pre-miRNA Information
pre-miRNA hsa-mir-640   
Genomic Coordinates chr19: 19435063 - 19435158
Synonyms MIRN640, hsa-mir-640, MIR640
Description Homo sapiens miR-640 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-640
Sequence 61| AUGAUCCAGGAACCUGCCUCU |81
Evidence Experimental
Experiments RT-PCR
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30153378 1 COSMIC
COSN23015356 12 COSMIC
COSN30513185 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs111726405 1 dbSNP
rs765622881 2 dbSNP
rs1249744889 6 dbSNP
rs752995186 12 dbSNP
rs758746736 13 dbSNP
rs918887970 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol EIF2A   
Synonyms CDA02, EIF-2A, MST089, MSTP004, MSTP089
Description eukaryotic translation initiation factor 2A
Transcript NM_032025   
Expression
Putative miRNA Targets on EIF2A
3'UTR of EIF2A
(miRNA target sites are highlighted)
>EIF2A|NM_032025|3'UTR
   1 AGATTCACGGAAAGCAAGTTGATGACCAGAAATCAGTGCAAACACATCTTCTGTTAAACCCATTGGTATACACAGAATAT
  81 TCCTGTGCCCACACTTAATGTCAATCTATAATTTTAACCATTTATCCAAGATTCTACTAAGTGTAAAATTATTTAATAAT
 161 GTCTATTAAATTGATATTTATATCTTGCATCCTATATCATGTCAATATGTGATATAGAAAAGAGATACGTGAATTTTTTA
 241 GCTAAGCTTGACAGATTGAAAGACAAGTGTCATTTTTTTTTGTAGAGGGTGATATATACCATGTAAATGAATAAAGACAT
 321 TTTAAATTTAATCACTGTTTTTATTATAAGTTCCTTAGTTCAGATATCCTTTATTAATTTATAAGATGTGTAAAACTACT
 401 TAATTCTCACAAGACTCTATGAAGTAATTCTTTTAATCTCTATTTTATAAATGAAAAAACTAAGGCCATAAATTTAAGAA
 481 ATTTGTCAGTGTCTCAAAGCTAGGAAATGGCCATCTAATCCCAGAGCCTATGCTTTAGGTCACTATGATATATACTACTC
 561 CTGTATCCTCAAGTAATGTATCATTTAGTAACACTAAGCACCCTGCTTAGTTTTCATGGATACTGCCAAATTGCCCTATC
 641 TCAAGCTTTATACTTGCACCATTTAAAGTTTTCCACACTGTTGGCAATATCAGAAGTGATAAGGCTTTGAAATGTTCGCC
 721 ACTTTGATAAAGAGGAAATGATTGTTTGTTACTGTTATATACATGTATTTTTATCAGAGATGGGTTATGTACTTTTCCAC
 801 GTTTGATAGTTGGTTGTATTTCTTTAGTGAATTGATTTTTCTTTTCCTTTGCCCATTTTTCTGTTTGGATGTTTGACTTT
 881 CTTCTTAATTTGTAAGAGTATCCTATGTAGTAACAAAATCCTTTTTTAAAAATTTTTAAAGAAAAAGTATACACACAGGA
 961 CTTTTTTTTTTCTAATTCAAAAAATACAAAGGCATGCAATGAAAATTAAGTCTGTTCCACTACCACATTTTCCAGTTTTT
1041 TGTGTATCTTTCTAATGATAGATACCATATGAGTATTCAAATATACATACACATACACTTAAAAAAAAAAGATGGCATAT
1121 ACTAACTGTTCTGTTTGGGGCTTTTTGGTGGTGGTGTTTGTTTGACAGGGTCTCACTCTGCCTCCCAGGTTGGAGTGCAC
1201 CTTGAACTCCTGGACTCAAGTGATCCTTCACCTCCTCCTTCCAAGTATCTGACACTACAGGCTTGCATCACTATGCCCAG
1281 CTTATACTCACCATAGTGGTTCTGTACTCCCTTAAAATATTCTGGAGGCCAGGCATGCTGGCTCACACCTGTAATCCCAG
1361 CACCTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGATCAACATGGTGAAACCCCATC
1441 TCTACTAAAAATACAAAAGTATCCAGGCGTGGTAGCACATACCTGTAATCCCAGCTACTTGGGAGGCTGAGGTAGGAAAA
1521 TTGTTTGAACCCGGCAGACAGAGGTTGCAGTGAGCCGACATCGTGCCATTGCACTCCAAGCCTGGGCAACAAGAGTGAAA
1601 CCGTCTCACACACACACAAAAAAAAATATTTTGGAGCTCCTTCTATATGAGTCTCTCTCTCTTATCTCTCTCAGGATGTG
1681 TGTATGTGTTTGTTTCTCTGGAAAACCCTGACTAATACAGATTAGCTATGTATTAGGTAATACATAATGCCTAATACATA
1761 ACTAATATATGGACAGGAAGTTAATAGACTGACTGTGCCACCTTAAAACTCGTATGTTGAAGCCCTAACCTCCAACGTGG
1841 TGGTATTGGGAGATGGGCCTTTTGGAAGGTAAGTGTGTTTGAATGAGGTGAAGAGGTTGGGGACTTCGTGATGGGATTAT
1921 TGTCCTTACAAGAAAAGACACCAGAGAGCTTGTTCTGTCTCTTTGGGCCATGTGAAGACATGGTGAGAAAGCAGCCAGCT
2001 GTAAGCCAGAGAGTCCTCACCAGAACCTAACCATGCTGGTGATATCCTCATCTCAGACTTCTAACCTCCAGAACTGTGAG
2081 AAAATAAACTTCTTTGTTTAAACCAAAAAAAAAAAAAAAA
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' ucUCCG--UCCAAGGACCUAGUa 5'
            ||||  ||||   ||||||| 
Target 5' ggAGGCCAAGGTGGGTGGATCAc 3'
1368 - 1390 161.00 -20.90
2
miRNA  3' ucUCC-GUCC-AAGGACCUAGUa 5'
            ||| ||||  | |||| ||| 
Target 5' ggAGGCCAGGCATGCTGGCTCAc 3'
1324 - 1346 131.00 -18.70
3
miRNA  3' ucuccGUCCAAGGACCUAGUa 5'
               ||||  |:|| |||| 
Target 5' cactaCAGG--CTTGCATCAc 3'
