miRTarBase - #MIRT479073


—
pre-miRNA Information
pre-miRNA hsa-mir-4640   
Genomic Coordinates chr6: 30890883 - 30890972
Description Homo sapiens miR-4640 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4640-5p
Sequence 9| UGGGCCAGGGAGCAGCUGGUGGG |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1392105945 7 dbSNP
rs939712790 9 dbSNP
rs762825841 15 dbSNP
rs71552023 20 dbSNP
rs1305909531 21 dbSNP
rs750017220 21 dbSNP
rs1375436057 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B32FZJ miR-4640 Safety Biomarker (SAF) Clinical/Experimental Data Expression lower Urine Quantitative polymerase chain reaction
Gene Information
Gene Symbol CNNM4   
Synonyms ACDP4
Description cyclin and CBS domain divalent metal cation transport mediator 4
Transcript NM_020184   
Expression
Putative miRNA Targets on CNNM4
3'UTR of CNNM4
(miRNA target sites are highlighted)		 
>CNNM4|NM_020184|3'UTR
   1 CAGGAGGGCCCGGGGCCCCCTGCCCACCCTGCGGGGGCCTCCCCAGTGGGCCCACATGAAGAGAGGGAACCTGTTAGTCC
  81 AGAAAGGATACGGATAGATAGCCTGTCTGACTGAACAGCCAGATGGCCCCCAGCCTATGGGGGATCTGGCCTCTGCCAGG
 161 GACCTCTGAGTAGCTCTGAGGTGGCACTGTCCAGCCCTGGATAGGGGGGGCAGTGGGCCAGCTACCGTAAGCAAAGGCTG
 241 TTTTTTACTGAGAGAATTTCTAAAGTAGGCTCATCACTTTTTTTTAAATATCATTTTGGGAAGGGAAGACAGGGTTAAGG
 321 AACTTTATTTAAAAAAAAAATATTTTTTTCCTAAAAACTATAAAAGAGGAAGGGTTTCTTGTCCCGGGAAGCAACGGACA
 401 TAATCTGTTCCCAGCCATGGCCTTCCAGCTTGTGTCCCTGATTCAGGGAGCTCTCCCTTCCTCCTCCTCCTCCTCCTCCG
 481 GAGGTGGGATCCCAGAGCCTGCCAGTGGAGGCTTATCTGTTGGGAGGAAGACAGCTCTTCACAGAAGCAAAGAACAAAAT
 561 GGCATGGAGATCAGCTGCCTGAGCACCTGCGCTGTAGCTTATCTGACAACGCTGAGGCCACGAGCTCCTGGGTAGCTGTG
 641 ATCAGGGACATGATAATCTGAGCTATGCAGAGGAGCACATCTGTTGTCAACTGCTGTACCCAGAAATCTAGAACTCTGCC
 721 GACAGCCTCTCCTGGTGAGTCGGGACTCAGCTGAGGACACATCCCCACCCTGCCTCCCATCTGGCCCTTTGGACAACTGG
 801 CCCTTTGTGACAGGGCTGACTCAAGTGTTAGGCAGGGTCTCAGGCCTTTGATTGCTCACCCCTGCTCCCCAGGCCCTGCC
 881 CTCACTTTTACCAAAGGTTCTCCCTCGGCGGGAGGGCATCTGTGTTGGAGGTGATTTGTCTGGGTTCTTCCTTTTGGTTC
 961 CAGAAGGAACTGTCAGTCATCAGCATCTGCGTTGTTAGCAGTCAGTACCACCCCCGCCCCACAATGACAGTCAAGGCTGA
1041 CTTGTTGACTGAAGCCTTTTTCCCAGACCCCTTATTTCGAATCCCCAAGCTTCAGTCCCTCTTGGGGGTGGAGACAAGAG
1121 GACATGTGGGAAGCCACGGAAGCAGGTTCTTTATGTCCTCTCCTCTGTGGCTGGCAAGGCTCACCTGGCCTTATCCACCC
1201 ACTTATGGAACCTCAGGAGAGGAGGGCTCCTCCTAAAGGCATGCAGCTTGCAGCCCCTCTTTCTCACACGTGTGATCCTA
1281 GCGTGAGAGGTCATCCTGCCCTTGCTGAAGTTAGTAGTACTGTACTAAGAGCTCTGCCCTCATGTGAATTCCTGCCCTGG
1361 CGCCTCTTCCCTGGGGCTGAATCAGGCCCTGCTGCAAAACTCCAGGCTTCCCAGGGTTGGGGAGGCTGTGGGACCAAGGT
1441 CCATGTTGGTCCTTCCACTGGGTGCAGCAGGAGCTGGGTCCCGAGAGCCTGGCAGGTGAAACTCTGCAGGCCTTCCGCCT
1521 GATTATTATTTATTCACTCCTTTCCTCACCCCAAGTGCCCTGCTCTCCAGGTGCCTAGAGTATCCTAACTCTTAGGACCA
1601 GGGATTGTCTTGCACCAAGTATGCCTACCCCTGGCCAGTCTGAGGTCTCCTAGCCATAGAACTGACTCCTGGAAGCCTGG
