miRTarBase - #MIRT469166


—
pre-miRNA Information
pre-miRNA hsa-mir-3616   
Genomic Coordinates chr20: 47166967 - 47167058
Description Homo sapiens miR-3616 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3616-3p
Sequence 60| CGAGGGCAUUUCAUGAUGCAGGC |82
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 3 20 + 47167028 29233923 MiREDiBase
A-to-I 20 20 + 47167045 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1241656567 2 dbSNP
rs1336777739 8 dbSNP
rs1288261512 13 dbSNP
rs750749182 21 dbSNP
rs751652021 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol RNF111   
Synonyms ARK, hRNF111
Description ring finger protein 111
Transcript NM_017610   
Expression
Putative miRNA Targets on RNF111
3'UTR of RNF111
(miRNA target sites are highlighted)		 
>RNF111|NM_017610|3'UTR
   1 CACCATGTTTCAGAACTCTTGCCCTCCCTCTCATTCCCATCCTTCCTGGTACTGCAGTCAACCAAAGATGGCATGACTTA
  81 CCTGCGCAGATTTGGAAGCATTGAACTTAGAGTGCTGGCTCTGCTATATGGTACAACTAATGCTAGACCTACAGTTTATG
 161 TATACAGTTGATTTTGATGTATTTATAAAAGCTTTTTTTTCTAGATTTGACATTTTTCTGTATCATTTTACTGTATTTTT
 241 GCATGGTTCCTTGTATTGCATTTCTTTGCACATATTATGGGCTTGTGACCCTAAACTTGCAGGCAAGGTTAGCTGCTTTA
 321 GTAAGTAGAATTTTGTGGTCTTTTTGTTTTTTACATAGTACCAAGCCTTGATAATTATGAATTTTTTATCCATTACTAAC
 401 CTTTAATTTAATCAATCATGTACTTTAGTTTAATGTATAAAGATCCTCTAGAAAATGATAATATTGTGTATTAAGACATT
 481 CCTTAATTAGGACAAAATGGCTGCTGTATATTTACTATATGGAGTTCTGAGTTAAATACCATCCTTAATACTGGGAACAG
 561 AATACAACCCATATAAATCAGATGCAGGTGGTAGTCACATCACCAGAGTGATCAGTATAAATTTTCTTGGTGTATCCTTT
 641 TCCTTTCAACACAGTGCAGATAAGAGTTGAATATTGATATCATACATTTAGACTGCTGTTCTGATTGCATTTATCTTTTT
 721 CCTACATCATTTAGAATTTTATTTCCCTGATTCAGTTTTTGCTGCTGTGAAACAGCTCTGATGAACACTAAATATTAATT
 801 TCAATTAGCTAGATTGTACATACTTGCAGATTTAACAAAATTTTAGGGAAATTGAAAAAGACATGTAGAATTTGTTGTCT
 881 TCTGCTAAGCACGAAAAGTTAAGATATCTGCTTACATTGATTTTGTAGACACATTAAGTCAAGATTTGGAATTTAAGTCA
 961 CTGGCAGGTATCTGTGCATTCATAGAACTTATAAAGGTCCCAGGATCACTTTTAAGGGATTTTTATTAGTTTAAAGGTAA
1041 ATAAAGTCAGCTGAATCTACATGTCTCTTGTTTTATTTCTCTCTAAACTTGAAAACAGTAAATCTGCAGATACTGTGAGG
1121 CACAAATTATACTGTCAACCTACTGTTGCTATGGTTATATACTCCCACTTCATACATTACCAAGAGTCGATCACTGATTT
1201 AAAATTTTTAATTTCTATAGTTAAGATTTACTGCATAATATAGAATATAAAGTTAAGTTAACATACTAACATTTCTCCTT
1281 TGGAGGAAGTTTTAATCTACTTCAGGATGCATATTATTATCAAGATACTTTCATATACAGGATAGCCTAATTTTATTTGT
1361 TTAAATATGCTTAATATGCCCCAGATTGCAAATGCATCCAGTCAGTAATATCACTGTCTGTATGTGGAGGACATGTTCCC
1441 ATGGATCATATGTGAAGATGTCAATAAGCTTGCATTAAGCCACCTGCTTTGTAAGTGGATTGATTAATAAATAACTTATA
1521 TTTCTATTGTCTTTGTGTTTCATAATTAGTTTTTATAAAAACAGTTTACATTAAACATCTTGGAATTCAACAATAGTGAT
