pre-miRNA Information
pre-miRNA hsa-mir-6501   
Genomic Coordinates chr21: 33550662 - 33550728
Description Homo sapiens miR-6501 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6501-5p
Sequence 3| AGUUGCCAGGGCUGCCUUUGGU |24
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
1055619 20 ClinVar
COSM5974214 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs756127353 5 dbSNP
rs764400023 6 dbSNP
rs753967693 8 dbSNP
rs1283296362 14 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TIPRL   
Synonyms TIP, TIP41, TIPRL1
Description TOR signaling pathway regulator
Transcript NM_152902   
Other Transcripts NM_001031800   
Expression
Putative miRNA Targets on TIPRL
3'UTR of TIPRL
(miRNA target sites are highlighted)
>TIPRL|NM_152902|3'UTR
   1 AATGTGATACAACATATACTCACTATGGAATCTGACTGGACACCTTGGCTATTTGTAAGGGGTTATTTTTATTATGAGAA
  81 TTAATTGCCTTGTTTATGTACAGATTTTCTGTAGCCTTAAAGGAAAAAAAAATAAAGATCGTTACAGGCAGGTTTCACTC
 161 AACTGCTGTTTGTACTGTCTGTCTTCACATTCATATTCCAGATTTATATTTTCTGGAGTTAAATTTGGATGATTTCTAAA
 241 TTATCACAAAGTGGGACCTCAGCAGTAGTGATGTGTGTGTCTCATGAGCAGTGAGCACAGTCTGCATTCATCATGAAACA
 321 CTATCTTCTACCAGGAGGAGGTTAATGTAAATCACCAAATCCCAATGCCTTGTGACTTTCATAGGATTCCTGATCATGCA
 401 TGTTGATGTACTGGCTCTTCACTTTGGGCTTTCTGATGTTTATTCACACCTTTGGAGAGTTGCAACTTGCCACATACGAA
 481 ATTAGTCTCATAGTGTAGTGAACTTCAACCCCAAAATTTTAAAAATGTATTTCCCCCCAGTTTTAAATTGCCTTTGAAAT
 561 TTAAAAAAAAAAAATTTAGACTTAGTACCAGAACCAAAAATACCTAGATTTTTGGAGAACTTATTACATACATAGAAACA
 641 TGAATATGGTTTACCACTGTGTGTGTGTAGGATGTTAGAATTATCTGTCCTCCATCTTTAGGTGCTTTTTCTTAAATGTG
 721 GTTCTACTTATACTGATATTTTTAATTTCCATCTTCCATGCAACCTCAGAGTGAATAAACCCCTTAAATTTGGTGCTGGT
 801 TCGAAAAAGTCTAAAGGGTTTATTAGGGGTTGTTTTTCGCAAATATTACATCAATCCTTAAAGCAACAAGATTAATTTTC
 881 TGCTTAAAATATTTGGGAAGATAGGTAAGGAGGAGGGGGTTTTAAAATATAAAAGCAAGTTTTTCTATTTTAAGGTGCAT
 961 ATTTGTAACATTACAGGGGATGAAGTAAAATGTAATTAATTAGCACAAGACTTAGGGAGTACAGAAAATACACAGAAGTA
1041 AATTTCAAATCCATTTGATTGTTTTCATAGTGACCCCTTAGTCATTTTATATTCTTGTCTGCCTTTCTAGAAAAATGGTT
1121 GTCATAAAGTGGAAAGTGATTAAAAAGCATCAAATAAGAAATTATTTCAAGTGGATTTTTAAAAATATTTTTTTGAAGGG
1201 CAGGGGGAAAATTCACCCCTTTTCTGATTTGAAATATGTTGTACATATTTCCATTTGATGGATAAATCATTAAGTAAGAA
1281 TATTTGATTTAAAGTATTAGCCAACCTCTTCAGGTATTAGCCTGAAGATAAATTTTAACAAAACATATACACTTGGGTAT
1361 CCGTCATTGCTCAAACTCTATAGTGTATTGCTGGAGCCAATAGGCAGGGTATATTTTATTAGCTAAATTTGATATTTGTC
1441 TTCTGCCTTCTGTATCACCTCCAAGCTATAGGAAATCAGGATTTTGTTGGCTTTAAGAAAACACATGGTATGTTCACTGT
1521 ATATTAAATATACCTGTATTTAATGTTTTCTCTTAGGACAGAAAAGTAGACACACACACACACACACACACACATGTTGT
1601 GTTCAGCTTTCTGTTTTATATTATTTGCCATTGAGATTAGAATAGAACAGGCTCTATTCATGCAAACTATATGAAATGAA
1681 AAACTTTTAAGACTCTTCATTAATTGGAGCTTCTGGGCAACATCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
1761 ATACAGACATTTTTTTTTTAACTTGTTGATTCAGATGTCTTGGTCCCTGAATAGTCCTAGATTACTTATTTTGAGAATTC
1841 ATTGTTAAAAATTACAGGGAATTAAAATAATTGCCTTTTTTTTTTTTAGAGGGTAAGAGATGGGTAGAAGAGTATGCCTC
1921 TGAAAATTTTATTAGTTTATTCTTGTGGAGAATACCAAGAAAATGTGTATTTGCCCATTGCTAAATATGATATATGCCAT
