 258 dbSNP
rs967724685 264 dbSNP
rs12570798 273 dbSNP
rs1021134644 287 dbSNP
rs548332100 292 dbSNP
rs890966287 298 dbSNP
rs1029466573 310 dbSNP
rs913786997 328 dbSNP
rs3740293 335 dbSNP
rs1309417227 344 dbSNP
rs1350936791 347 dbSNP
rs957872605 355 dbSNP
rs1017835932 366 dbSNP
rs774613764 374 dbSNP
rs954605300 389 dbSNP
rs1228746701 395 dbSNP
rs1030041650 404 dbSNP
rs993126841 413 dbSNP
rs1280781749 420 dbSNP
rs898089334 447 dbSNP
rs572931233 450 dbSNP
rs1220595513 454 dbSNP
rs770039469 454 dbSNP
rs1483623292 460 dbSNP
rs1181897428 461 dbSNP
rs554375437 493 dbSNP
rs1203357991 498 dbSNP
rs942055761 499 dbSNP
rs887756952 500 dbSNP
rs1047820943 502 dbSNP
rs1412472460 503 dbSNP
rs894670710 504 dbSNP
rs1056358614 505 dbSNP
rs1170138715 505 dbSNP
rs1428640026 508 dbSNP
rs938817026 509 dbSNP
rs138687876 510 dbSNP
rs907239377 512 dbSNP
rs1448697872 516 dbSNP
rs929355428 528 dbSNP
rs1041708665 530 dbSNP
rs1448247191 531 dbSNP
rs1360560522 533 dbSNP
rs1243863509 534 dbSNP
rs1317890577 534 dbSNP
rs918094985 536 dbSNP
rs1456256879 537 dbSNP
rs1343160781 538 dbSNP
rs769203006 538 dbSNP
rs1160627929 539 dbSNP
rs1166270721 540 dbSNP
rs1180061665 540 dbSNP
rs1187450850 540 dbSNP
rs1189954054 540 dbSNP
rs1204623059 540 dbSNP
rs1211501141 540 dbSNP
rs1237382348 540 dbSNP
rs1270522185 540 dbSNP
rs1271368632 540 dbSNP
rs1442315594 540 dbSNP
rs1444440558 540 dbSNP
rs1448529242 540 dbSNP
rs1491446952 540 dbSNP
rs56147683 540 dbSNP
rs57745482 540 dbSNP
rs59162775 540 dbSNP
rs796899631 540 dbSNP
rs1227068084 541 dbSNP
rs913837907 541 dbSNP
rs946021874 541 dbSNP
rs140171142 542 dbSNP
rs1211078671 545 dbSNP
rs1248126117 546 dbSNP
rs938192254 547 dbSNP
rs926893958 554 dbSNP
rs979677001 555 dbSNP
rs1378999819 566 dbSNP
rs34172607 569 dbSNP
rs1171798384 570 dbSNP
rs1239433187 571 dbSNP
rs1020577430 579 dbSNP
rs1458782578 580 dbSNP
rs1321086413 586 dbSNP
rs987895068 589 dbSNP
rs910420985 595 dbSNP
rs955141230 598 dbSNP
rs192799507 599 dbSNP
rs996705628 600 dbSNP
rs954488962 602 dbSNP
rs538980638 604 dbSNP
rs1288817152 605 dbSNP
rs1321790205 608 dbSNP
rs1017277939 610 dbSNP
rs146617579 614 dbSNP
rs1202840049 615 dbSNP
rs571826543 617 dbSNP
rs1047687605 618 dbSNP
rs1006505799 624 dbSNP
rs1266537184 627 dbSNP
rs547019950 631 dbSNP
rs528467338 642 dbSNP
rs1433695129 643 dbSNP
rs1284892804 644 dbSNP
rs1056458441 647 dbSNP
rs938188552 648 dbSNP
rs567610381 651 dbSNP
rs1392917962 652 dbSNP
rs1044370205 658 dbSNP
rs946953823 659 dbSNP
rs914148048 661 dbSNP
rs907298558 662 dbSNP
rs142904487 672 dbSNP
rs531001409 673 dbSNP
rs188178616 682 dbSNP
rs975161439 689 dbSNP
rs1356378981 690 dbSNP
rs1054378526 692 dbSNP
rs1448907037 693 dbSNP
rs936642656 718 dbSNP
rs910421514 720 dbSNP
rs985991990 732 dbSNP
rs1189469490 734 dbSNP
rs370099084 736 dbSNP
rs1458442894 737 dbSNP
rs550782594 744 dbSNP
rs1016730116 745 dbSNP
rs923036150 746 dbSNP
rs1005891279 748 dbSNP
rs1272015278 749 dbSNP
rs1373006563 762 dbSNP
rs532492859 763 dbSNP
rs1390191642 768 dbSNP
rs1227271269 769 dbSNP
rs971831635 781 dbSNP
rs1025515292 790 dbSNP
rs993485209 793 dbSNP
rs1205349051 795 dbSNP