1601 CTCACTCAAATTGACATTTGCATAATTTGACATTTATATTCATTCAGTTATGACTACTTGCCCTTTTCTTCATATTAGTA
1681 AATGTTACACTGTAGTAGTTGTCAATGTTAACAGGCTTCAACATAGTATGTGTGCAGATGGACGATGGATTTAAAGAGCA
1761 TACCTTATGATTAAACCGAGGTTATAGAAGGTCAGGGGAGAGTGAAGGAGTCAGTGACCTATGTCTGCCATCTTACTGGG
1841 GAAAAGAGCAAGTAGCCTGTCTTCCTTTAAGTAAGTAGCCTGTAATGGATGTACTACTTTGCCACTGGAATACCCCGGGT
1921 CTGTGCCAAGGGACTGAAGAAGTGTAAGATGGGGAGAACTGTATGTCATGGAGTCCTCTTGACGTTCCCCCAGATACAAG
2001 TAAAGCACAGGTGGATTTCTCTATTTTTGAATACTACATCAGATTTAGATGCACGACTACCTGTTGACTTGTTTTATAAT
2081 TGCTACTGATTTTTTTAATGTAGGCAAAGCTTTGTTACTTTGAAATTTATTTAATAAAAGTATTTGTGACATAAACCTGA
2161 ATTGTTAATATAGGAGCTTATTAAGCTACTGCCATTAGTTATCGAAAAATGTGATAAGTAATGAAGAAAGTAAGGAAGAA
2241 AATGACTTTGAACATTTTGACTTTTTGTGCTTTGTTTTGGTGTCTTCCATATCCTGCTGCATCTTATATGTCAAAATGAA
2321 CATTTCAGTGGTAGCTGTCCAAATACATAAAAACTAAAATTCTTTTGTTAGCAAGTCCTTATTTTTATTGTTGTTAACAT
2401 GCAAGTGATAAACTGATAATTTGAAACATTTTTCTTACTCTGGTGACTTTCTTTTAGCTGCTAGCACACTTCAGCATTTG
2481 AACCATAACAGTTGTGATAAACTGATCGTTTGAAACGTT
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' cggACGUAGUACUU---UACGGGAGc 5'
             ||: ||| |||    ||||||| 
Target 5' ccaTGTTTCA-GAACTCTTGCCCTCc 3'
 3 - 27 155.00 -16.00
2 
miRNA  3' cggACGU-AGUACU--U-UACGGGAGc 5'
             | || |:||||  |  ||||||: 
Target 5' tcaTTCAGTTATGACTACTTGCCCTTt 3'
 1640 - 1666 138.00 -12.70
3 
miRNA  3' cgGACGU--AGUACUUUACGGGAGc 5'
            |||:|  |||||:|  |:|||| 
Target 5' aaCTGTATGTCATGGA--GTCCTCt 3'
 1957 - 1979 130.00 -17.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN24399762 6 COSMIC
COSN30153430 12 COSMIC
COSN31533380 24 COSMIC
COSN30537655 29 COSMIC
COSN30190054 30 COSMIC
COSN30455832 43 COSMIC
COSN19188556 44 COSMIC
COSN26552341 58 COSMIC
COSN16692508 68 COSMIC
COSN5266714 86 COSMIC
COSN30126407 87 COSMIC
COSN31522460 101 COSMIC
COSN30138942 108 COSMIC
COSN30493413 162 COSMIC
COSN31578814 184 COSMIC
COSN31524207 247 COSMIC
COSN30165212 329 COSMIC
COSN31530221 333 COSMIC
COSN9627068 463 COSMIC
COSN17805098 808 COSMIC
COSN30539616 966 COSMIC
COSN15717233 1127 COSMIC
COSN31568052 1646 COSMIC
COSN29840892 1676 COSMIC
COSN25803856 1771 COSMIC
COSN24657858 2395 COSMIC
COSN24859168 2517 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1201673173 5 dbSNP
rs544806880 6 dbSNP
rs1477905632 7 dbSNP
rs762664082 10 dbSNP
rs189017652 12 dbSNP
rs759048789 16 dbSNP
rs767520088 18 dbSNP
rs752526355 19 dbSNP
rs755982775 21 dbSNP
rs530876743 22 dbSNP
rs763763519 27 dbSNP
rs750706640 28 dbSNP
rs758601692 34 dbSNP
rs757587213 40 dbSNP
rs1466832774 41 dbSNP