2001 TTTGTATTTATTTGTCCCAAGTGTCTTTTTGTAAGAGGAGAATAAACAATAAGGAATTACTGATCAAA
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' ugGUUUCCGUCG-GGA-CCGUUGa 5'
            :||  | ||| :|| |||||| 
Target 5' atTAATTGGAGCTTCTGGGCAACa 3'
1699 - 1722 128.00 -15.30
2
miRNA  3' ugGUUUCCGUCGGGACCGUUGa 5'
            :::||  ||   | ||||| 
Target 5' ttTGGAG--AG---TTGCAACt 3'
451 - 467 109.00 -8.30
3
miRNA  3' ugguuUCCGUCGGGACCGUUGa 5'
               :| || ||:|||| |: 
Target 5' tgactGGACA-CCTTGGCTATt 3'
33 - 53 108.00 -12.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN18725393 62 COSMIC
COSN31515163 79 COSMIC
COSN30117522 87 COSMIC
COSN31589656 106 COSMIC
COSN30530408 137 COSMIC
COSN31586701 167 COSMIC
COSN26710315 261 COSMIC
COSN31531389 266 COSMIC
COSN14471974 401 COSMIC
COSN1412013 468 COSMIC
COSN25404722 496 COSMIC
COSN30441880 516 COSMIC
COSN17326637 522 COSMIC
COSN20825589 527 COSMIC
COSN20095555 575 COSMIC
COSN22293090 855 COSMIC
COSN20095556 1592 COSMIC
COSN1412014 1669 COSMIC
COSN27487136 1761 COSMIC
COSN8648740 1762 COSMIC
COSN23891290 1807 COSMIC
COSN20095558 1888 COSMIC
COSN27315250 1888 COSMIC
COSN21557282 1970 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs759670703 10 dbSNP
rs1307614154 11 dbSNP
rs1228970747 17 dbSNP
rs772117498 18 dbSNP
rs775449070 19 dbSNP
rs760639270 21 dbSNP
rs1270710880 23 dbSNP
rs1322884344 24 dbSNP
rs763892824 25 dbSNP
rs1192902274 33 dbSNP
rs372916134 37 dbSNP
rs1319771750 43 dbSNP
rs761453717 44 dbSNP
rs765010226 46 dbSNP
rs750074584 47 dbSNP
rs758017907 49 dbSNP
rs1360852638 50 dbSNP
rs766015993 51 dbSNP
rs950671007 56 dbSNP
rs1005094595 58 dbSNP
rs1020016560 60 dbSNP
rs145150142 62 dbSNP
rs1175215022 74 dbSNP
rs534307301 75 dbSNP
rs963565101 77 dbSNP
rs1449514725 79 dbSNP
rs1166537923 80 dbSNP
rs191274194 89 dbSNP
rs747365248 91 dbSNP
rs1391639670 92 dbSNP
rs1460528693 93 dbSNP
rs1202886983 99 dbSNP
rs745665101 102 dbSNP
rs1484496573 115 dbSNP
rs574389487 117 dbSNP
rs1257109814 124 dbSNP
rs201890300 124 dbSNP
rs974139815 124 dbSNP
rs976084309 126 dbSNP
rs763548107 130 dbSNP
rs916029898 131 dbSNP
rs1293467518 133 dbSNP
rs970042521 133 dbSNP
rs1397875935 139 dbSNP
rs928853831 142 dbSNP
rs1303422992 147 dbSNP
rs1465345966 148 dbSNP
rs934948876 158 dbSNP
rs2072776 169 dbSNP
rs952859696 176 dbSNP
rs947592247 178 dbSNP
rs1038759000 190 dbSNP
rs1257468570 200 dbSNP
rs1230227123 214 dbSNP
rs900265098 225 dbSNP
rs997103816 227 dbSNP
rs1310932085 237 dbSNP
rs373862549 239 dbSNP
rs907659048 249 dbSNP
rs1334446717 253 dbSNP
rs940407573 264 dbSNP
rs991862137 266 dbSNP
rs917590355 267 dbSNP
rs1247075413 269 dbSNP
rs758751580 272 dbSNP
rs1341202548 276 dbSNP
rs1219265299 278 dbSNP
rs575655525 289 dbSNP
rs750752956 289 dbSNP
rs1414130469 300 dbSNP
rs1045392359 310 dbSNP
rs1353518924 310 dbSNP
rs1004782470 311 dbSNP
rs1459001443 314 dbSNP
rs1410222299 324 dbSNP
rs1202399975 327 dbSNP
rs1165853399 331 dbSNP
rs556284148 332 dbSNP
rs1368581139 341 dbSNP
rs1163498759 343 dbSNP