1253 - 1271 124.00 -10.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30109146 4 COSMIC
COSN30157077 7 COSMIC
COSN30499385 9 COSMIC
COSN31582598 32 COSMIC
COSN26465357 57 COSMIC
COSN31491974 78 COSMIC
COSN31553836 102 COSMIC
COSN19299746 105 COSMIC
COSN31573579 131 COSMIC
COSN31571103 145 COSMIC
COSN32061975 282 COSMIC
COSN26491215 479 COSMIC
COSN15859791 806 COSMIC
COSN25243080 989 COSMIC
COSN32057413 1098 COSMIC
COSN1921272 1173 COSMIC
COSN28316241 1281 COSMIC
COSN17421884 1331 COSMIC
COSN17213314 1332 COSMIC
COSN29754486 1422 COSMIC
COSN19474305 1564 COSMIC
COSN23524840 1729 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1054450414 7 dbSNP
rs762693824 9 dbSNP
rs750567464 10 dbSNP
rs1474536950 11 dbSNP
rs774894748 11 dbSNP
rs751231892 14 dbSNP
rs1424015383 20 dbSNP
rs754604496 23 dbSNP
rs1169250447 25 dbSNP
rs1334538267 27 dbSNP
rs948879861 29 dbSNP
rs944594740 32 dbSNP
rs7627786 56 dbSNP
rs1429310911 60 dbSNP
rs1045915003 66 dbSNP
rs907365484 67 dbSNP
rs1004441086 74 dbSNP
rs1234790390 75 dbSNP
rs1036605808 86 dbSNP
rs1016280007 94 dbSNP
rs1178086997 102 dbSNP
rs897711387 127 dbSNP
rs994731991 128 dbSNP
rs746092927 131 dbSNP
rs1455644967 134 dbSNP
rs547106775 150 dbSNP
rs1422998908 154 dbSNP
rs535471633 157 dbSNP
rs113868009 158 dbSNP
rs1263786079 165 dbSNP
rs1461713714 165 dbSNP
rs1223007969 166 dbSNP
rs1310641086 170 dbSNP
rs897473645 171 dbSNP
rs1224680337 175 dbSNP
rs1373133061 176 dbSNP
rs1329748310 181 dbSNP
rs894174532 183 dbSNP
rs1329339557 184 dbSNP
rs1335438561 191 dbSNP
rs1464151851 192 dbSNP
rs570401441 195 dbSNP
rs994536323 204 dbSNP
rs532894305 210 dbSNP
rs549853555 216 dbSNP
rs1418160287 218 dbSNP
rs1378176342 227 dbSNP
rs1330082743 229 dbSNP
rs1242510009 230 dbSNP
rs1371003449 244 dbSNP
rs1013072631 250 dbSNP
rs1442496205 251 dbSNP
rs1482355794 251 dbSNP
rs1216698062 254 dbSNP
rs918150668 255 dbSNP
rs985881060 257 dbSNP
rs1307480789 260 dbSNP
rs971559525 265 dbSNP
rs1018748159 266 dbSNP
rs1032272190 273 dbSNP
rs1393789158 273 dbSNP
rs957584228 273 dbSNP
rs1288944018 274 dbSNP
rs1452549833 276 dbSNP
rs1215503738 282 dbSNP
rs966284498 288 dbSNP
rs553704464 289 dbSNP
rs1445058819 294 dbSNP
rs1384528219 304 dbSNP
rs990423305 307 dbSNP
rs1430252929 309 dbSNP
rs1275623333 310 dbSNP
rs14434 313 dbSNP
rs1225150077 317 dbSNP
rs199516831 317 dbSNP
rs766416449 317 dbSNP
rs747083981 330 dbSNP
rs924546674 331 dbSNP
rs987287063 332 dbSNP
rs912608479 335 dbSNP
rs940107450 336 dbSNP
rs1295609013 342 dbSNP
rs1036176109 345 dbSNP
rs1337921242 349 dbSNP
rs535686595 354 dbSNP
rs1425046974 366 dbSNP
rs1364665180 373 dbSNP
rs1161249615 374 dbSNP
rs187348281 378 dbSNP
rs1196882895 379 dbSNP
rs375996691 389 dbSNP
rs1244879058 390 dbSNP
rs565860010 391 dbSNP
rs990141896 404 dbSNP
rs1261302424 408 dbSNP
rs1201941833 411 dbSNP
rs915991317 415 dbSNP
rs755169666 416 dbSNP
rs1267058771 420 dbSNP
rs190644335 427 dbSNP
rs1421469746 431 dbSNP
rs771272848 431 dbSNP
rs1049001943 448 dbSNP
rs1252447685 450 dbSNP
rs1226053329 454 dbSNP
rs7638500 463 dbSNP
rs907347574 473 dbSNP
rs779334666 476 dbSNP
rs1045818650 478 dbSNP
rs940208601 489 dbSNP
rs1462532911 493 dbSNP
rs1321283920 505 dbSNP
rs1321072183 510 dbSNP
rs1392970844 514 dbSNP
rs577130353 518 dbSNP
rs1167336450 520 dbSNP
rs1465159538 530 dbSNP
rs1421503666 537 dbSNP
rs1178712823 539 dbSNP
rs999027791 542 dbSNP
rs1432195975 543 dbSNP
rs1031824280 546 dbSNP
rs545899486 550 dbSNP
rs1439986532 552 dbSNP
rs893335375 559 dbSNP
rs1338830524 561 dbSNP
rs1011825322 563 dbSNP
rs1456827172 574 dbSNP
rs1264419540 577 dbSNP
rs1223618928 582 dbSNP
rs1218431204 584 dbSNP
rs1322374655 592 dbSNP
rs1028618929 603 dbSNP
rs183173051 605 dbSNP
rs1336191978 613 dbSNP