1681 AGAGAAGGTGGTGACACCCATGGGTTCTCAACTGTAAGGAAAAAAGACACCAGACTTTTGTTCCCTAGTGGGGGAAAGCC
1761 CTTAGTCTTGTACAGGAGCAGCTTGCTCCCAAGTCCTTTTGGAAGCTGGCAGAGCTATATTCCTGACAGCCCTGACTGCC
1841 AGGTAGAGCAAAAGACATTGGTGGGGGTATGTGAAGCAAAAGGGGCAGGTGCACACACCTCCACAGTGACCTCTGTGCAC
1921 ACGGTTACCACCAACTGGCTGGCCCTCCTCCTCTTCCCTGGCCCATTGATCATCCCTTCTCACAGAGGGTCATCATTATT
2001 TCCAAATATTGTTTGTCTGATGACTTCCTCTTCCCAGTGCAATTTTTCCCTTCCTATTTCAACCTCTGGTTCCTGGGATG
2081 AGCCATACCCTGGAACTGGCCCACCCACTGTGTCTTCCACGTAAGGGAGACCTTTGCAAAGGGCATCCAAATGGGTAGGC
2161 AGGTGACAGCCGCCGTATTTATTTTGCATAATATTTTAATTTGTATATTTTTGTGATTTATTTTGGCGTTATGAGTTTGA
2241 CTCTCGGGGAGTTTTGTTGTTATGACTCTTGTGTCTTTTGTCACAAAACAATGATATTTGCTAAACGATATATGGAATTT
2321 ATTTTTGATTGGTAATAAAAAATCAAATATGTATAAATCCTGGTGAATCTACAAAAAAAAAAAAAAAA
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' ggGUGGUCGACGAGGGACCGGGu 5'
            | ||  || :|||||||||| 
Target 5' ccCTCCTCCTCTTCCCTGGCCCa 3'
 1943 - 1965 169.00 -34.90
2 
miRNA  3' ggGUGGUCGAC-GAGG---GACCGGGu 5'
            ||||  ||| ||||   ||||||| 
Target 5' ccCACC--CTGCCTCCCATCTGGCCCt 3'
 764 - 788 165.00 -31.60
3 
miRNA  3' ggGUGG-UCG-AC-GA--GGGACCGGgu 5'
            |||| ||: || ||  ||||||||  
Target 5' tgCACCAAGTATGCCTACCCCTGGCCag 3'
 1611 - 1638 147.00 -26.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
337595 92 ClinVar
337596 96 ClinVar
895113 190 ClinVar
337597 203 ClinVar
895114 205 ClinVar
895115 253 ClinVar
895116 287 ClinVar
337598 365 ClinVar
337599 459 ClinVar
337600 476 ClinVar
896548 480 ClinVar
337601 561 ClinVar
896549 638 ClinVar
896550 754 ClinVar
337602 925 ClinVar
337603 966 ClinVar
337604 1046 ClinVar
337605 1057 ClinVar
898176 1060 ClinVar
898177 1127 ClinVar
337606 1159 ClinVar
337607 1245 ClinVar
337608 1363 ClinVar
898178 1431 ClinVar
337609 1483 ClinVar
337610 1517 ClinVar
337611 1518 ClinVar
337612 1566 ClinVar
337613 1694 ClinVar
337614 1755 ClinVar
899278 1837 ClinVar
899279 1925 ClinVar
337615 1938 ClinVar
337616 1975 ClinVar
337617 1991 ClinVar
337618 2121 ClinVar
895189 2122 ClinVar
337619 2254 ClinVar
COSN30544281 9 COSMIC
COSN30105629 13 COSMIC
COSN31526261 30 COSMIC
COSN14014804 33 COSMIC
COSN30101670 46 COSMIC
COSN30492081 52 COSMIC
COSN31539262 90 COSMIC
COSN19658206 228 COSMIC
COSN9393868 286 COSMIC
COSN31591635 332 COSMIC
COSN29825651 342 COSMIC
COSN18723944 358 COSMIC
COSN24299038 369 COSMIC
COSN15743646 380 COSMIC
COSN2531894 478 COSMIC
COSN31553259 623 COSMIC
COSN31482750 628 COSMIC
COSN30107943 784 COSMIC
COSN10010514 802 COSMIC
COSN1244797 834 COSMIC
COSN31591992 851 COSMIC
COSN27614697 1011 COSMIC
COSN14488001 1526 COSMIC
COSN23876860 1592 COSMIC
COSN31603293 2019 COSMIC
COSN31537084 2039 COSMIC
COSN20853606 2129 COSMIC
COSN31571558 2176 COSMIC
COSN31546578 2212 COSMIC
COSN5963232 2232 COSMIC