rs936545334 355 dbSNP
rs1483490720 362 dbSNP
rs867655295 362 dbSNP
rs1052209366 364 dbSNP
rs892575593 366 dbSNP
rs1248668022 371 dbSNP
rs1211904705 372 dbSNP
rs564341337 381 dbSNP
rs1264893861 392 dbSNP
rs1001913117 396 dbSNP
rs1023015656 398 dbSNP
rs1170717869 399 dbSNP
rs1471435400 402 dbSNP
rs761479660 408 dbSNP
rs1410202015 410 dbSNP
rs899840833 421 dbSNP
rs1335002130 423 dbSNP
rs1326411300 432 dbSNP
rs376269489 443 dbSNP
rs1027689105 447 dbSNP
rs1035677305 448 dbSNP
rs1408682407 454 dbSNP
rs952931720 458 dbSNP
rs1160624456 460 dbSNP
rs1360105495 461 dbSNP
rs1450550413 464 dbSNP
rs982977191 474 dbSNP
rs1015751405 475 dbSNP
rs956266522 478 dbSNP
rs1452352527 495 dbSNP
rs960170626 501 dbSNP
rs1211823350 505 dbSNP
rs992328657 514 dbSNP
rs917640063 521 dbSNP
rs989070999 525 dbSNP
rs540625325 539 dbSNP
rs914849868 540 dbSNP
rs755055482 560 dbSNP
rs1277508745 563 dbSNP
rs1331262801 563 dbSNP
rs35037221 563 dbSNP
rs397732493 563 dbSNP
rs947711568 563 dbSNP
rs562406628 564 dbSNP
rs1302325427 574 dbSNP
rs1280134055 575 dbSNP
rs1390261375 581 dbSNP
rs1321769401 596 dbSNP
rs1400589088 597 dbSNP
rs1316191065 610 dbSNP
rs1212726964 615 dbSNP
rs1174616972 618 dbSNP
rs974888055 621 dbSNP
rs1394696586 627 dbSNP
rs1272290119 660 dbSNP
rs980458215 665 dbSNP
rs769230888 673 dbSNP
rs1211908928 681 dbSNP
rs772796351 699 dbSNP
rs1255168009 702 dbSNP
rs1485118303 704 dbSNP
rs1051971050 717 dbSNP
rs529570493 731 dbSNP
rs1345525492 738 dbSNP
rs1052283223 741 dbSNP
rs1302206727 754 dbSNP
rs892314137 757 dbSNP
rs535705429 770 dbSNP
rs147159475 782 dbSNP
rs1336791540 784 dbSNP
rs1474179466 784 dbSNP
rs1415388506 793 dbSNP
rs555357870 804 dbSNP
rs1431809179 814 dbSNP
rs1166813856 818 dbSNP
rs899083162 819 dbSNP
rs1041530258 825 dbSNP
rs1474508648 825 dbSNP
rs1240274271 828 dbSNP
rs1012059260 829 dbSNP
rs1416674397 830 dbSNP
rs1172117021 834 dbSNP
rs530535024 839 dbSNP
rs1208490582 840 dbSNP
rs1343779398 841 dbSNP
rs1400807446 842 dbSNP
rs1274914525 847 dbSNP
rs1300342203 851 dbSNP
rs997289538 852 dbSNP
rs762431031 857 dbSNP
rs1455275457 859 dbSNP
rs888723475 862 dbSNP
rs1291655949 866 dbSNP
rs1355410439 871 dbSNP
rs1311380390 872 dbSNP
rs148561543 883 dbSNP
rs1275531229 885 dbSNP
rs1371400661 897 dbSNP
rs1036220105 898 dbSNP
rs1015823607 903 dbSNP
rs368794324 905 dbSNP
rs1416107043 907 dbSNP
rs960201656 911 dbSNP
rs570432588 919 dbSNP
rs775150928 924 dbSNP
rs1256731160 930 dbSNP
rs1389931508 934 dbSNP
rs1025181946 936 dbSNP
rs969153894 948 dbSNP
rs1233083407 959 dbSNP
rs1346943674 960 dbSNP
rs980872312 971 dbSNP
rs534356638 978 dbSNP
rs1216869687 979 dbSNP
rs1203435487 981 dbSNP
rs1305441051 982 dbSNP
rs1287633191 987 dbSNP
rs1228409070 989 dbSNP
rs1334696760 992 dbSNP
rs968953477 1004 dbSNP
rs1230612364 1012 dbSNP
rs1351542738 1013 dbSNP
rs974856738 1017 dbSNP
rs1440238469 1026 dbSNP
rs1351856074 1033 dbSNP
rs1324216033 1035 dbSNP
rs1191783249 1042 dbSNP
rs924969533 1049 dbSNP
rs1460986962 1050 dbSNP