rs1327956977 618 dbSNP
rs898776453 626 dbSNP
rs1408236537 632 dbSNP
rs986783086 637 dbSNP
rs576118905 643 dbSNP
rs1470365296 644 dbSNP
rs1273999814 645 dbSNP
rs1424719499 656 dbSNP
rs1171097267 661 dbSNP
rs546913021 666 dbSNP
rs542053323 673 dbSNP
rs557955699 682 dbSNP
rs1027286031 688 dbSNP
rs749279883 689 dbSNP
rs1438332924 696 dbSNP
rs771696822 699 dbSNP
rs770591315 700 dbSNP
rs961467030 701 dbSNP
rs1203717842 705 dbSNP
rs774219572 716 dbSNP
rs561926158 718 dbSNP
rs745452993 719 dbSNP
rs1276056492 726 dbSNP
rs1193724573 731 dbSNP
rs527999354 734 dbSNP
rs1350953910 742 dbSNP
rs1308193274 743 dbSNP
rs973258790 744 dbSNP
rs1384860846 745 dbSNP
rs888793752 754 dbSNP
rs771760611 761 dbSNP
rs930518696 763 dbSNP
rs541668686 769 dbSNP
rs1192724764 774 dbSNP
rs965887445 776 dbSNP
rs563927776 778 dbSNP
rs1385978198 785 dbSNP
rs915797993 788 dbSNP
rs948660666 793 dbSNP
rs868332383 801 dbSNP
rs1045381300 802 dbSNP
rs1184817120 807 dbSNP
rs1160945767 821 dbSNP
rs1235176966 832 dbSNP
rs977686809 835 dbSNP
rs34217437 849 dbSNP
rs1447191380 858 dbSNP
rs1284911436 871 dbSNP
rs1214167242 881 dbSNP
rs1361400593 885 dbSNP
rs532990337 893 dbSNP
rs761684936 897 dbSNP
rs1359216957 898 dbSNP
rs1282453773 903 dbSNP
rs1433044091 911 dbSNP
rs990027326 921 dbSNP
rs1341327406 922 dbSNP
rs915876635 927 dbSNP
rs549793879 928 dbSNP
rs1294341276 933 dbSNP
rs1357591842 942 dbSNP
rs1011712309 945 dbSNP
rs565541098 948 dbSNP
rs1283820097 955 dbSNP
rs1351414888 957 dbSNP
rs1008919993 962 dbSNP
rs890013633 962 dbSNP
rs1206993617 973 dbSNP
rs1288040022 975 dbSNP
rs1487297854 976 dbSNP
rs4518155 977 dbSNP
rs1215615382 979 dbSNP
rs569798697 986 dbSNP
rs1019600131 987 dbSNP
rs928742572 996 dbSNP
rs9830228 1000 dbSNP
rs1184885978 1008 dbSNP
rs1026989920 1017 dbSNP
rs1275079692 1025 dbSNP
rs777088608 1026 dbSNP
rs984561689 1027 dbSNP
rs1398315768 1034 dbSNP
rs1037645350 1036 dbSNP
rs1347658637 1040 dbSNP
rs915765286 1047 dbSNP
rs549219532 1056 dbSNP
rs948644408 1062 dbSNP
rs1401592386 1064 dbSNP
rs1278630833 1066 dbSNP
rs1411026858 1068 dbSNP
rs187643928 1069 dbSNP
rs1422201115 1079 dbSNP
rs920109688 1083 dbSNP
rs1159973855 1095 dbSNP
rs1481185303 1097 dbSNP
rs928310600 1098 dbSNP
rs1487422681 1101 dbSNP
rs550982988 1101 dbSNP
rs934359157 1108 dbSNP
rs2903961 1111 dbSNP
rs1052773635 1113 dbSNP
rs1457267421 1119 dbSNP
rs931519694 1124 dbSNP
rs1133494 1125 dbSNP
rs1377579825 1127 dbSNP
rs1216903005 1132 dbSNP
rs888759530 1137 dbSNP
rs1049898103 1145 dbSNP
rs889981439 1146 dbSNP
rs765467267 1151 dbSNP
rs879070241 1152 dbSNP
rs1333693770 1154 dbSNP
rs1008472487 1155 dbSNP
rs1041734102 1161 dbSNP
rs200765501 1165 dbSNP
rs1040111001 1167 dbSNP
rs1400241944 1173 dbSNP
rs1328659333 1175 dbSNP
rs901620592 1191 dbSNP
rs1336623301 1192 dbSNP
rs1359377302 1194 dbSNP
rs1241249637 1196 dbSNP
rs1431109395 1203 dbSNP
rs1380371074 1204 dbSNP
rs1294598517 1208 dbSNP
rs73001357 1220 dbSNP
rs750809026 1232 dbSNP
rs1351420178 1246 dbSNP
rs763297811 1255 dbSNP
rs1438958250 1259 dbSNP
rs1236323251 1263 dbSNP
rs957207731 1271 dbSNP
rs1239252903 1274 dbSNP
rs1462755912 1286 dbSNP
rs1280975446 1289 dbSNP
rs766612621 1294 dbSNP
rs1011426328 1303 dbSNP
rs1209598834 1309 dbSNP
rs1022861775 1315 dbSNP
rs1309541619 1329 dbSNP
rs1026957380 1336 dbSNP
rs1376771985 1345 dbSNP
rs1198551790 1358 dbSNP
rs1307800978 1359 dbSNP
rs1255007425 1361 dbSNP
rs192572270 1365 dbSNP
rs970020164 1366 dbSNP
rs1464198643 1369 dbSNP
rs1012311479 1371 dbSNP
rs1378019712 1374 dbSNP
rs1159006293 1378 dbSNP
rs140720861 1379 dbSNP
rs970327431 1384 dbSNP
rs928733846 1388 dbSNP
rs1445168334 1391 dbSNP
rs556123655 1396 dbSNP
rs972850437 1399 dbSNP