rs961781805 807 dbSNP
rs896479908 808 dbSNP
rs1015975530 810 dbSNP
rs1202143838 813 dbSNP
rs1256766243 824 dbSNP
rs1424530532 830 dbSNP
rs1183077863 831 dbSNP
rs1383388366 832 dbSNP
rs565204466 833 dbSNP
rs984822413 837 dbSNP
rs1384585901 838 dbSNP
rs41280404 841 dbSNP
rs1460759126 844 dbSNP
rs1034986044 850 dbSNP
rs1293515595 853 dbSNP
rs182419981 854 dbSNP
rs1043933187 855 dbSNP
rs144469305 857 dbSNP
rs1294364899 858 dbSNP
rs373158284 858 dbSNP
rs1235125720 860 dbSNP
rs762544582 861 dbSNP
rs560910376 862 dbSNP
rs149246701 863 dbSNP
rs1431581590 868 dbSNP
rs893220160 869 dbSNP
rs1466292560 870 dbSNP
rs796420303 871 dbSNP
rs1191749005 877 dbSNP
rs1054464191 896 dbSNP
rs1419069148 896 dbSNP
rs1178712387 897 dbSNP
rs574977812 903 dbSNP
rs1469770875 909 dbSNP
rs1335286918 911 dbSNP
rs1390251142 913 dbSNP
rs780398864 915 dbSNP
rs756890889 916 dbSNP
rs1388084082 922 dbSNP
rs757441751 926 dbSNP
rs889054605 943 dbSNP
rs975572068 950 dbSNP
rs1483147615 952 dbSNP
rs374112958 960 dbSNP
rs1269909625 963 dbSNP
rs140338614 965 dbSNP
rs1230417057 967 dbSNP
rs933235488 973 dbSNP
rs1485019964 977 dbSNP
rs923130903 984 dbSNP
rs1036193209 997 dbSNP
rs1480295095 1001 dbSNP
rs909617200 1003 dbSNP
rs538846240 1020 dbSNP
rs542756076 1021 dbSNP
rs984012980 1026 dbSNP
rs763633046 1030 dbSNP
rs369876802 1039 dbSNP
rs1157739728 1041 dbSNP
rs1342886798 1043 dbSNP
rs1025547872 1046 dbSNP
rs1243902424 1050 dbSNP
rs1286781455 1059 dbSNP
rs1402867545 1060 dbSNP
rs1290202319 1061 dbSNP
rs1351051744 1068 dbSNP
rs1223082000 1072 dbSNP
rs1014099372 1073 dbSNP
rs960695918 1084 dbSNP
rs958591760 1085 dbSNP
rs1409604698 1090 dbSNP
rs1371397824 1092 dbSNP
rs1300176879 1094 dbSNP
rs1292771912 1100 dbSNP
rs926960513 1103 dbSNP
rs578225876 1113 dbSNP
rs41280402 1116 dbSNP
rs535279982 1118 dbSNP
rs1177084692 1126 dbSNP
rs1405224874 1137 dbSNP
rs1481350701 1158 dbSNP
rs1061859 1159 dbSNP
rs905313941 1164 dbSNP
rs1181110997 1168 dbSNP
rs1472827367 1177 dbSNP
rs1020450108 1183 dbSNP
rs1198410424 1190 dbSNP
rs1309631118 1190 dbSNP
rs1022782349 1194 dbSNP
rs1277666684 1199 dbSNP
rs371668773 1199 dbSNP
rs554269336 1199 dbSNP
rs1011101824 1201 dbSNP
rs1256022186 1213 dbSNP
rs1230084773 1215 dbSNP
rs879280246 1216 dbSNP
rs111909088 1227 dbSNP
rs368702396 1232 dbSNP
rs1287076788 1245 dbSNP
rs889809499 1249 dbSNP
rs1228152468 1259 dbSNP
rs1204489950 1264 dbSNP
rs1231669379 1266 dbSNP
rs1473526986 1268 dbSNP
rs1183684759 1274 dbSNP
rs934192671 1276 dbSNP
rs1384011458 1280 dbSNP
rs1442433041 1284 dbSNP
rs900847883 1285 dbSNP
rs1390614876 1288 dbSNP
rs1039406100 1289 dbSNP
rs942359131 1290 dbSNP
rs1326836644 1294 dbSNP
rs754860741 1295 dbSNP
rs1448576117 1296 dbSNP
rs1337505294 1302 dbSNP
rs1382063605 1305 dbSNP
rs1309384057 1307 dbSNP
rs1244117618 1309 dbSNP
rs909657500 1310 dbSNP
rs1378752010 1319 dbSNP
rs1340586844 1322 dbSNP
rs549365010 1324 dbSNP
rs997472730 1326 dbSNP
rs373369032 1334 dbSNP
rs115251193 1335 dbSNP
rs138190774 1336 dbSNP
rs992710111 1356 dbSNP
rs556890647 1358 dbSNP
rs908980667 1359 dbSNP
rs114598671 1361 dbSNP
rs368848312 1372 dbSNP