rs957675015 1050 dbSNP
rs1417073959 1059 dbSNP
rs1162777925 1065 dbSNP
rs142903441 1073 dbSNP
rs540627303 1076 dbSNP
rs1479271139 1078 dbSNP
rs568015485 1082 dbSNP
rs907655421 1090 dbSNP
rs1248099075 1092 dbSNP
rs535322715 1098 dbSNP
rs913782305 1099 dbSNP
rs1467689219 1100 dbSNP
rs559317422 1114 dbSNP
rs943908861 1118 dbSNP
rs1037779953 1119 dbSNP
rs899060018 1122 dbSNP
rs1382996782 1128 dbSNP
rs1040876116 1130 dbSNP
rs575365174 1132 dbSNP
rs1440243266 1138 dbSNP
rs183391126 1138 dbSNP
rs1392435872 1142 dbSNP
rs1045032578 1143 dbSNP
rs932734177 1151 dbSNP
rs1048483889 1154 dbSNP
rs558274288 1168 dbSNP
rs1442983602 1169 dbSNP
rs1158021398 1175 dbSNP
rs1417154950 1181 dbSNP
rs151127489 1182 dbSNP
rs1426818335 1183 dbSNP
rs1301234155 1187 dbSNP
rs1370161919 1188 dbSNP
rs1453238797 1188 dbSNP
rs888461024 1198 dbSNP
rs1260653805 1199 dbSNP
rs1214081325 1202 dbSNP
rs1311211359 1203 dbSNP
rs1314366636 1206 dbSNP
rs906359867 1208 dbSNP
rs1204223476 1210 dbSNP
rs1369090084 1211 dbSNP
rs141096147 1217 dbSNP
rs1057179718 1224 dbSNP
rs891884043 1228 dbSNP
rs1284028099 1236 dbSNP
rs1037287599 1239 dbSNP
rs75496339 1243 dbSNP
rs1021596633 1254 dbSNP
rs1440865146 1255 dbSNP
rs78336291 1256 dbSNP
rs187322589 1258 dbSNP
rs767443860 1275 dbSNP
rs1362457705 1295 dbSNP
rs996369361 1306 dbSNP
rs574403606 1313 dbSNP
rs544892786 1314 dbSNP
rs77810784 1328 dbSNP
rs1428661653 1334 dbSNP
rs1261623253 1339 dbSNP
rs1185334594 1344 dbSNP
rs754073262 1348 dbSNP
rs1258606218 1352 dbSNP
rs1210634976 1353 dbSNP
rs1345911712 1360 dbSNP
rs757566389 1363 dbSNP
rs1228231007 1364 dbSNP
rs145433951 1379 dbSNP
rs868766348 1379 dbSNP
rs962121414 1381 dbSNP
rs1380422981 1383 dbSNP
rs1357317336 1388 dbSNP
rs1460003854 1400 dbSNP
rs1313198799 1402 dbSNP
rs1325316127 1409 dbSNP
rs973174115 1410 dbSNP
rs563018443 1411 dbSNP
rs920245830 1413 dbSNP
rs779061841 1422 dbSNP
rs1447461805 1433 dbSNP
rs1372039182 1440 dbSNP
rs987764208 1441 dbSNP
rs557776596 1445 dbSNP
rs913855731 1452 dbSNP
rs1237857463 1453 dbSNP
rs1284490136 1455 dbSNP
rs1196646114 1460 dbSNP
rs965310170 1469 dbSNP
rs1247107759 1471 dbSNP
rs1336771200 1491 dbSNP
rs1293899788 1494 dbSNP
rs1230868045 1503 dbSNP
rs939166066 1505 dbSNP
rs977014748 1516 dbSNP
rs921124114 1539 dbSNP
rs932447452 1545 dbSNP
rs1391569631 1546 dbSNP
rs533609494 1547 dbSNP
rs545262052 1549 dbSNP
rs1395352778 1553 dbSNP
rs1295880319 1555 dbSNP
rs1462623727 1562 dbSNP
rs1201119052 1568 dbSNP
rs1273710185 1570 dbSNP
rs1469008148 1570 dbSNP
rs150597538 1570 dbSNP
rs397981867 1570 dbSNP
rs59196293 1570 dbSNP
rs66543118 1570 dbSNP
rs71866574 1570 dbSNP
rs761326086 1570 dbSNP
rs878940107 1570 dbSNP
rs1248834821 1573 dbSNP
rs61809618 1574 dbSNP
rs1188502843 1578 dbSNP
rs1332623725 1580 dbSNP
rs1370356959 1583 dbSNP
rs1474361760 1590 dbSNP
rs1164249773 1592 dbSNP
rs1334801229 1592 dbSNP
rs1442440206 1594 dbSNP
rs891853643 1594 dbSNP
rs1048516563 1596 dbSNP
rs1460295718 1598 dbSNP
rs909927266 1611 dbSNP