rs780195312 42 dbSNP
rs747100788 47 dbSNP
rs762038159 50 dbSNP
rs1308971171 54 dbSNP
rs1270836349 60 dbSNP
rs936855275 62 dbSNP
rs1213870211 74 dbSNP
rs1345866998 75 dbSNP
rs1054389332 79 dbSNP
rs1487322271 82 dbSNP
rs1232456543 83 dbSNP
rs549104133 86 dbSNP
rs1258538468 87 dbSNP
rs1475003071 90 dbSNP
rs948276538 92 dbSNP
rs1163887449 98 dbSNP
rs1046647470 99 dbSNP
rs906836581 100 dbSNP
rs1366436979 102 dbSNP
rs1174969083 103 dbSNP
rs1452248437 113 dbSNP
rs1394108316 115 dbSNP
rs1178824683 129 dbSNP
rs1455282988 134 dbSNP
rs1230942491 140 dbSNP
rs767778166 145 dbSNP
rs1442934183 153 dbSNP
rs551771857 156 dbSNP
rs1208840123 161 dbSNP
rs1347154812 163 dbSNP
rs879268798 174 dbSNP
rs1310299844 175 dbSNP
rs1371688298 177 dbSNP
rs1279305360 179 dbSNP
rs1449490009 190 dbSNP
rs1361391309 191 dbSNP
rs1311530993 193 dbSNP
rs1432363026 225 dbSNP
rs1374273441 226 dbSNP
rs1359369033 244 dbSNP
rs143673628 246 dbSNP
rs1314145407 248 dbSNP
rs1176401711 250 dbSNP
rs1472972570 259 dbSNP
rs1259538813 265 dbSNP
rs1047461072 266 dbSNP
rs1208588229 267 dbSNP
rs1485396871 278 dbSNP
rs374995639 283 dbSNP
rs1315345355 299 dbSNP
rs1413726465 301 dbSNP
rs1006033460 307 dbSNP
rs753560165 308 dbSNP
rs750795200 314 dbSNP
rs565151759 328 dbSNP
rs1343089092 347 dbSNP
rs1455079425 347 dbSNP
rs996458067 353 dbSNP
rs1352112337 354 dbSNP
rs1030262349 356 dbSNP
rs1419692965 368 dbSNP
rs141914801 369 dbSNP
rs1213199809 373 dbSNP
rs1188344205 378 dbSNP
rs4145892 379 dbSNP
rs1485473588 380 dbSNP
rs924006246 381 dbSNP
rs1337471040 382 dbSNP
rs1253852347 396 dbSNP
rs570266165 399 dbSNP
rs1233283875 402 dbSNP
rs780683893 402 dbSNP
rs916710203 412 dbSNP
rs1182229811 416 dbSNP
rs1298301756 417 dbSNP
rs1379656890 418 dbSNP
rs368888025 421 dbSNP
rs878936878 424 dbSNP
rs753437068 427 dbSNP
rs1046596217 428 dbSNP
rs537900610 429 dbSNP
rs1175036045 433 dbSNP
rs1375451126 436 dbSNP
rs1465262044 441 dbSNP
rs1460909105 444 dbSNP
rs1424263878 453 dbSNP
rs569439722 465 dbSNP
rs938346834 468 dbSNP
rs1172360474 469 dbSNP
rs1398159813 473 dbSNP
rs1426846608 482 dbSNP
rs1418867839 492 dbSNP
rs537646935 494 dbSNP
rs1192035996 501 dbSNP
rs1469990137 506 dbSNP
rs1392379662 507 dbSNP
rs1047408606 518 dbSNP
rs1458445555 528 dbSNP
rs536982767 531 dbSNP
rs1237074474 535 dbSNP
rs1225809890 536 dbSNP
rs1305303403 537 dbSNP
rs1294191174 538 dbSNP
rs1304255755 545 dbSNP
rs1347187484 589 dbSNP
rs1006354331 591 dbSNP
rs1396891154 593 dbSNP
rs1299867390 607 dbSNP
rs1037460322 610 dbSNP
rs551516378 611 dbSNP
rs1196225131 615 dbSNP