rs144607574 1404 dbSNP
rs1353512463 1407 dbSNP
rs947101569 1421 dbSNP
rs1049540521 1422 dbSNP
rs931486711 1456 dbSNP
rs535528136 1457 dbSNP
rs1393845351 1459 dbSNP
rs755079621 1469 dbSNP
rs1449368634 1470 dbSNP
rs1399023925 1471 dbSNP
rs1329572346 1484 dbSNP
rs781454615 1490 dbSNP
rs1376180943 1494 dbSNP
rs943042306 1506 dbSNP
rs753781353 1512 dbSNP
rs1441766162 1520 dbSNP
rs1304017539 1521 dbSNP
rs1313922398 1522 dbSNP
rs555700455 1526 dbSNP
rs1422206389 1532 dbSNP
rs1265594713 1533 dbSNP
rs1194587098 1534 dbSNP
rs1488089980 1535 dbSNP
rs1255251379 1536 dbSNP
rs184285810 1538 dbSNP
rs757233520 1544 dbSNP
rs1052885515 1547 dbSNP
rs1041227258 1549 dbSNP
rs892955242 1550 dbSNP
rs765868613 1557 dbSNP
rs1235989719 1558 dbSNP
rs994399433 1561 dbSNP
rs1278279985 1563 dbSNP
rs1217588034 1564 dbSNP
rs1337991601 1565 dbSNP
rs1304706633 1575 dbSNP
rs1193749441 1591 dbSNP
rs1011395343 1603 dbSNP
rs1022830671 1604 dbSNP
rs113119063 1607 dbSNP
rs3086798 1607 dbSNP
rs542802141 1607 dbSNP
rs775056640 1607 dbSNP
rs1425784713 1609 dbSNP
rs1024177424 1612 dbSNP
rs969990387 1612 dbSNP
rs1421823541 1615 dbSNP
rs369645211 1616 dbSNP
rs66935400 1616 dbSNP
rs761383198 1616 dbSNP
rs776605912 1616 dbSNP
rs199687978 1617 dbSNP
rs1208501827 1618 dbSNP
rs1491028440 1618 dbSNP
rs78246755 1618 dbSNP
rs970838314 1618 dbSNP
rs28578086 1620 dbSNP
rs564839058 1622 dbSNP
rs1284877482 1636 dbSNP
rs1399879450 1637 dbSNP
rs1462002995 1644 dbSNP
rs1233688222 1645 dbSNP
rs778503986 1646 dbSNP
rs1295410393 1650 dbSNP
rs796710208 1652 dbSNP
rs1385074041 1661 dbSNP
rs1036067305 1665 dbSNP
rs578246069 1676 dbSNP
rs1465207582 1677 dbSNP
rs1220257145 1683 dbSNP
rs988750918 1683 dbSNP
rs745669955 1685 dbSNP
rs920030522 1687 dbSNP
rs968411949 1689 dbSNP
rs1266770808 1691 dbSNP
rs1239360963 1693 dbSNP
rs952843184 1697 dbSNP
rs1487223948 1698 dbSNP
rs1197452806 1708 dbSNP
rs985660191 1710 dbSNP
rs771819683 1713 dbSNP
rs944246064 1714 dbSNP
rs779656997 1715 dbSNP
rs910928701 1717 dbSNP
rs1343894108 1719 dbSNP
rs943816753 1726 dbSNP
rs753491019 1731 dbSNP
rs746700729 1734 dbSNP
rs977037630 1742 dbSNP
rs754592838 1744 dbSNP
rs922899845 1745 dbSNP
rs1485006992 1746 dbSNP
rs1263073776 1755 dbSNP
rs1377516449 1759 dbSNP
rs1478984995 1773 dbSNP
rs764858811 1787 dbSNP
rs1374668140 1790 dbSNP
rs1336276532 1798 dbSNP
rs1415204684 1799 dbSNP
rs768110272 1806 dbSNP
rs1171151508 1812 dbSNP
rs548654630 1813 dbSNP
rs892924607 1824 dbSNP
rs762165406 1831 dbSNP
rs930217758 1832 dbSNP
rs947221725 1835 dbSNP
rs151337458 1837 dbSNP
rs1438389932 1841 dbSNP
rs905704683 1844 dbSNP
rs1348127546 1847 dbSNP
rs888443184 1856 dbSNP
rs948015616 1861 dbSNP
rs1253695135 1869 dbSNP
rs563243673 1880 dbSNP
rs1218517274 1891 dbSNP
rs1354228679 1892 dbSNP
rs74970637 1893 dbSNP
rs187608491 1898 dbSNP
rs1003647375 1908 dbSNP
rs897128112 1909 dbSNP
rs1448897708 1914 dbSNP
rs1340090613 1922 dbSNP
rs1276136135 1930 dbSNP
rs891662581 1938 dbSNP
rs1010154914 1943 dbSNP
rs1361496813 1946 dbSNP
rs1158453478 1953 dbSNP
rs994208361 1956 dbSNP
rs1027063286 1962 dbSNP
rs1163303842 1964 dbSNP
rs2626 1970 dbSNP
rs985503763 1977 dbSNP
rs1319357366 1982 dbSNP
rs140591420 1989 dbSNP
rs1195327512 1995 dbSNP
rs985542420 2001 dbSNP
rs1018418458 2002 dbSNP
rs1453221314 2008 dbSNP
rs73001358 2008 dbSNP
rs571543680 2010 dbSNP
rs1355658993 2013 dbSNP
rs924247108 2017 dbSNP
rs1220652255 2019 dbSNP
rs910101153 2028 dbSNP
rs538552519 2035 dbSNP
rs1398586042 2054 dbSNP
rs1183753781 2059 dbSNP
rs536926601 2065 dbSNP
rs988475539 2069 dbSNP
rs150465172 2078 dbSNP
rs939418895 2089 dbSNP
rs947106837 2092 dbSNP
rs1159974139 2093 dbSNP