rs1185167946 1374 dbSNP
rs1426959872 1390 dbSNP
rs1414991652 1396 dbSNP
rs1422817641 1404 dbSNP
rs1405490697 1408 dbSNP
rs532214042 1409 dbSNP
rs1322873149 1411 dbSNP
rs1256427486 1415 dbSNP
rs565042235 1428 dbSNP
rs1268822656 1437 dbSNP
rs1184898105 1439 dbSNP
rs1347519468 1442 dbSNP
rs1034676746 1444 dbSNP
rs539046548 1451 dbSNP
rs146989764 1468 dbSNP
rs969780080 1475 dbSNP
rs767162212 1487 dbSNP
rs560755376 1489 dbSNP
rs1022386773 1491 dbSNP
rs1010956741 1495 dbSNP
rs1480622728 1501 dbSNP
rs1198687593 1502 dbSNP
rs1427099378 1503 dbSNP
rs988952602 1504 dbSNP
rs957513687 1507 dbSNP
rs542193874 1516 dbSNP
rs141233100 1517 dbSNP
rs563036947 1518 dbSNP
rs1316081417 1528 dbSNP
rs1333234652 1528 dbSNP
rs1400410529 1533 dbSNP
rs901447762 1533 dbSNP
rs1405914892 1554 dbSNP
rs148116168 1560 dbSNP
rs1454623429 1565 dbSNP
rs1040356474 1579 dbSNP
rs578112986 1596 dbSNP
rs1230729821 1602 dbSNP
rs553506857 1606 dbSNP
rs751269863 1607 dbSNP
rs1214442952 1613 dbSNP
rs759858329 1621 dbSNP
rs764349323 1623 dbSNP
rs1470232464 1628 dbSNP
rs1349303360 1630 dbSNP
rs954148812 1634 dbSNP
rs1353803078 1635 dbSNP
rs1291573101 1637 dbSNP
rs1490469126 1638 dbSNP
rs888073933 1639 dbSNP
rs1266427054 1640 dbSNP
rs1167740243 1642 dbSNP
rs1048164028 1646 dbSNP
rs1182379591 1652 dbSNP
rs34529973 1654 dbSNP
rs1419805035 1659 dbSNP
rs766372958 1665 dbSNP
rs998150773 1667 dbSNP
rs764409025 1671 dbSNP
rs901771809 1678 dbSNP
rs1349831922 1687 dbSNP
rs1185761859 1688 dbSNP
rs761148867 1692 dbSNP
rs1251180482 1693 dbSNP
rs1202545552 1698 dbSNP
rs1004784871 1699 dbSNP
rs1309325448 1700 dbSNP
rs775560608 1701 dbSNP
rs1245483468 1702 dbSNP
rs918324241 1704 dbSNP
rs1316919383 1708 dbSNP
rs1453044197 1709 dbSNP
rs767455524 1720 dbSNP
rs1372529359 1728 dbSNP
rs772404601 1730 dbSNP
rs1443817221 1733 dbSNP
rs992645136 1735 dbSNP
rs938516495 1736 dbSNP
rs1048877361 1743 dbSNP
rs1221228522 1746 dbSNP
rs1289352310 1746 dbSNP
rs1483902436 1759 dbSNP
rs1196354937 1760 dbSNP
rs1249732135 1765 dbSNP
rs535025760 1768 dbSNP
rs1188667697 1772 dbSNP
rs1387121222 1776 dbSNP
rs1445490125 1780 dbSNP
rs980393182 1781 dbSNP
rs905573780 1782 dbSNP
rs1045382093 1786 dbSNP
rs1299302178 1791 dbSNP
rs574261746 1792 dbSNP
rs567448773 1793 dbSNP
rs949692902 1796 dbSNP
rs1382824950 1799 dbSNP
rs117050535 1803 dbSNP
rs989048974 1805 dbSNP
rs1344138731 1806 dbSNP
rs989576861 1811 dbSNP
rs1250482216 1813 dbSNP
rs143732128 1823 dbSNP
rs537431294 1829 dbSNP
Experimental Support 1 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 GSM1084045. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep3 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' agUGUCAACGGUCGACUCUAAu 5'
            :||| ||  |||||||||| 
Target 5' uuGCAG-UG--AGCUGAGAUUg 3'
4 - 22
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 GSM1084045
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep3
Location of target site ENST00000372873.4 | 3UTR | AGCUUGCAGUGAGCUGAGAUUGCGCCACUGCACUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
GSE21849 B cell lymphoma -0.409 1.4e-2 0.302 5.6e-2 29 Click to see details