COSN21954098 2234 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs759145970 2 dbSNP
rs1200627793 4 dbSNP
rs764778181 7 dbSNP
rs1460796630 8 dbSNP
rs752438896 9 dbSNP
rs758078718 12 dbSNP
rs369622669 13 dbSNP
rs1447674575 17 dbSNP
rs750802395 24 dbSNP
rs1423921363 26 dbSNP
rs1179588448 28 dbSNP
rs756548433 29 dbSNP
rs780676562 32 dbSNP
rs749313626 33 dbSNP
rs376793247 34 dbSNP
rs1414528423 38 dbSNP
rs778967812 39 dbSNP
rs1303998725 43 dbSNP
rs1284358380 46 dbSNP
rs1162488886 47 dbSNP
rs1404718921 49 dbSNP
rs1380900057 50 dbSNP
rs748337052 51 dbSNP
rs1341396119 52 dbSNP
rs1216117682 57 dbSNP
rs1354650595 64 dbSNP
rs1280004931 82 dbSNP
rs7581456 92 dbSNP
rs1220502525 93 dbSNP
rs138947618 96 dbSNP
rs543105550 99 dbSNP
rs1047538989 126 dbSNP
rs1450151186 131 dbSNP
rs912563112 135 dbSNP
rs943978863 141 dbSNP
rs1038822275 144 dbSNP
rs1362051407 147 dbSNP
rs1224967130 171 dbSNP
rs1162344226 177 dbSNP
rs1404178146 178 dbSNP
rs1269949616 190 dbSNP
rs562289410 203 dbSNP
rs901782791 203 dbSNP
rs1047391883 204 dbSNP
rs1195042842 204 dbSNP
rs1476493600 204 dbSNP
rs375409792 206 dbSNP
rs776740619 217 dbSNP
rs540683887 222 dbSNP
rs868661418 226 dbSNP
rs560492957 227 dbSNP
rs1016007030 228 dbSNP
rs1290716889 247 dbSNP
rs778510289 253 dbSNP
rs759582452 256 dbSNP
rs1315963025 273 dbSNP
rs1277555389 274 dbSNP
rs1400379047 278 dbSNP
rs1053942261 286 dbSNP
rs532504125 287 dbSNP
rs1426994856 288 dbSNP
rs1303376446 289 dbSNP
rs1359568353 291 dbSNP
rs1397527380 293 dbSNP
rs1299532333 294 dbSNP
rs1009815578 297 dbSNP
rs1362509737 298 dbSNP
rs1435337615 304 dbSNP
rs895340133 307 dbSNP
rs1324923754 310 dbSNP
rs1463655518 315 dbSNP
rs1227652088 324 dbSNP
rs1310535699 328 dbSNP
rs1012439740 331 dbSNP
rs572669200 331 dbSNP
rs772129031 332 dbSNP
rs779765519 338 dbSNP
rs746489405 340 dbSNP
rs1353260353 343 dbSNP
rs1215620352 350 dbSNP
rs1214495949 351 dbSNP
rs529730765 352 dbSNP
rs1456553701 358 dbSNP
rs886056476 365 dbSNP
rs1219189920 375 dbSNP
rs765477717 383 dbSNP
rs1033407945 384 dbSNP
rs768243592 386 dbSNP
rs149420732 387 dbSNP
rs541457628 389 dbSNP
rs1367846714 396 dbSNP
rs919087720 397 dbSNP
rs989548489 402 dbSNP
rs1164625557 412 dbSNP
rs768578227 436 dbSNP
rs911327703 438 dbSNP
rs1417506510 450 dbSNP
rs1433027016 459 dbSNP
rs202044868 459 dbSNP
rs886056477 459 dbSNP
rs923067516 459 dbSNP
rs942761254 459 dbSNP
rs1160897218 465 dbSNP
rs1426130323 470 dbSNP
rs886056478 476 dbSNP
rs1345235777 477 dbSNP
rs1446736662 480 dbSNP
rs569563923 481 dbSNP
rs776557480 482 dbSNP
rs1481559588 496 dbSNP
rs1254232960 498 dbSNP
rs987407316 501 dbSNP
rs560073812 502 dbSNP
rs911775274 505 dbSNP
rs1209153588 512 dbSNP
rs886133178 514 dbSNP
rs1305096621 518 dbSNP
rs941673411 520 dbSNP
rs1037347794 536 dbSNP
rs1453012032 536 dbSNP
rs1392674332 542 dbSNP