rs1455603052 616 dbSNP
rs1237327783 618 dbSNP
rs1437762642 633 dbSNP
rs1195382825 635 dbSNP
rs1440725107 661 dbSNP
rs1253071730 664 dbSNP
rs1194625589 665 dbSNP
rs1250325145 675 dbSNP
rs747765927 675 dbSNP
rs150220686 678 dbSNP
rs1030251015 687 dbSNP
rs1300844328 697 dbSNP
rs1336171304 708 dbSNP
rs1308874065 725 dbSNP
rs1389661265 727 dbSNP
rs1173307355 737 dbSNP
rs1395705323 748 dbSNP
rs373196097 749 dbSNP
rs1313345387 751 dbSNP
rs1436698501 753 dbSNP
rs1373661276 754 dbSNP
rs1173297896 756 dbSNP
rs1454472025 776 dbSNP
rs778889005 805 dbSNP
rs1365977593 815 dbSNP
rs954636237 816 dbSNP
rs1418803647 818 dbSNP
rs764838039 831 dbSNP
rs1190645727 835 dbSNP
rs1486378981 836 dbSNP
rs999516260 839 dbSNP
rs1398469439 849 dbSNP
rs1209795986 854 dbSNP
rs1443789395 856 dbSNP
rs1350926635 861 dbSNP
rs1262063990 863 dbSNP
rs1327102425 865 dbSNP
rs1030980152 881 dbSNP
rs1293857381 883 dbSNP
rs958084196 892 dbSNP
rs989930198 893 dbSNP
rs745800 894 dbSNP
rs1403608966 906 dbSNP
rs1312344146 907 dbSNP
rs1401559014 918 dbSNP
rs1387428112 930 dbSNP
rs1044674 933 dbSNP
rs1217582945 935 dbSNP
rs1297806394 936 dbSNP
rs1453534463 939 dbSNP
rs571235806 943 dbSNP
rs1167796541 945 dbSNP
rs1474511268 951 dbSNP
rs532813954 958 dbSNP
rs982283298 960 dbSNP
rs1263452451 964 dbSNP
rs928200784 966 dbSNP
rs1202954713 973 dbSNP
rs750233886 975 dbSNP
rs138766434 976 dbSNP
rs1273544237 978 dbSNP
rs1297877727 982 dbSNP
rs1456241869 984 dbSNP
rs930255538 985 dbSNP
rs552603579 987 dbSNP
rs1292533468 992 dbSNP
rs1431576444 994 dbSNP
rs1253590606 997 dbSNP
rs1328233794 1001 dbSNP
rs983007586 1018 dbSNP
rs577328492 1019 dbSNP
rs1316522390 1026 dbSNP
rs1488116555 1029 dbSNP
rs746802331 1031 dbSNP
rs1328331798 1047 dbSNP
rs1460149216 1058 dbSNP
rs1189011802 1063 dbSNP
rs1263154794 1064 dbSNP
rs1168962684 1068 dbSNP
rs1475471243 1075 dbSNP
rs544796353 1081 dbSNP
rs534222109 1085 dbSNP
rs1464155992 1089 dbSNP
rs1253453169 1096 dbSNP
rs1169462375 1102 dbSNP
rs941714442 1107 dbSNP
rs1421957336 1111 dbSNP
rs3751539 1115 dbSNP
rs900290261 1121 dbSNP
rs1341619956 1128 dbSNP
rs931787747 1134 dbSNP
rs1227043658 1138 dbSNP
rs184272463 1139 dbSNP
rs370533517 1141 dbSNP
rs1394148480 1150 dbSNP
rs1434926415 1155 dbSNP
rs999421531 1165 dbSNP
rs1290725299 1166 dbSNP
rs1283266983 1169 dbSNP
rs1448286740 1176 dbSNP
rs1362669057 1184 dbSNP
rs776585022 1185 dbSNP
rs759423189 1190 dbSNP
rs1337186880 1194 dbSNP
rs1010938612 1197 dbSNP
rs1024134859 1207 dbSNP
rs1205184268 1211 dbSNP
rs1439479227 1218 dbSNP
rs758480558 1232 dbSNP