GSE21687 Ependynoma primary tumors 0.206 5.1e-2 0.023 4.3e-1 64 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.284 8.4e-2 -0.131 2.7e-1 25 Click to see details
GSE28260 Renal cortex and medulla -0.33 1.4e-1 -0.554 2.5e-2 13 Click to see details
GSE27834 Pluripotent stem cells -0.29 1.4e-1 -0.250 1.8e-1 16 Click to see details
GSE38226 Liver fibrosis -0.22 1.7e-1 -0.137 2.8e-1 21 Click to see details
GSE28544 Breast cancer 0.203 1.7e-1 0.291 8.4e-2 24 Click to see details
GSE14794 Lymphoblastoid cells 0.099 1.8e-1 0.186 4.0e-2 90 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.191 1.8e-1 0.386 2.8e-2 25 Click to see details
GSE42095 Differentiated embryonic stem cells 0.153 2.4e-1 -0.167 2.2e-1 23 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.102 3.3e-1 -0.098 3.4e-1 20 Click to see details
GSE19350 CNS germ cell tumors 0.03 4.6e-1 0.281 1.9e-1 12 Click to see details
GSE17306 Multiple myeloma -0.013 4.6e-1 0.417 1.4e-3 49 Click to see details
GSE32688 Pancreatic cancer 0.01 4.8e-1 0.055 3.8e-1 32 Click to see details
GSE17498 Multiple myeloma 0.008 4.8e-1 -0.022 4.5e-1 40 Click to see details
GSE26953 Aortic valvular endothelial cells -0.009 4.8e-1 -0.009 4.8e-1 24 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
THCA 0.334 0.01 0.124 0.2 47 Click to see details
ESCA -0.958 0.02 -0.800 0.1 4 Click to see details
BRCA 0.375 0.03 0.411 0.02 25 Click to see details
KICH 0.459 0.08 0.464 0.08 11 Click to see details
LIHC -0.154 0.16 -0.100 0.26 45 Click to see details
LUSC -0.21 0.19 -0.274 0.12 20 Click to see details
KIRP 0.203 0.21 -0.055 0.41 18 Click to see details
KIRC -0.152 0.22 -0.224 0.12 29 Click to see details
STAD 0.123 0.3 0.065 0.39 20 Click to see details
PAAD -0.38 0.31 -0.400 0.3 4 Click to see details
HNSC 0.108 0.31 -0.130 0.28 23 Click to see details
CHOL -0.193 0.32 -0.095 0.41 8 Click to see details
UCEC 0.132 0.36 -0.164 0.33 10 Click to see details
LUAD 0.111 0.39 0.117 0.38 9 Click to see details
PRAD -0.045 0.41 -0.156 0.2 31 Click to see details
BLCA -0.057 0.44 -0.200 0.29 10 Click to see details
BLCA -0.057 0.44 -0.200 0.29 10 Click to see details
BLCA -0.057 0.44 -0.200 0.29 10 Click to see details
148 hsa-miR-216a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT000534 PTEN phosphatase and tensin homolog 4 3
MIRT005018 SIRT1 sirtuin 1 3 1
MIRT005964 CDC42 cell division cycle 42 2 1
MIRT005969 CD44 CD44 molecule (Indian blood group) 2 1
MIRT007154 SMAD7 SMAD family member 7 1 1
MIRT054887 BECN1 beclin 1 5 3
MIRT067588 METAP2 methionyl aminopeptidase 2 2 6
MIRT099144 MYLIP myosin regulatory light chain interacting protein 2 12
MIRT162313 TGFBR2 transforming growth factor beta receptor 2 2 2
MIRT230668 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT256274 PHAX phosphorylated adaptor for RNA export 2 2
MIRT386817 RAD51L3-RFFL RAD51L3-RFFL readthrough 2 2
MIRT386825 RFFL ring finger and FYVE like domain containing E3 ubiquitin protein ligase 2 2
MIRT438816 HNF4A hepatocyte nuclear factor 4 alpha 1 1