rs1387798261 1619 dbSNP
rs940040622 1622 dbSNP
rs1394057463 1628 dbSNP
rs1362260934 1644 dbSNP
rs1037024106 1645 dbSNP
rs190665725 1647 dbSNP
rs1334588540 1652 dbSNP
rs1252410046 1653 dbSNP
rs950350177 1663 dbSNP
rs1412575919 1668 dbSNP
rs1045015895 1677 dbSNP
rs1467039173 1680 dbSNP
rs528126831 1686 dbSNP
rs143621204 1688 dbSNP
rs546081197 1691 dbSNP
rs1230248019 1695 dbSNP
rs35934819 1698 dbSNP
rs955136461 1700 dbSNP
rs1371311309 1702 dbSNP
rs567682584 1718 dbSNP
rs906041059 1721 dbSNP
rs904678663 1722 dbSNP
rs1400465671 1724 dbSNP
rs1488451335 1724 dbSNP
rs1491386999 1724 dbSNP
rs562164244 1724 dbSNP
rs1231417648 1725 dbSNP
rs1259344643 1725 dbSNP
rs1271251012 1725 dbSNP
rs1340920770 1725 dbSNP
rs1348075923 1725 dbSNP
rs141290927 1725 dbSNP
rs200296252 1725 dbSNP
rs397981868 1725 dbSNP
rs71981720 1725 dbSNP
rs746355653 1725 dbSNP
rs796803916 1725 dbSNP
rs962266307 1728 dbSNP
rs529169740 1729 dbSNP
rs750390747 1729 dbSNP
rs1491034674 1730 dbSNP
rs973141711 1733 dbSNP
rs893549973 1734 dbSNP
rs1187561895 1736 dbSNP
rs920383953 1742 dbSNP
rs1263978764 1749 dbSNP
rs1478879753 1751 dbSNP
rs1411702255 1752 dbSNP
rs1167433690 1760 dbSNP
rs1420271437 1760 dbSNP
rs1168426260 1762 dbSNP
rs1421398937 1764 dbSNP
rs550876916 1767 dbSNP
rs139315904 1769 dbSNP
rs761575824 1769 dbSNP
rs781102579 1769 dbSNP
rs1020600158 1770 dbSNP
rs1337942837 1770 dbSNP
rs1491578143 1770 dbSNP
rs927876104 1770 dbSNP
rs569050611 1771 dbSNP
rs1481868038 1780 dbSNP
rs1461444480 1783 dbSNP
rs1181090316 1786 dbSNP
rs1355269652 1798 dbSNP
rs1311477783 1805 dbSNP
rs115895993 1812 dbSNP
rs1355354550 1815 dbSNP
rs557623120 1824 dbSNP
rs1328190645 1826 dbSNP
rs1052384924 1832 dbSNP
rs1054720 1841 dbSNP
rs1432455755 1875 dbSNP
rs1167072180 1876 dbSNP
rs1416843663 1876 dbSNP
rs35549590 1876 dbSNP
rs398049692 1876 dbSNP
rs1311954988 1877 dbSNP
rs946602992 1884 dbSNP
rs1383347784 1888 dbSNP
rs1470925413 1888 dbSNP
rs953903879 1888 dbSNP
rs1292850245 1889 dbSNP
rs1203201562 1892 dbSNP
rs1326315488 1892 dbSNP
rs1456104705 1895 dbSNP
rs1043119778 1905 dbSNP
rs369433109 1911 dbSNP
rs983951014 1919 dbSNP
rs1214821611 1921 dbSNP
rs909999413 1928 dbSNP
rs904618438 1929 dbSNP
rs1291759625 1930 dbSNP
rs1225840754 1932 dbSNP
rs1234653769 1936 dbSNP
rs931949395 1936 dbSNP
rs1282885210 1946 dbSNP
rs1279255056 1948 dbSNP
rs940071883 1955 dbSNP
rs747534580 1957 dbSNP
rs1440079255 1958 dbSNP
rs972791189 1981 dbSNP
rs1373334817 1991 dbSNP
rs534253412 2011 dbSNP
rs374701086 2019 dbSNP
rs1286924059 2026 dbSNP
rs1054721 2032 dbSNP
rs1402298396 2036 dbSNP
rs1044655216 2050 dbSNP
rs76072625 2051 dbSNP
rs1427824236 2053 dbSNP
rs936206922 2056 dbSNP
rs183233356 2060 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
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 Chi_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BCBL-1
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 GSM1015448. RNA binding protein: AGO2. Condition:BCBL-1 mRNA ...

- Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al., 2012, PLoS pathogens.

Article - Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al.
- PLoS pathogens, 2012
KSHV is the etiological agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentricCastleman's disease (MCD). The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. MiRNA-mediated regulation of gene expression is a complex network with each miRNA having many potential targets, and to date only few KSHV miRNA targets have been experimentally determined. A detailed understanding of KSHV miRNA functions requires high-through putribonomics to globally analyze putative miRNA targets in a cell type-specific manner. We performed Ago HITS-CLIP to identify viral and cellular miRNAs and their cognate targets in two latently KSHV-infected PEL cell lines. Ago HITS-CLIP recovered 1170 and 950 cellular KSHV miRNA targets from BCBL-1 and BC-3, respectively. Importantly, enriched clusters contained KSHV miRNA seed matches in the 3'UTRs of numerous well characterized targets, among them THBS1, BACH1, and C/EBPbeta. KSHV miRNA targets were strongly enriched for genes involved in multiple pathways central for KSHV biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in KSHV pathogenesis and potentially tumorigenesis. A limited number of viral transcripts were also enriched by HITS-CLIP including vIL-6 expressed only in a subset of PEL cells during latency. Interestingly, Ago HITS-CLIP revealed extremely high levels of Ago-associated KSHV miRNAs especially in BC-3 cells where more than 70% of all miRNAs are of viral origin. This suggests that in addition to seed match-specific targeting of cellular genes, KSHV miRNAs may also function by hijacking RISCs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human miRNAs. In summary, we provide an extensive list of cellular and viral miRNA targets representing an important resource to decipher KSHV miRNA function.
LinkOut: [PMID: 22927820]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Hela
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 GSM1048187. RNA binding protein: AGO2. Condition:Hela_AGO2_CLIP_control ...

- Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al., 2013, Cell.

Article - Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al.
- Cell, 2013
The induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. Here, we report that repression of a single RNA binding polypyrimidine-tract-binding (PTB) protein, which occurs during normal brain development via the action of miR-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we show that PTB has a previously undocumented function in the regulation of microRNA functions, suppressing or enhancing microRNA targeting by competitive binding on target mRNA or altering local RNA secondary structure. A key event during neuronal induction is the relief of PTB-mediated blockage of microRNA action on multiple components of the REST complex, thereby derepressing a large array of neuronal genes, including miR-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. This converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.
LinkOut: [PMID: 23313552]
Experimental Support 4 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 GSM1084041. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep1 HITS-CLIP data was present in GSM1084042. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep2 HITS-CLIP data was present in GSM1084043. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep2 HITS-CLIP data was present in GSM1084044. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep3 HITS-CLIP data was present in GSM1084045. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep3 HITS-CLIP data was present in GSM1084046. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep4 HITS-CLIP data was present in GSM1084047. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep4 HITS-CLIP data was present in GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb HITS-CLIP data was present in GSM1084066. RNA binding protein: AGO2. Condition:CLIP_noemetine_SantaCruzAb HITS-CLIP data was present in GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb HITS-CLIP data was present in GSM1084072. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_AbnovaAb HITS-CLIP data was present in GSM1084073. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_AbnovaAb HITS-CLIP data was present in GSM1084074. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_SantaCruzAb HITS-CLIP data was present in GSM1084075. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_SantaCruzAb HITS-CLIP data was present in GSM1084076. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_SigmaAb HITS-CLIP data was present in GSM1084077. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_SigmaAb HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084079. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084080. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SantaCruzAb HITS-CLIP data was present in GSM1084081. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SantaCruzAb HITS-CLIP data was present in GSM1084082. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SigmaAb HITS-CLIP data was present in GSM1084083. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SigmaAb ...