rs1477927473 2106 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 GSM1084040. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep1 HITS-CLIP data was present in GSM1084042. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep2 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ucUCCGUCCAAGGACCUAGUa 5'
            |||::||    ||||||| 
Target 5' caAGGUGGG----UGGAUCAc 3'
1 - 17
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 GSM1084040
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep1
Location of target site ENST00000460851.1 | 3UTR | AGGCCAAGGUGGGUGGAUCACCUGAGGUCAGGAGUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084042
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep2
Location of target site ENST00000460851.1 | 3UTR | CAAGGUGGGUGGAUCACCUGAGGUCAGGAGUUCAAG
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
GSE32688 Pancreatic cancer 0.601 1.4e-4 0.602 1.3e-4 32 Click to see details
GSE28544 Breast cancer -0.533 3.7e-3 -0.402 2.6e-2 24 Click to see details
GSE28260 Renal cortex and medulla 0.552 2.5e-2 0.342 1.3e-1 13 Click to see details
GSE27834 Pluripotent stem cells 0.466 3.4e-2 0.432 4.7e-2 16 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.353 6.3e-2 0.021 4.6e-1 20 Click to see details
GSE19783 ER+ ER+ breast cancer 0.307 9.4e-2 0.349 6.6e-2 20 Click to see details
GSE26953 Aortic valvular endothelial cells -0.259 1.1e-1 -0.359 4.2e-2 24 Click to see details
GSE19350 CNS germ cell tumors -0.335 1.4e-1 0.084 4.0e-1 12 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.209 1.6e-1 -0.252 1.1e-1 25 Click to see details
GSE17306 Multiple myeloma -0.12 2.1e-1 -0.078 3.0e-1 49 Click to see details
GSE21687 Ependynoma primary tumors 0.089 2.4e-1 0.090 2.4e-1 64 Click to see details
GSE42095 Differentiated embryonic stem cells 0.149 2.5e-1 0.000 5.0e-1 23 Click to see details
GSE19783 ER- ER- breast cancer -0.052 3.2e-1 -0.111 1.7e-1 79 Click to see details
GSE35602 Colorectal cancer stromal tissue -0.094 3.3e-1 -0.012 4.8e-1 25 Click to see details
GSE21849 B cell lymphoma -0.06 3.8e-1 0.178 1.8e-1 29 Click to see details
GSE38226 Liver fibrosis 0.06 4.0e-1 -0.050 4.1e-1 21 Click to see details
GSE14794 Lymphoblastoid cells 0.018 4.3e-1 -0.057 3.0e-1 90 Click to see details
GSE19536 Breast cancer 0.016 4.4e-1 0.025 4.0e-1 100 Click to see details
GSE19536 Breast cancer 0.016 4.4e-1 0.025 4.0e-1 100 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
194 hsa-miR-640 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT097121 TNPO1 transportin 1 2 2
MIRT115090 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 4
MIRT204603 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 8
MIRT204634 MOB4 MOB family member 4, phocein 2 8
MIRT344451 MTRNR2L1 MT-RNR2-like 1 2 2
MIRT405772 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT445876 SENP6 SUMO1/sentrin specific peptidase 6 2 2
MIRT497418 FAM46A family with sequence similarity 46 member A 2 2
MIRT504394 HMX2 H6 family homeobox 2 2 4
MIRT504691 SLCO2B1 solute carrier organic anion transporter family member 2B1 2 8
MIRT512386 MTRNR2L3 MT-RNR2-like 3 2 6
MIRT513003 MAN1A2 mannosidase alpha class 1A member 2 2 2
MIRT513084 USP9X ubiquitin specific peptidase 9, X-linked 2 2
MIRT519122 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) 2 2
MIRT523836 F2RL1 F2R like trypsin receptor 1 2 2
MIRT565356 TMCC1 transmembrane and coiled-coil domain family 1 2 2
MIRT575895 Dis3 DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease 2 3
MIRT576894 Poteg POTE ankyrin domain family, member G 2 2
MIRT613780 RPS6 ribosomal protein S6 2 2
MIRT613934 POLR3A RNA polymerase III subunit A 2 2
MIRT614348 LOH12CR1 BLOC-1 related complex subunit 5 2 2