MIRT464699 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465962 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466046 TMEM189 transmembrane protein 189 2 2
MIRT466482 TECPR2 tectonin beta-propeller repeat containing 2 2 7
MIRT472209 NGFRAP1 brain expressed X-linked 3 2 4
MIRT472562 NACC1 nucleus accumbens associated 1 2 4
MIRT478921 CPS1 carbamoyl-phosphate synthase 1 2 2
MIRT480121 CALR calreticulin 2 2
MIRT497754 OXGR1 oxoglutarate receptor 1 2 2
MIRT497967 TWISTNB TWIST neighbor 2 2
MIRT502882 CDK4 cyclin dependent kinase 4 2 8
MIRT510191 MON1B MON1 homolog B, secretory trafficking associated 2 4
MIRT512407 CD84 CD84 molecule 2 2
MIRT513739 PSD3 pleckstrin and Sec7 domain containing 3 2 4
MIRT526257 DROSHA drosha ribonuclease III 2 2
MIRT528968 FAM19A3 family with sequence similarity 19 member A3, C-C motif chemokine like 2 2
MIRT529599 C6orf132 chromosome 6 open reading frame 132 2 2
MIRT529776 ZNF486 zinc finger protein 486 2 2
MIRT530110 PSAPL1 prosaposin like 1 (gene/pseudogene) 2 2
MIRT530504 FADS6 fatty acid desaturase 6 2 2
MIRT531437 PAK1 p21 (RAC1) activated kinase 1 2 2
MIRT534445 SDR16C5 short chain dehydrogenase/reductase family 16C member 5 2 2
MIRT537286 GABPB1 GA binding protein transcription factor beta subunit 1 2 2
MIRT538451 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT543085 ACTB actin beta 2 2
MIRT550982 ZNF254 zinc finger protein 254 2 2
MIRT556259 MAPRE2 microtubule associated protein RP/EB family member 2 2 2
MIRT556639 LAMC1 laminin subunit gamma 1 2 2
MIRT559127 C11orf57 chromosome 11 open reading frame 57 2 2
MIRT561405 TUBB2A tubulin beta 2A class IIa 2 2
MIRT569677 SEC23B Sec23 homolog B, coat complex II component 2 4
MIRT574660 KLHL15 kelch like family member 15 2 2
MIRT575030 Tecpr2 tectonin beta-propeller repeat containing 2 2 5
MIRT617683 JRKL JRK like 2 2
MIRT618540 SEMA5A semaphorin 5A 2 2
MIRT620805 C1orf27 chromosome 1 open reading frame 27 2 2
MIRT621569 ZBTB7A zinc finger and BTB domain containing 7A 2 2
MIRT622133 SP4 Sp4 transcription factor 2 2
MIRT624913 CTCFL CCCTC-binding factor like 2 2
MIRT625010 PAK4 p21 (RAC1) activated kinase 4 2 2
MIRT626644 ZNF551 zinc finger protein 551 2 2
MIRT626646 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT626672 NOM1 nucleolar protein with MIF4G domain 1 2 2
MIRT627945 NNT nicotinamide nucleotide transhydrogenase 2 2
MIRT627963 NLK nemo like kinase 2 2
MIRT628767 SRSF7 serine and arginine rich splicing factor 7 2 2
MIRT629261 KDM2B lysine demethylase 2B 2 2
MIRT629422 ADM2 adrenomedullin 2 2 2
MIRT630238 SORD sorbitol dehydrogenase 2 2
MIRT631272 CENPM centromere protein M 2 4
MIRT631793 CLK4 CDC like kinase 4 2 2
MIRT632058 ATF7IP activating transcription factor 7 interacting protein 2 2
MIRT632485 RPS15A ribosomal protein S15a 2 2
MIRT632611 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT632708 MTA3 metastasis associated 1 family member 3 2 2
MIRT632815 INO80 INO80 complex subunit 2 2
MIRT635956 PLA2G12A phospholipase A2 group XIIA 2 2
MIRT636152 UBXN2A UBX domain protein 2A 2 2
MIRT636899 C5orf45 MRN complex interacting protein 2 4