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

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]
Experimental Support 5 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Liver Tissue
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 GSM2550620. RNA binding protein: AGO2. Condition:Patient 2 Tumor 1 HITS-CLIP data was present in GSM2550619. RNA binding protein: AGO2. Condition:Patient 1 Tumor 2 HITS-CLIP data was present in GSM2550618. RNA binding protein: AGO2. Condition:Patient 1 Tumor 1 ...

- Luna JM; Barajas JM; Teng KY; Sun HL; Moore et al., 2017, Molecular cell.

Article - Luna JM; Barajas JM; Teng KY; Sun HL; Moore et al.
- Molecular cell, 2017
MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Argonaute [Ago]-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3' UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122-dependent binding revealed a G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma.
LinkOut: [PMID: 28735896]
CLIP-seq Support 1 for dataset Chi_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000367833.2 | 3UTR | AUUGGAGCUUCUGGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset Chi_ControlB_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control B
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1015448
Method / RBP HITS-CLIP / AGO2
Cell line / Condition BCBL-1 / BCBL-1 mRNA
Location of target site ENST00000367833.2 | 3UTR | CAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22927820 / GSE41357
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1048187
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Hela / Hela_AGO2_CLIP_control
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23313552 / GSE42701
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1084040
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep1
Location of target site ENST00000367833.2 | 3UTR | AACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1084041
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep1
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1084042
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep2
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM1084043
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep2
Location of target site ENST00000367833.2 | 3UTR | AACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM1084044
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep3
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM1084045
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep3
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1084046
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep4
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset GSM1084047
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep4
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUAUAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | AACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 15 for dataset GSM1084066
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_SantaCruzAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 16 for dataset GSM1084067
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SantaCruzAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 17 for dataset GSM1084068
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | AUUGGAGCUUCUGGGCAACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 18 for dataset GSM1084069
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | AACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 19 for dataset GSM1084072
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 20 for dataset GSM1084073
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep1_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 21 for dataset GSM1084074
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_SantaCruzAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 22 for dataset GSM1084075
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep1_SantaCruzAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 23 for dataset GSM1084076
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 24 for dataset GSM1084077
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep1_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | AACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 25 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 26 for dataset GSM1084079
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_AbnovaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 27 for dataset GSM1084081
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SantaCruzAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 28 for dataset GSM1084082
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 29 for dataset GSM1084083
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SigmaAb
Location of target site ENST00000367833.2 | 3UTR | ACAUCGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU
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