MIRT614534 NOA1 nitric oxide associated 1 2 2
MIRT617019 ZBTB8B zinc finger and BTB domain containing 8B 2 2
MIRT618247 MANEAL mannosidase endo-alpha like 2 2
MIRT619051 TTC4 tetratricopeptide repeat domain 4 2 2
MIRT619442 ZNF517 zinc finger protein 517 2 2
MIRT619723 FPR2 formyl peptide receptor 2 2 2
MIRT620179 TRIM72 tripartite motif containing 72 2 2
MIRT620370 ANKRD62 ankyrin repeat domain 62 2 2
MIRT621263 RTN2 reticulon 2 2 2
MIRT621463 APOH apolipoprotein H 2 2
MIRT621571 ZBTB43 zinc finger and BTB domain containing 43 2 2
MIRT621683 TSPYL1 TSPY like 1 2 2
MIRT622866 PDE7A phosphodiesterase 7A 2 2
MIRT624669 ARHGEF39 Rho guanine nucleotide exchange factor 39 2 2
MIRT625607 ZNF84 zinc finger protein 84 2 2
MIRT626111 IL23R interleukin 23 receptor 2 2
MIRT628380 CACNB2 calcium voltage-gated channel auxiliary subunit beta 2 2 2
MIRT628553 MELK maternal embryonic leucine zipper kinase 2 2
MIRT628671 C2orf72 chromosome 2 open reading frame 72 2 2
MIRT628747 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT628776 TMEM154 transmembrane protein 154 2 2
MIRT628918 ZNF430 zinc finger protein 430 2 2
MIRT629174 ALDOA aldolase, fructose-bisphosphate A 2 2
MIRT629209 C12orf66 chromosome 12 open reading frame 66 2 2
MIRT629267 SLC5A8 solute carrier family 5 member 8 2 2
MIRT629498 AS3MT arsenite methyltransferase 2 2
MIRT629665 USP1 ubiquitin specific peptidase 1 2 2
MIRT629760 STK25 serine/threonine kinase 25 2 2
MIRT630899 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT631105 SLC15A2 solute carrier family 15 member 2 2 2
MIRT631112 ATCAY ATCAY, caytaxin 2 2
MIRT631450 DLEU1 deleted in lymphocytic leukemia 1 (non-protein coding) 2 2
MIRT631505 FFAR4 free fatty acid receptor 4 2 2
MIRT631580 ITGAL integrin subunit alpha L 2 2
MIRT631836 CMBL carboxymethylenebutenolidase homolog 2 2
MIRT632342 SWSAP1 SWIM-type zinc finger 7 associated protein 1 2 2
MIRT633214 ZNF584 zinc finger protein 584 2 2
MIRT633223 ZNF43 zinc finger protein 43 2 2
MIRT633480 ARIH2OS ariadne RBR E3 ubiquitin protein ligase 2 opposite strand 2 2
MIRT633511 LRRC27 leucine rich repeat containing 27 2 2
MIRT633615 CWF19L1 CWF19 like 1, cell cycle control (S. pombe) 2 2
MIRT633652 SLC28A1 solute carrier family 28 member 1 2 2
MIRT633677 ZNF576 zinc finger protein 576 2 2
MIRT634196 TMOD2 tropomodulin 2 2 4
MIRT634388 PLSCR1 phospholipid scramblase 1 2 2
MIRT635817 OPA3 OPA3, outer mitochondrial membrane lipid metabolism regulator 2 2
MIRT635962 TTC31 tetratricopeptide repeat domain 31 2 2
MIRT636114 YPEL1 yippee like 1 2 2
MIRT636164 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT636768 CLUAP1 clusterin associated protein 1 2 2
MIRT637092 CXorf23 BCLAF1 and THRAP3 family member 3 2 2
MIRT637316 FAM9B family with sequence similarity 9 member B 2 2
MIRT637540 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT637628 ZNF431 zinc finger protein 431 2 2
MIRT637826 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT637945 IVD isovaleryl-CoA dehydrogenase 2 2
MIRT637968 IRF1 interferon regulatory factor 1 2 2
MIRT638321 RNF11 ring finger protein 11 2 2
MIRT638386 RAB11FIP1 RAB11 family interacting protein 1 2 2
MIRT639244 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT642608 APOPT1 apoptogenic 1, mitochondrial 2 2
MIRT642793 SLC1A5 solute carrier family 1 member 5 2 2
MIRT643847 LACTB lactamase beta 2 4
MIRT644705 ZNF321P zinc finger protein 321, pseudogene 2 2
MIRT645148 DIS3 DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease 2 3
MIRT646671 CCDC69 coiled-coil domain containing 69 2 2
MIRT647780 ASB8 ankyrin repeat and SOCS box containing 8 2 2