MIRT636930 AGAP9 ArfGAP with GTPase domain, ankyrin repeat and PH domain 9 2 2
MIRT637457 ZNF324B zinc finger protein 324B 2 2
MIRT637900 SLC19A3 solute carrier family 19 member 3 2 2
MIRT639826 ZNF638 zinc finger protein 638 2 2
MIRT640445 ERVMER34-1 endogenous retrovirus group MER34 member 1, envelope 2 2
MIRT640681 ARSK arylsulfatase family member K 2 2
MIRT641611 CAPN7 calpain 7 2 2
MIRT641676 AKR7A2 aldo-keto reductase family 7 member A2 2 2
MIRT646786 IL23R interleukin 23 receptor 2 2
MIRT648352 A2ML1 alpha-2-macroglobulin like 1 2 2
MIRT649144 SPATA5 spermatogenesis associated 5 2 2
MIRT649254 TRIM65 tripartite motif containing 65 2 2
MIRT652491 TMEM178B transmembrane protein 178B 2 2
MIRT653308 SMU1 DNA replication regulator and spliceosomal factor 2 2
MIRT653945 SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase 2 2
MIRT654212 RNF19B ring finger protein 19B 2 2
MIRT654839 PPM1L protein phosphatase, Mg2+/Mn2+ dependent 1L 2 2
MIRT655159 PHF21A PHD finger protein 21A 2 2
MIRT655316 PDCD11 programmed cell death 11 2 2
MIRT655375 PAX3 paired box 3 2 2
MIRT657301 HOXB5 homeobox B5 2 2
MIRT657593 GRIN2A glutamate ionotropic receptor NMDA type subunit 2A 2 2
MIRT658460 FAM117B family with sequence similarity 117 member B 2 2
MIRT658716 ELOVL4 ELOVL fatty acid elongase 4 2 2
MIRT661640 UGT2B28 UDP glucuronosyltransferase family 2 member B28 2 2
MIRT661712 MTO1 mitochondrial tRNA translation optimization 1 2 4
MIRT661833 ZNF793 zinc finger protein 793 2 2
MIRT663805 BET1L Bet1 golgi vesicular membrane trafficking protein like 2 2
MIRT663884 CXorf56 chromosome X open reading frame 56 2 2
MIRT664672 L2HGDH L-2-hydroxyglutarate dehydrogenase 2 2
MIRT665814 TMEM168 transmembrane protein 168 2 2
MIRT668159 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT668430 FAM20B FAM20B, glycosaminoglycan xylosylkinase 2 2
MIRT672306 GP2 glycoprotein 2 2 2
MIRT673101 SYNPO2L synaptopodin 2 like 2 2
MIRT673437 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT673584 KDELC2 KDEL motif containing 2 2 2
MIRT673718 SLU7 SLU7 homolog, splicing factor 2 2
MIRT673777 MRPL17 mitochondrial ribosomal protein L17 2 2
MIRT674316 IMP4 IMP4, U3 small nucleolar ribonucleoprotein 2 2
MIRT674820 FAM229B family with sequence similarity 229 member B 2 2
MIRT675179 BPTF bromodomain PHD finger transcription factor 2 2
MIRT675586 WWC1 WW and C2 domain containing 1 2 2
MIRT675812 MED28 mediator complex subunit 28 2 2
MIRT677632 ALG1 ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase 2 2
MIRT683914 PSMB9 proteasome subunit beta 9 2 2
MIRT687135 QPCTL glutaminyl-peptide cyclotransferase like 2 2
MIRT691973 PLCXD1 phosphatidylinositol specific phospholipase C X domain containing 1 2 2
MIRT693078 AS3MT arsenite methyltransferase 2 2
MIRT694084 RNASEH2B ribonuclease H2 subunit B 2 2
MIRT696292 IER3IP1 immediate early response 3 interacting protein 1 2 2
MIRT696541 C3 complement C3 2 2
MIRT701955 MITF melanogenesis associated transcription factor 2 2
MIRT703276 GNG12 G protein subunit gamma 12 2 2
MIRT706852 DNAJB13 DnaJ heat shock protein family (Hsp40) member B13 2 2