rs1290314825 1249 dbSNP
rs1321066240 1250 dbSNP
rs1348634527 1251 dbSNP
rs533581746 1253 dbSNP
rs780072407 1265 dbSNP
rs1305930041 1268 dbSNP
rs1232344991 1274 dbSNP
rs1370778607 1276 dbSNP
rs1280503787 1278 dbSNP
rs1445058970 1285 dbSNP
rs1334519168 1286 dbSNP
rs969523724 1293 dbSNP
rs115696726 1296 dbSNP
rs541331180 1299 dbSNP
rs768738102 1301 dbSNP
rs1175176235 1303 dbSNP
rs1432444933 1308 dbSNP
rs1424283523 1312 dbSNP
rs1485878376 1319 dbSNP
rs147502614 1336 dbSNP
rs763458060 1337 dbSNP
rs1471001473 1338 dbSNP
rs1231138118 1339 dbSNP
rs774423808 1346 dbSNP
rs910170822 1348 dbSNP
rs941689739 1350 dbSNP
rs973117304 1359 dbSNP
rs1486069317 1361 dbSNP
rs921666718 1365 dbSNP
rs1189163742 1369 dbSNP
rs1209083234 1370 dbSNP
rs554021078 1371 dbSNP
rs762007880 1374 dbSNP
rs1413452356 1382 dbSNP
rs1285143390 1386 dbSNP
rs1225834306 1389 dbSNP
rs1371577357 1395 dbSNP
rs931693176 1398 dbSNP
rs144080108 1409 dbSNP
rs1415910828 1411 dbSNP
rs1355587732 1412 dbSNP
rs1404101283 1421 dbSNP
rs1161852980 1422 dbSNP
rs1346285829 1423 dbSNP
rs1412318376 1431 dbSNP
rs1051529380 1433 dbSNP
rs1159332400 1434 dbSNP
rs749999952 1434 dbSNP
rs1405497688 1435 dbSNP
rs747075522 1440 dbSNP
rs879177659 1442 dbSNP
rs1296417443 1444 dbSNP
rs1357667134 1449 dbSNP
rs1185910746 1452 dbSNP
rs890255740 1453 dbSNP
rs1482926640 1458 dbSNP
rs574126871 1465 dbSNP
rs1242944336 1492 dbSNP
rs1218150405 1498 dbSNP
rs1315556081 1506 dbSNP
rs1267859097 1516 dbSNP
rs1052771971 1518 dbSNP
rs767767290 1520 dbSNP
rs1337567539 1525 dbSNP
rs118119186 1527 dbSNP
rs1289140457 1532 dbSNP
rs1225387973 1534 dbSNP
rs1432424283 1537 dbSNP
rs74017355 1543 dbSNP
rs1319630789 1546 dbSNP
rs1378127682 1548 dbSNP
rs905214478 1555 dbSNP
rs1419939546 1565 dbSNP
rs1003559221 1571 dbSNP
rs1286314969 1574 dbSNP
rs1420286996 1581 dbSNP
rs1354287469 1584 dbSNP
rs1485013224 1590 dbSNP
rs1247858073 1592 dbSNP
rs1035076317 1594 dbSNP
rs1214712706 1600 dbSNP
rs1470075201 1601 dbSNP
rs1271853012 1606 dbSNP
rs1244673621 1611 dbSNP
rs1320637763 1612 dbSNP
rs551175433 1621 dbSNP
rs559482153 1622 dbSNP
rs1283244746 1623 dbSNP
rs1296327520 1626 dbSNP
rs1441400595 1632 dbSNP
rs1259041592 1642 dbSNP
rs74017356 1647 dbSNP
rs1457315175 1654 dbSNP
rs578164814 1657 dbSNP
rs1426751464 1662 dbSNP
rs1389817857 1664 dbSNP
rs189215505 1668 dbSNP
rs1455893508 1701 dbSNP
rs1043912899 1706 dbSNP
rs1179288700 1718 dbSNP
rs1253540863 1722 dbSNP
rs1409444464 1724 dbSNP
rs1206008032 1731 dbSNP
rs1448561282 1735 dbSNP
rs1439611329 1739 dbSNP
rs555895628 1744 dbSNP