MIRT648554 WDR92 WD repeat domain 92 2 2
MIRT648990 MRPL49 mitochondrial ribosomal protein L49 2 2
MIRT649099 KCNMB1 potassium calcium-activated channel subfamily M regulatory beta subunit 1 2 2
MIRT650141 ZNF426 zinc finger protein 426 2 2
MIRT650791 GSR glutathione-disulfide reductase 2 2
MIRT654967 PLEKHA2 pleckstrin homology domain containing A2 2 2
MIRT655099 PHLDA3 pleckstrin homology like domain family A member 3 2 2
MIRT655516 PAG1 phosphoprotein membrane anchor with glycosphingolipid microdomains 1 2 2
MIRT656289 METTL14 methyltransferase like 14 2 2
MIRT656497 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT657074 JPH2 junctophilin 2 2 2
MIRT657314 HOOK3 hook microtubule tethering protein 3 2 2
MIRT657419 HIF1AN hypoxia inducible factor 1 alpha subunit inhibitor 2 4
MIRT659032 DHTKD1 dehydrogenase E1 and transketolase domain containing 1 2 2
MIRT659535 CHCHD5 coiled-coil-helix-coiled-coil-helix domain containing 5 2 2
MIRT661532 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT662029 FUT2 fucosyltransferase 2 2 2
MIRT663206 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT663357 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT663557 CCR6 C-C motif chemokine receptor 6 2 2
MIRT663650 POLM DNA polymerase mu 2 2
MIRT663694 ABHD17B abhydrolase domain containing 17B 2 2
MIRT664370 CYB5A cytochrome b5 type A 2 2
MIRT664783 LIAS lipoic acid synthetase 2 4
MIRT665561 TXNL1 thioredoxin like 1 2 2
MIRT665950 TAOK1 TAO kinase 1 2 2
MIRT667338 MSANTD3 Myb/SANT DNA binding domain containing 3 2 2
MIRT667804 ITIH5 inter-alpha-trypsin inhibitor heavy chain family member 5 2 2
MIRT668804 CYP20A1 cytochrome P450 family 20 subfamily A member 1 2 2
MIRT669470 ARPC2 actin related protein 2/3 complex subunit 2 2 2
MIRT669599 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT669806 STOML1 stomatin like 1 2 2
MIRT669944 FBXL2 F-box and leucine rich repeat protein 2 2 2
MIRT670292 RBBP4 RB binding protein 4, chromatin remodeling factor 2 2
MIRT670381 EMP2 epithelial membrane protein 2 2 2
MIRT670481 DCUN1D2 defective in cullin neddylation 1 domain containing 2 2 2
MIRT670531 KIF1C kinesin family member 1C 2 4
MIRT670565 GLTP glycolipid transfer protein 2 2
MIRT670603 NPHP1 nephrocystin 1 2 2
MIRT670880 CYTIP cytohesin 1 interacting protein 2 2
MIRT670931 LIPG lipase G, endothelial type 2 2
MIRT671261 MTRNR2L5 MT-RNR2-like 5 2 2
MIRT671794 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 2 2
MIRT671897 GBP4 guanylate binding protein 4 2 2
MIRT672000 SLC35F6 solute carrier family 35 member F6 2 4
MIRT672074 KIR3DX1 killer cell immunoglobulin like receptor, three Ig domains X1 2 2
MIRT672319 C9orf3 chromosome 9 open reading frame 3 2 2
MIRT672853 C22orf29 retrotransposon Gag like 10 2 2
MIRT673395 WNT7B Wnt family member 7B 2 2
MIRT673537 DEGS1 delta 4-desaturase, sphingolipid 1 2 2
MIRT674285 ZNF724P zinc finger protein 724 2 2
MIRT674494 TIRAP TIR domain containing adaptor protein 2 2
MIRT675460 NUBPL nucleotide binding protein like 2 2
MIRT675569 TRIP11 thyroid hormone receptor interactor 11 2 2
MIRT676068 TIMM50 translocase of inner mitochondrial membrane 50 2 2
MIRT676254 PBOV1 prostate and breast cancer overexpressed 1 2 2
MIRT676377 SEC24D SEC24 homolog D, COPII coat complex component 2 2
MIRT676758 SNX2 sorting nexin 2 2 2
MIRT676773 NPHS1 NPHS1, nephrin 2 2
MIRT676874 ENSA endosulfine alpha 2 2
MIRT676918 KLHDC8A kelch domain containing 8A 2 2
MIRT676944 S1PR3 sphingosine-1-phosphate receptor 3 2 2
MIRT676957 HFE hemochromatosis 2 2
MIRT676967 RNF19B ring finger protein 19B 2 2
MIRT676972 ZNF708 zinc finger protein 708 2 2