rs74411759 561 dbSNP
rs1301674630 566 dbSNP
rs1011969048 573 dbSNP
rs1025187943 587 dbSNP
rs1353199805 590 dbSNP
rs548805987 591 dbSNP
rs1238222525 592 dbSNP
rs373408309 602 dbSNP
rs568316186 611 dbSNP
rs1181217432 612 dbSNP
rs1483425076 622 dbSNP
rs936758768 623 dbSNP
rs200119917 631 dbSNP
rs1031652726 632 dbSNP
rs1240556626 635 dbSNP
rs776449781 651 dbSNP
rs1209580799 659 dbSNP
rs1399435320 660 dbSNP
rs1254713562 666 dbSNP
rs1315126498 667 dbSNP
rs1398561658 678 dbSNP
rs1463054195 692 dbSNP
rs958293226 697 dbSNP
rs1455403322 704 dbSNP
rs1414856626 711 dbSNP
rs892633522 712 dbSNP
rs945497968 713 dbSNP
rs1046639497 721 dbSNP
rs1424287387 722 dbSNP
rs1438269281 742 dbSNP
rs964101595 743 dbSNP
rs1178571265 748 dbSNP
rs79109340 754 dbSNP
rs976801161 755 dbSNP
rs761317131 759 dbSNP
rs1413345996 761 dbSNP
rs34156246 763 dbSNP
rs923162747 772 dbSNP
rs546253122 778 dbSNP
rs1244919933 788 dbSNP
rs898943203 790 dbSNP
rs1173347962 799 dbSNP
rs1295666474 803 dbSNP
rs994592371 815 dbSNP
rs1340365358 823 dbSNP
rs771331667 826 dbSNP
rs1384178927 830 dbSNP
rs983409124 832 dbSNP
rs774576916 838 dbSNP
rs1470277027 842 dbSNP
rs868333395 845 dbSNP
rs143881459 847 dbSNP
rs1419858807 853 dbSNP
rs1374348611 858 dbSNP
rs1444204387 860 dbSNP
rs1449474516 862 dbSNP
rs1281476911 863 dbSNP
rs538653848 869 dbSNP
rs1018894561 872 dbSNP
rs941897724 874 dbSNP
rs964607973 879 dbSNP
rs767154388 898 dbSNP
rs1469419731 907 dbSNP
rs1218654697 908 dbSNP
rs1275589340 910 dbSNP
rs975442758 911 dbSNP
rs1317652538 913 dbSNP
rs1299324026 914 dbSNP
rs1037377950 919 dbSNP
rs558251134 923 dbSNP
rs886056479 925 dbSNP
rs1055644084 933 dbSNP
rs575534145 935 dbSNP
rs1456706937 957 dbSNP
rs1329198360 963 dbSNP
rs989583695 964 dbSNP
rs3731941 966 dbSNP
rs1169379808 975 dbSNP
rs945578591 978 dbSNP
rs1476924537 980 dbSNP
rs547692372 985 dbSNP
rs1046530512 986 dbSNP
rs906821795 988 dbSNP
rs1233025353 991 dbSNP
rs1455179859 992 dbSNP
rs1235875224 994 dbSNP
rs938256654 999 dbSNP
rs1156617745 1000 dbSNP
rs771233581 1001 dbSNP
rs1177505406 1016 dbSNP
rs1477508431 1017 dbSNP
rs1274341577 1025 dbSNP
rs1054756711 1045 dbSNP
rs886056480 1046 dbSNP
rs554806901 1049 dbSNP
rs183039738 1057 dbSNP
rs139799133 1060 dbSNP
rs1255615251 1065 dbSNP
rs894059137 1068 dbSNP
rs1011076502 1071 dbSNP
rs1480502910 1079 dbSNP
rs1309757266 1080 dbSNP
rs1026074043 1082 dbSNP
rs1336214462 1086 dbSNP
rs886166885 1098 dbSNP
rs1412537843 1105 dbSNP
rs560544737 1106 dbSNP
rs1398103231 1115 dbSNP
rs1411392322 1116 dbSNP
rs141670657 1127 dbSNP
rs1378125107 1135 dbSNP
rs998252856 1138 dbSNP
rs546215807 1139 dbSNP
rs974656742 1158 dbSNP
rs760774484 1159 dbSNP
rs878907878 1160 dbSNP
rs983701667 1164 dbSNP
rs1257307961 1181 dbSNP
rs1212084575 1183 dbSNP
rs764110329 1190 dbSNP
rs1350261911 1197 dbSNP