rs534280073 1745 dbSNP
rs1234540868 1751 dbSNP
rs1372961080 1759 dbSNP
rs1298915333 1767 dbSNP
rs552591377 1776 dbSNP
rs987183595 1778 dbSNP
rs748443632 1779 dbSNP
rs911676858 1785 dbSNP
rs1435610854 1786 dbSNP
rs1373985849 1790 dbSNP
rs1333692431 1796 dbSNP
rs1299775122 1800 dbSNP
rs766809048 1801 dbSNP
rs1370004840 1811 dbSNP
rs571008596 1816 dbSNP
rs1445588590 1827 dbSNP
rs1376346000 1830 dbSNP
rs1281065659 1831 dbSNP
rs1377628794 1835 dbSNP
rs144464225 1836 dbSNP
rs1254903188 1844 dbSNP
rs1052297585 1846 dbSNP
rs115033971 1849 dbSNP
rs1200511376 1850 dbSNP
rs575361060 1851 dbSNP
rs1253318611 1858 dbSNP
rs1175939433 1861 dbSNP
rs1277526473 1868 dbSNP
rs1250382785 1871 dbSNP
rs946625940 1880 dbSNP
rs1349581850 1887 dbSNP
rs755482466 1892 dbSNP
rs1239111874 1895 dbSNP
rs1317240930 1896 dbSNP
rs74017357 1897 dbSNP
rs752244521 1898 dbSNP
rs905162191 1901 dbSNP
rs1177274482 1905 dbSNP
rs1003534718 1907 dbSNP
rs1396996174 1909 dbSNP
rs1313547557 1910 dbSNP
rs148402169 1917 dbSNP
rs887216275 1918 dbSNP
rs1454649712 1921 dbSNP
rs573181525 1924 dbSNP
rs1472547511 1926 dbSNP
rs1017076571 1932 dbSNP
rs1411851055 1933 dbSNP
rs963225036 1936 dbSNP
rs545068963 1939 dbSNP
rs1028589626 1943 dbSNP
rs1486328961 1944 dbSNP
rs1253670993 1957 dbSNP
rs953015017 1959 dbSNP
rs1486096013 1960 dbSNP
rs1262268817 1964 dbSNP
rs1400671927 1966 dbSNP
rs565324248 1977 dbSNP
rs911623154 1985 dbSNP
rs1373055758 1990 dbSNP
rs1235254913 1993 dbSNP
rs1338721517 1995 dbSNP
rs34338282 1998 dbSNP
rs988308541 2013 dbSNP
rs142488594 2020 dbSNP
rs757069129 2022 dbSNP
rs1456991116 2024 dbSNP
rs1342459243 2025 dbSNP
rs1473522026 2030 dbSNP
rs1366171072 2035 dbSNP
rs1186486028 2036 dbSNP
rs946543513 2037 dbSNP
rs1249442539 2049 dbSNP
rs1044980877 2050 dbSNP
rs572388027 2052 dbSNP
rs1259149876 2054 dbSNP
rs939336960 2055 dbSNP
rs1273765777 2056 dbSNP
rs1317631350 2061 dbSNP
rs1197112490 2062 dbSNP
rs1354378389 2064 dbSNP
rs1283666623 2070 dbSNP
rs562865599 2072 dbSNP
rs1328439218 2085 dbSNP
rs887125024 2087 dbSNP
rs191668810 2089 dbSNP
rs1038865040 2100 dbSNP
rs1328567693 2111 dbSNP
rs1395644748 2111 dbSNP
rs1452684232 2113 dbSNP
rs1198317575 2131 dbSNP
rs1404093256 2140 dbSNP
rs1244994374 2141 dbSNP
rs1476515262 2147 dbSNP
rs1186231484 2149 dbSNP
rs898631231 2152 dbSNP
rs1448692321 2158 dbSNP
rs1253358921 2165 dbSNP
rs1200992137 2172 dbSNP
rs1449778997 2175 dbSNP
rs997456060 2178 dbSNP
rs1028575037 2179 dbSNP
rs1196459553 2180 dbSNP
rs530273341 2181 dbSNP
rs1008552443 2182 dbSNP
rs150961347 2184 dbSNP