MIRT706993 XPO5 exportin 5 2 2
MIRT710716 KRTAP6-1 keratin associated protein 6-1 2 2
MIRT711305 ACOX1 acyl-CoA oxidase 1 2 2
MIRT711514 ESCO1 establishment of sister chromatid cohesion N-acetyltransferase 1 2 2
MIRT711648 LIPG lipase G, endothelial type 2 2
MIRT711772 CCDC59 coiled-coil domain containing 59 2 2
MIRT714280 COQ7 coenzyme Q7, hydroxylase 2 2
MIRT715048 PRPF38A pre-mRNA processing factor 38A 2 2
MIRT716934 INCENP inner centromere protein 2 2
MIRT717220 OTUD3 OTU deubiquitinase 3 2 2
MIRT717865 BICD2 BICD cargo adaptor 2 2 2
MIRT718836 SNX20 sorting nexin 20 2 2
MIRT720243 GPBP1 GC-rich promoter binding protein 1 2 2
MIRT721969 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 2
MIRT724000 LMTK2 lemur tyrosine kinase 2 2 2
MIRT725193 SDAD1 SDA1 domain containing 1 2 2
MIRT731669 CBL Cbl proto-oncogene 3 1
MIRT732776 AQP4 aquaporin 4 3 0
MIRT733158 ITGA5 integrin subunit alpha 5 1 0
MIRT735623 TLR4 toll like receptor 4 4 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-216a Curcumin NULL 969516 Quantitative real-time PCR Y79 RB cells. 22510010 2012 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-216a Cisplatin 5460033 NSC119875 approved resistant cell line (CIS)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant High Ovarian Cancer cell line (SKOV3, 2008, OVCAR10, OVCAR3, HeLa, MCF7, MDA-MB-468)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-216a-5p Verapamil 2520 NSC272366 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved sensitive High Small Cell Lung Cancer cell line (NCI-H69)
hsa-miR-216a-5p Sorafenib 216239 NSC747971 approved resistant Low Hepatocellular Carcinoma tissue and cell line (HepG2, Hep3B, Huh-7, PLC/PRF/5, HCCLM3, Bel-7404, HLE, SK-HEP-1, SNU-449)
hsa-miR-216a-5p Fluorouracil 3385 NSC19893 approved resistant High Colorectal Cancer tissue
hsa-miR-216a-5p Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer tissue
hsa-miR-216a-5p Sorafenib 216239 NSC747971 approved resistant High Hepatocellular Carcinoma cell line (Huh-7)
hsa-miR-216a-5p Doxorubicin 31703 NSC123127 approved resistant Low Small Cell Lung Cancer cell line (H69, H446)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant Low Ovarian Cancer cell line (SKOV3, OVCA433)
hsa-miR-216a-5p Oxaliplatin 6857599 NSC266046 approved resistant Low Gastric Cancer cell line (MGC, SGC)
hsa-miR-216a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM11)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM17)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM47)
hsa-miR-216a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (LM43)
hsa-miR-216a-5p Exemestane 60198 NSC713563 approved sensitive cell line (MCF-7)
hsa-miR-216a-5p Testosterone+Tamoxifen sensitive cell line (MCF-7)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved resistant cell line (RPMI2650)
hsa-miR-216a-5p Tamoxifen 2733525 NSC180973 approved sensitive cell line (TamR8)
hsa-miR-216a-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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