rs907666369 1199 dbSNP
rs958072693 1206 dbSNP
rs989858311 1207 dbSNP
rs1281193279 1212 dbSNP
rs1445790015 1226 dbSNP
rs562732091 1233 dbSNP
rs963292486 1234 dbSNP
rs1278055812 1239 dbSNP
rs7565577 1245 dbSNP
rs1358163399 1250 dbSNP
rs916278651 1259 dbSNP
rs945439185 1270 dbSNP
rs947684245 1282 dbSNP
rs1046042658 1283 dbSNP
rs927718372 1284 dbSNP
rs1417799751 1289 dbSNP
rs1189022761 1291 dbSNP
rs1486858973 1293 dbSNP
rs982278697 1296 dbSNP
rs1053039132 1301 dbSNP
rs893973873 1306 dbSNP
rs1011145346 1312 dbSNP
rs548429663 1323 dbSNP
rs1226708694 1324 dbSNP
rs938140317 1332 dbSNP
rs1055310666 1335 dbSNP
rs1334000501 1336 dbSNP
rs920813944 1350 dbSNP
rs1338225781 1352 dbSNP
rs1297177594 1355 dbSNP
rs1431064975 1358 dbSNP
rs757351430 1362 dbSNP
rs561958044 1363 dbSNP
rs1404253688 1369 dbSNP
rs1270687132 1378 dbSNP
rs1417687824 1384 dbSNP
rs1490367966 1388 dbSNP
rs998157896 1395 dbSNP
rs1476381878 1418 dbSNP
rs531490342 1429 dbSNP
rs549999969 1431 dbSNP
rs1040272332 1449 dbSNP
rs1475839022 1471 dbSNP
rs10172803 1483 dbSNP
rs1219383719 1498 dbSNP
rs1476370058 1499 dbSNP
rs1468146435 1503 dbSNP
rs1004260807 1506 dbSNP
rs1215539397 1508 dbSNP
rs995977257 1513 dbSNP
rs1032941547 1514 dbSNP
rs116742732 1517 dbSNP
rs538345373 1518 dbSNP
rs973341219 1519 dbSNP
rs1272720311 1523 dbSNP
rs146209406 1531 dbSNP
rs1435118651 1534 dbSNP
rs949741558 1544 dbSNP
rs886056481 1566 dbSNP
rs568713096 1569 dbSNP
rs966804922 1583 dbSNP
rs538151165 1592 dbSNP
rs1228687290 1604 dbSNP
rs1410886682 1614 dbSNP
rs1297689343 1615 dbSNP
rs1421914706 1615 dbSNP
rs139348243 1616 dbSNP
rs928017368 1622 dbSNP
rs959543713 1630 dbSNP
rs927614322 1631 dbSNP
rs1195612551 1632 dbSNP
rs935117881 1637 dbSNP
rs987899276 1640 dbSNP
rs780174878 1641 dbSNP
rs561603076 1650 dbSNP
rs1271327933 1654 dbSNP
rs1356089786 1656 dbSNP
rs946866596 1657 dbSNP
rs1371048826 1678 dbSNP
rs1304934316 1680 dbSNP
rs1293426870 1692 dbSNP
rs77892978 1694 dbSNP
rs1215212816 1702 dbSNP
rs1298177721 1705 dbSNP
rs900106360 1714 dbSNP
rs534007068 1715 dbSNP
rs1356695700 1718 dbSNP
rs1174181184 1729 dbSNP
rs920881795 1731 dbSNP
rs569416889 1734 dbSNP
rs930881801 1736 dbSNP
rs1193803693 1750 dbSNP
rs1047425514 1751 dbSNP
rs887113108 1753 dbSNP
rs1471654943 1755 dbSNP
rs886056482 1755 dbSNP
rs537549930 1759 dbSNP
rs549449886 1760 dbSNP
rs186965169 1761 dbSNP
rs536720636 1764 dbSNP
rs545980459 1773 dbSNP
rs1040156113 1774 dbSNP
rs1425556040 1782 dbSNP
rs898560205 1784 dbSNP
rs1348087561 1791 dbSNP
rs567669594 1797 dbSNP
rs562906004 1798 dbSNP
rs994686863 1802 dbSNP
rs142615598 1819 dbSNP
rs1392522918 1822 dbSNP
rs969298498 1823 dbSNP
rs1376205450 1826 dbSNP
rs996029514 1829 dbSNP
rs982050899 1833 dbSNP
rs1035135225 1839 dbSNP
rs1019162304 1847 dbSNP
rs1054682251 1849 dbSNP