rs745812172 2189 dbSNP
rs1018592611 2190 dbSNP
rs1306069623 2192 dbSNP
rs956591449 2203 dbSNP
rs769719630 2204 dbSNP
rs1022470273 2205 dbSNP
rs1387222680 2215 dbSNP
rs1371849749 2216 dbSNP
rs967906148 2222 dbSNP
rs1322313645 2223 dbSNP
rs111463749 2229 dbSNP
rs774353166 2230 dbSNP
rs1432492080 2232 dbSNP
rs926530861 2246 dbSNP
rs1395523518 2247 dbSNP
rs1174122565 2255 dbSNP
rs1476881232 2270 dbSNP
rs1246086794 2271 dbSNP
rs939243583 2283 dbSNP
rs992057638 2288 dbSNP
rs908512579 2299 dbSNP
rs1484100358 2300 dbSNP
rs940026364 2302 dbSNP
rs1249709005 2308 dbSNP
rs184249998 2310 dbSNP
rs898611633 2316 dbSNP
rs541105599 2321 dbSNP
rs1348883523 2322 dbSNP
rs772222469 2329 dbSNP
rs1217861347 2330 dbSNP
rs1344689519 2336 dbSNP
rs1280690977 2340 dbSNP
rs561623124 2343 dbSNP
rs546164654 2347 dbSNP
rs1408629309 2350 dbSNP
rs1375685177 2357 dbSNP
rs1044673 2368 dbSNP
rs1412568847 2373 dbSNP
rs1424181362 2374 dbSNP
rs1357686744 2388 dbSNP
rs1473523880 2389 dbSNP
rs1008459262 2393 dbSNP
rs1209695214 2403 dbSNP
rs1486015963 2405 dbSNP
rs1239451738 2406 dbSNP
rs1208249445 2419 dbSNP
rs1442242338 2420 dbSNP
rs1285394017 2421 dbSNP
rs1230836080 2422 dbSNP
rs538261519 2425 dbSNP
rs1288201546 2426 dbSNP
rs1448761642 2429 dbSNP
rs1304277305 2442 dbSNP
rs1445349516 2455 dbSNP
rs892096743 2468 dbSNP
rs139850173 2473 dbSNP
rs1262826481 2485 dbSNP
rs1386396885 2489 dbSNP
rs1158266119 2493 dbSNP
rs1475603205 2496 dbSNP
rs1416008955 2502 dbSNP
rs568859513 2503 dbSNP
rs1472586838 2505 dbSNP
rs1476957417 2508 dbSNP
rs561580286 2509 dbSNP
rs1463795479 2513 dbSNP
rs968232005 2517 dbSNP
rs760928833 2518 dbSNP
rs536402914 2520 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cggacguaguacuuuacGGGAGc 5'
                           ||||| 
Target 5' -----------------CCCUCc 3'
 		1 - 6
2 
miRNA  3' cggacguaguacuuuacGGGAGC---- 5'
                           ||:||     
Target 5' cucccucucauucccauCCUUCCUGGU 3'
 		3 - 29
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HCT116
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 ERX177633. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_4_11 PAR-CLIP data was present in ERX177605. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_2_7 PAR-CLIP data was present in ERX177616. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_6 PAR-CLIP data was present in ERX177626. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_4 ...

- Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research.

Article - Krell J; Stebbing J; Carissimi C; Dabrowska et al.
- Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000348370.4 | 3UTR | CCCUCCCUCUCAUUCCCAUCCUUCCUGGUACUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
STAD 0.988 0.05 1.000 0.5 3 Click to see details
PRAD -0.985 0.06 -1.000 0.5 3 Click to see details
UCEC 0.417 0.13 0.150 0.35 9 Click to see details
THCA 0.18 0.24 0.074 0.39 17 Click to see details
BRCA 0.179 0.37 0.257 0.31 6 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
KIRP -0.147 0.41 -0.300 0.31 5 Click to see details
65 hsa-miR-3616-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT064769 CCND2 cyclin D2 2 2
MIRT066953 ATXN7L3B ataxin 7 like 3B 2 8
MIRT109451 KLHL15 kelch like family member 15 2 4
MIRT110074 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 2
MIRT253112 BCL2L12 BCL2 like 12 2 2
MIRT444698 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT445748 AGO1 argonaute 1, RISC catalytic component 2 2
MIRT446453 CHST15 carbohydrate sulfotransferase 15 2 2
MIRT451956 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452332 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT453115 HOXC4 homeobox C4 2 2
MIRT455167 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT457105 DCX doublecortin 2 2
MIRT458349 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT461635 ZSWIM4 zinc finger SWIM-type containing 4 2 2
MIRT462354 BCL7B BCL tumor suppressor 7B 2 2
MIRT462750 EFNB1 ephrin B1 2 2
MIRT465801 TMEM91 transmembrane protein 91 2 2
MIRT468741 SDC2 syndecan 2 2 2
MIRT468935 RPS24 ribosomal protein S24 2 2
MIRT469166 RNF111 ring finger protein 111 2 2
MIRT469466 REEP5 receptor accessory protein 5 2 2
MIRT469605 RALGAPA2 Ral GTPase activating protein catalytic alpha subunit 2 2 2
MIRT470600 POTEM POTE ankyrin domain family member M 2 2
MIRT470630 POTEG POTE ankyrin domain family member G 2 2
MIRT471061 PIM2 Pim-2 proto-oncogene, serine/threonine kinase 2 2
MIRT473179 MLEC malectin 2 2
MIRT474351 KMT2D lysine methyltransferase 2D 2 2
MIRT477386 ENTPD7 ectonucleoside triphosphate diphosphohydrolase 7 2 2
MIRT477452 ELOVL1 ELOVL fatty acid elongase 1 2 2
MIRT479938 CBX5 chromobox 5 2 2
MIRT481633 ARF1 ADP ribosylation factor 1 2 2
MIRT485404 MIDN midnolin 2 2
MIRT486996 ZFAND2B zinc finger AN1-type containing 2B 2 2
MIRT488315 LDOC1 LDOC1, regulator of NFKB signaling 2 2
MIRT490609 SLC47A1 solute carrier family 47 member 1 2 4
MIRT490686 SSTR1 somatostatin receptor 1 2 2
MIRT490864 UPK2 uroplakin 2 2 2
MIRT492572 PPM1L protein phosphatase, Mg2+/Mn2+ dependent 1L 2 2
MIRT492687 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT492939 NEUROD2 neuronal differentiation 2 2 2
MIRT494944 IFFO2 intermediate filament family orphan 2 2 2
MIRT503137 ATG9A autophagy related 9A 2 6
MIRT507792 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT512248 ARPP19 cAMP regulated phosphoprotein 19 2 4
MIRT512585 ZNF223 zinc finger protein 223 2 2
MIRT531029 TDGF1P3 teratocarcinoma-derived growth factor 1 pseudogene 3 2 2
MIRT532014 NOX5 NADPH oxidase 5 2 2
MIRT534906 PUM2 pumilio RNA binding family member 2 2 2
MIRT555370 PPP1R12A protein phosphatase 1 regulatory subunit 12A 2 2
MIRT559524 ARHGAP12 Rho GTPase activating protein 12 2 4
MIRT560005 ZNF282 zinc finger protein 282 2 2
MIRT561566 SLC6A9 solute carrier family 6 member 9 2 2
MIRT565714 SESN3 sestrin 3 2 2
MIRT568365 AURKA aurora kinase A 2 2
MIRT570343 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT573036 GREM2 gremlin 2, DAN family BMP antagonist 2 2
MIRT629706 XKR4 XK related 4 2 2
MIRT649162 IQSEC1 IQ motif and Sec7 domain 1 2 2
MIRT660691 ANAPC1 anaphase promoting complex subunit 1 2 2
MIRT666940 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT694390 MTA1 metastasis associated 1 2 2
MIRT704066 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT704316 DCUN1D5 defective in cullin neddylation 1 domain containing 5 2 2
MIRT709848 SNX12 sorting nexin 12 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3616 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-3616-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3616-3p Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-3616-3p Gemcitabine 60750 NSC613327 approved resistant cell line (Panc1-GR4)
hsa-miR-3616-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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