MIRT677042 ZNF34 zinc finger protein 34 2 2
MIRT677070 VMAC vimentin type intermediate filament associated coiled-coil protein 2 2
MIRT677093 MFSD11 major facilitator superfamily domain containing 11 2 4
MIRT677134 P2RX7 purinergic receptor P2X 7 2 2
MIRT677179 ZNF786 zinc finger protein 786 2 2
MIRT677228 C15orf40 chromosome 15 open reading frame 40 2 2
MIRT677320 PIGO phosphatidylinositol glycan anchor biosynthesis class O 2 2
MIRT677455 PDLIM3 PDZ and LIM domain 3 2 2
MIRT677809 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT677937 ZNF519 zinc finger protein 519 2 2
MIRT678063 UBN2 ubinuclein 2 2 4
MIRT678072 EIF2A eukaryotic translation initiation factor 2A 2 2
MIRT678252 FXN frataxin 2 2
MIRT678315 FBLIM1 filamin binding LIM protein 1 2 2
MIRT678367 XIAP X-linked inhibitor of apoptosis 2 4
MIRT678372 RNF115 ring finger protein 115 2 2
MIRT678410 ANKRD36 ankyrin repeat domain 36 2 2
MIRT678518 ZNF347 zinc finger protein 347 2 2
MIRT678566 CDK4 cyclin dependent kinase 4 2 2
MIRT678580 PPP1R3B protein phosphatase 1 regulatory subunit 3B 2 2
MIRT678820 PDE6A phosphodiesterase 6A 2 2
MIRT678917 XPOT exportin for tRNA 2 2
MIRT679217 MAN2A2 mannosidase alpha class 2A member 2 2 2
MIRT679437 C19orf52 translocase of inner mitochondrial membrane 29 2 2
MIRT679595 HILPDA hypoxia inducible lipid droplet associated 2 2
MIRT679755 TLR6 toll like receptor 6 2 2
MIRT679800 APOBEC3A apolipoprotein B mRNA editing enzyme catalytic subunit 3A 2 2
MIRT680057 CD96 CD96 molecule 2 2
MIRT680116 CCDC30 coiled-coil domain containing 30 2 4
MIRT680181 ZNF554 zinc finger protein 554 2 2
MIRT680439 WDR12 WD repeat domain 12 2 2
MIRT680789 ZNF578 zinc finger protein 578 2 2
MIRT692464 APEX2 apurinic/apyrimidinic endodeoxyribonuclease 2 2 2
MIRT702952 HIP1 huntingtin interacting protein 1 2 2
MIRT706016 ZSCAN2 zinc finger and SCAN domain containing 2 2 2
MIRT706032 F2R coagulation factor II thrombin receptor 2 2
MIRT706135 MTRNR2L10 MT-RNR2-like 10 2 2
MIRT706394 HAS2 hyaluronan synthase 2 2 2
MIRT713293 DCP2 decapping mRNA 2 2 2
MIRT716583 BRAP BRCA1 associated protein 2 2
MIRT720433 C19orf47 chromosome 19 open reading frame 47 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-640 Paclitaxel 36314 NSC125973 approved resistant High Ovarian Cancer tissue and cell line (SKOV3)
hsa-miR-640 Cetuximab resistant High Colon Cancer cell line
hsa-miR-640 Trametinib 11707110 NSC758246 approved resistant High Melanoma cell line (WM266) (1uM)
hsa-miR-640 Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (WM266) (1uM)
hsa-miR-640 Mitoxantrone 4212 NSC279836 approved resistant High Breast Cancer cell line (BT-20, BT-474, BT-549, CAMA-1, HCC1143, HCC1395, HCC1569, HCC1806, HCC-1937, HCC1954, HCC202, HCC38, HCC70, Hs578T, MCF-7, MDA-MB-175VII, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-436, MDA-MB-468, SKBR3, T47D, UACC812, EVSA-T, MPE-600 , SK-BR-
hsa-miR-640 Sorafenib 216239 NSC747971 approved sensitive Low Clear Cell Renal Cell Carcinoma cell line (786-O)
hsa-mir-640 Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-mir-640 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-640 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-640 Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-640 Paclitaxel 36314 NSC125973 approved sensitive cell line (SKOV3)
hsa-miR-640 Tamoxifen 2733525 NSC180973 approved sensitive cell line (TamR8)
hsa-miR-640 Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-640 Cisplatin 5460033 NSC119875 approved sensitive cell line (IGROV-1)
hsa-miR-640 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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