rs1451704401 1859 dbSNP
rs1159701341 1862 dbSNP
rs893087089 1862 dbSNP
rs542136468 1864 dbSNP
rs1402593578 1869 dbSNP
rs1010565212 1876 dbSNP
rs562070315 1883 dbSNP
rs1485916219 1895 dbSNP
rs1259165925 1900 dbSNP
rs1214062171 1911 dbSNP
rs1020160161 1914 dbSNP
rs966688221 1919 dbSNP
rs1260763419 1925 dbSNP
rs886056483 1938 dbSNP
rs946438989 1948 dbSNP
rs975559600 1963 dbSNP
rs527962395 1965 dbSNP
rs1035082965 1969 dbSNP
rs1289469430 1974 dbSNP
rs538676167 1975 dbSNP
rs1392200728 1984 dbSNP
rs1164202496 1985 dbSNP
rs934276549 1990 dbSNP
rs7585552 1991 dbSNP
rs887132316 1995 dbSNP
rs1427507295 2002 dbSNP
rs1262011085 2011 dbSNP
rs1206314058 2017 dbSNP
rs774829651 2029 dbSNP
rs1487256479 2038 dbSNP
rs920755864 2039 dbSNP
rs1271809301 2046 dbSNP
rs1213673882 2053 dbSNP
rs940055133 2057 dbSNP
rs1038351957 2074 dbSNP
rs952371114 2075 dbSNP
rs984113803 2083 dbSNP
rs1296647010 2090 dbSNP
rs778058270 2091 dbSNP
rs1044960183 2101 dbSNP
rs1325103526 2111 dbSNP
rs12846 2121 dbSNP
rs566822382 2122 dbSNP
rs1461297466 2130 dbSNP
rs1373284157 2132 dbSNP
rs1178255248 2159 dbSNP
rs1003896737 2165 dbSNP
rs1034923367 2171 dbSNP
rs772384504 2172 dbSNP
rs975722462 2173 dbSNP
rs376267610 2176 dbSNP
rs1194436928 2190 dbSNP
rs1339206477 2194 dbSNP
rs551944590 2194 dbSNP
rs1402071174 2203 dbSNP
rs967773238 2204 dbSNP
rs775998994 2223 dbSNP
rs931711140 2225 dbSNP
rs761111607 2229 dbSNP
rs892962250 2233 dbSNP
rs1326848595 2241 dbSNP
rs373304929 2246 dbSNP
rs1407263216 2247 dbSNP
rs1446584974 2249 dbSNP
rs1169254290 2250 dbSNP
rs1304340137 2251 dbSNP
rs921466684 2252 dbSNP
rs1173651367 2254 dbSNP
rs886056484 2254 dbSNP
rs1455193686 2255 dbSNP
rs1248954951 2261 dbSNP
rs1180352972 2269 dbSNP
rs534231499 2272 dbSNP
rs1042037955 2275 dbSNP
rs1207769168 2290 dbSNP
rs1251640188 2290 dbSNP
rs907103162 2307 dbSNP
rs764159756 2308 dbSNP
rs1235106392 2309 dbSNP
rs1350217071 2312 dbSNP
rs1239083564 2314 dbSNP
rs568850832 2318 dbSNP
rs531306354 2320 dbSNP
rs1277678610 2322 dbSNP
rs190233534 2326 dbSNP
rs1205448034 2329 dbSNP
rs1263756327 2331 dbSNP
rs568400862 2331 dbSNP
rs1038383575 2333 dbSNP
rs1374397117 2348 dbSNP
rs1313178385 2352 dbSNP
rs919924397 2353 dbSNP
rs948819438 2354 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 GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ggguGGUCGACGAGGGAC-CGGGu 5'
              |||    | | ||| |:|: 
Target 5' ---cCCA----CCCACUGUGUCUu 3'
 		1 - 17
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 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' ggguggucgacGAGGGACCGGGu 5'
                     ||  ||||||| 
Target 5' ---------aaCUGGCUGGCCCu 3'
 		1 - 14
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]
CLIP-seq Support 1 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_020184 | 3UTR | AACUGGCCCUUUGUGACAGGGCUGACUCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000540067.1 | 3UTR | CCCACCCACUGUGUCUUCCACG
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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000540067.1 | 3UTR | AACUGGCUGGCCCUCCUCCUCUUCCCUG
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
87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100106 ABT1 activator of basal transcription 1 2 8
MIRT248144 LMBR1L limb development membrane protein 1 like 2 2
MIRT327062 KLHL15 kelch like family member 15 2 2
MIRT347231 GATAD2A GATA zinc finger domain containing 2A 2 2
MIRT450221 CENPN centromere protein N 2 2
MIRT451264 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT452701 C1orf226 chromosome 1 open reading frame 226 2 2
MIRT453212 CERS1 ceramide synthase 1 2 2
MIRT454822 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT454883 RAD50 RAD50 double strand break repair protein 2 2
MIRT455783 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT455858 TMEM254 transmembrane protein 254 2 2
MIRT457615 UPK3BL uroplakin 3B like 1 2 2
MIRT457822 ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein 2 4
MIRT458344 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458376 ITM2C integral membrane protein 2C 2 2
MIRT458928 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459066 WFIKKN2 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 2 2
MIRT460138 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460818 FSTL4 follistatin like 4 2 2
MIRT461285 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT462738 EFNB1 ephrin B1 2 2
MIRT464556 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT477910 DUSP2 dual specificity phosphatase 2 2 2
MIRT479073 CNNM4 cyclin and CBS domain divalent metal cation transport mediator 4 2 4
MIRT479534 CDC5L cell division cycle 5 like 2 4
MIRT485628 EEPD1 endonuclease/exonuclease/phosphatase family domain containing 1 2 2
MIRT489896 PPIC peptidylprolyl isomerase C 2 4
MIRT490737 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491201 MLLT1 MLLT1, super elongation complex subunit 2 4
MIRT492681 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT494593 ATG7 autophagy related 7 2 2
MIRT495061 PADI3 peptidyl arginine deiminase 3 2 4
MIRT496623 TMEM67 transmembrane protein 67 2 2
MIRT497177 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT498217 TLN2 talin 2 2 2
MIRT498306 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT499668 NPHP3 nephrocystin 3 2 2
MIRT508080 ANKRD52 ankyrin repeat domain 52 2 2
MIRT509707 ANKRD23 ankyrin repeat domain 23 2 2
MIRT509841 FOS Fos proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT512814 ARRDC2 arrestin domain containing 2 2 2
MIRT513353 SLIT1 slit guidance ligand 1 2 2
MIRT514293 FXYD5 FXYD domain containing ion transport regulator 5 2 2
MIRT516598 FAM89A family with sequence similarity 89 member A 2 4
MIRT516616 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT518348 CCL5 C-C motif chemokine ligand 5 2 2
MIRT520130 WSB1 WD repeat and SOCS box containing 1 2 2
MIRT522072 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT526461 OSBPL5 oxysterol binding protein like 5 2 2
MIRT528278 MBL2 mannose binding lectin 2 2 2
MIRT534844 RAB15 RAB15, member RAS oncogene family 2 4
MIRT542245 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT543299 ZNF585B zinc finger protein 585B 2 2
MIRT552456 ZNF410 zinc finger protein 410 2 2
MIRT553641 TJAP1 tight junction associated protein 1 2 2
MIRT557103 HOXA3 homeobox A3 2 2
MIRT570782 FANCA Fanconi anemia complementation group A 2 2
MIRT630912 ZMAT2 zinc finger matrin-type 2 2 2
MIRT631034 ZNF878 zinc finger protein 878 2 2
MIRT639017 AAK1 AP2 associated kinase 1 2 2
MIRT648596 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT648939 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT652834 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT659347 CSRP1 cysteine and glycine rich protein 1 2 2
MIRT664163 APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F 2 2
MIRT670511 ZSCAN22 zinc finger and SCAN domain containing 22 2 2
MIRT671246 TMEM41B transmembrane protein 41B 2 2
MIRT672120 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT672313 CD3D CD3d molecule 2 2
MIRT672543 BRMS1L breast cancer metastasis-suppressor 1 like 2 2
MIRT673036 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT673814 DARS aspartyl-tRNA synthetase 2 2
MIRT674858 GINM1 glycoprotein integral membrane 1 2 2
MIRT674970 SH3BP2 SH3 domain binding protein 2 2 2
MIRT675185 KIF1C kinesin family member 1C 2 2
MIRT675219 UGDH UDP-glucose 6-dehydrogenase 2 2
MIRT675558 MED16 mediator complex subunit 16 2 2
MIRT682566 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2 2
MIRT684640 PDE4C phosphodiesterase 4C 2 2
MIRT689722 ATXN2 ataxin 2 2 2
MIRT693594 SLC39A1 solute carrier family 39 member 1 2 2
MIRT704745 CDKN2B cyclin dependent kinase inhibitor 2B 2 2
MIRT712779 ZNF154 zinc finger protein 154 2 2
MIRT718118 OTOF otoferlin 2 2
MIRT720115 SAMD4A sterile alpha motif domain containing 4A 2 2
MIRT720275 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4640 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4640-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4640-5p Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4640-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4640-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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