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
167 hsa-miR-6501-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT156859 FAM126B family with sequence similarity 126 member B 2 2
MIRT173355 TP53INP1 tumor protein p53 inducible nuclear protein 1 2 2
MIRT369102 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT442037 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT442829 AZIN1 antizyme inhibitor 1 2 2
MIRT443729 CCND2 cyclin D2 2 2
MIRT453771 NUCB1 nucleobindin 1 2 10
MIRT453875 IFRD1 interferon related developmental regulator 1 2 12
MIRT454229 OSBPL10 oxysterol binding protein like 10 2 11
MIRT458829 RPUSD2 RNA pseudouridylate synthase domain containing 2 2 2
MIRT459898 PIGO phosphatidylinositol glycan anchor biosynthesis class O 2 10
MIRT464162 VMP1 vacuole membrane protein 1 2 15
MIRT495411 SMAD2 SMAD family member 2 2 2
MIRT496906 TRIM56 tripartite motif containing 56 2 2
MIRT498653 AP3B2 adaptor related protein complex 3 beta 2 subunit 2 6
MIRT498706 PGAM5 PGAM family member 5, mitochondrial serine/threonine protein phosphatase 2 10
MIRT499308 ZNF485 zinc finger protein 485 2 6
MIRT499707 NFATC2IP nuclear factor of activated T-cells 2 interacting protein 2 10
MIRT499755 CIRH1A UTP4, small subunit processome component 2 6
MIRT499827 PCSK9 proprotein convertase subtilisin/kexin type 9 2 8
MIRT503691 MAVS mitochondrial antiviral signaling protein 2 2
MIRT512418 LAYN layilin 2 4
MIRT516232 RAB3B RAB3B, member RAS oncogene family 2 2
MIRT522554 MCAM melanoma cell adhesion molecule 2 4
MIRT523760 FBXO27 F-box protein 27 2 4
MIRT525107 PRKD2 protein kinase D2 2 2
MIRT525919 KIAA0391 KIAA0391 2 2
MIRT527246 COMMD6 COMM domain containing 6 2 2
MIRT527564 ADCY7 adenylate cyclase 7 2 2
MIRT528764 CD1D CD1d molecule 2 2
MIRT529362 YWHAB tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta 2 4
MIRT529464 ZNF546 zinc finger protein 546 2 2
MIRT530676 CHRNB1 cholinergic receptor nicotinic beta 1 subunit 2 4
MIRT531635 C19orf52 translocase of inner mitochondrial membrane 29 2 4
MIRT531909 SLC4A1 solute carrier family 4 member 1 (Diego blood group) 2 2
MIRT532172 SEC14L5 SEC14 like lipid binding 5 2 4
MIRT534234 SLC25A16 solute carrier family 25 member 16 2 4
MIRT534561 RRAGD Ras related GTP binding D 2 2
MIRT534971 PSD3 pleckstrin and Sec7 domain containing 3 2 2
MIRT536738 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT538544 CELF1 CUGBP Elav-like family member 1 2 2
MIRT540462 ZNF71 zinc finger protein 71 2 2
MIRT540554 PPIC peptidylprolyl isomerase C 2 2
MIRT543593 KIAA1549 KIAA1549 2 2
MIRT543963 RNF20 ring finger protein 20 2 2
MIRT544047 C9orf64 chromosome 9 open reading frame 64 2 2
MIRT544670 AP1S1 adaptor related protein complex 1 sigma 1 subunit 2 2
MIRT550665 TRAF1 TNF receptor associated factor 1 2 2
MIRT558540 CSNK1G3 casein kinase 1 gamma 3 2 4
MIRT574917 Vmp1 vacuole membrane protein 1 2 9
MIRT575298 Osbpl10 oxysterol binding protein-like 10 2 7
MIRT607960 SNX22 sorting nexin 22 2 2
MIRT610649 TIPRL TOR signaling pathway regulator 2 8
MIRT615899 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT617438 CCS copper chaperone for superoxide dismutase 2 2
MIRT617510 C5orf45 MRN complex interacting protein 2 2
MIRT617548 MTO1 mitochondrial tRNA translation optimization 1 2 2
MIRT620565 WBSCR27 methyltransferase like 27 2 2
MIRT623166 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 2 2
MIRT624161 DGKE diacylglycerol kinase epsilon 2 2
MIRT626090 MKLN1 muskelin 1 2 2
MIRT627010 FIG4 FIG4 phosphoinositide 5-phosphatase 2 2
MIRT627073 SF3A1 splicing factor 3a subunit 1 2 2
MIRT627136 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 2 2
MIRT627340 TSHZ2 teashirt zinc finger homeobox 2 2 2
MIRT627436 TAS2R5 taste 2 receptor member 5 2 2
MIRT628273 CYB5D1 cytochrome b5 domain containing 1 2 2
MIRT629091 F2RL1 F2R like trypsin receptor 1 2 4
MIRT629282 UNC13A unc-13 homolog A 2 2
MIRT630122 ARHGEF5 Rho guanine nucleotide exchange factor 5 2 2
MIRT630247 SMTNL2 smoothelin like 2 2 2
MIRT631260 CENPM centromere protein M 2 2
MIRT631336 CD300E CD300e molecule 2 2
MIRT631399 IL2RA interleukin 2 receptor subunit alpha 2 2
MIRT632593 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT632991 DUSP18 dual specificity phosphatase 18 2 2
MIRT633079 CXorf21 chromosome X open reading frame 21 2 2
MIRT634223 TMEM132B transmembrane protein 132B 2 2
MIRT635046 MYH11 myosin heavy chain 11 2 2
MIRT636444 LRCH3 leucine rich repeats and calponin homology domain containing 3 2 2
MIRT636649 CDK4 cyclin dependent kinase 4 2 2
MIRT637129 BAMBI BMP and activin membrane bound inhibitor 2 2
MIRT637282 IBA57 IBA57 homolog, iron-sulfur cluster assembly 2 2
MIRT637527 RGS9BP regulator of G protein signaling 9 binding protein 2 2
MIRT637783 OLA1 Obg like ATPase 1 2 2
MIRT637920 LILRA2 leukocyte immunoglobulin like receptor A2 2 2
MIRT638238 SLC1A5 solute carrier family 1 member 5 2 2
MIRT638444 PLXDC2 plexin domain containing 2 2 2
MIRT639765 GPR45 G protein-coupled receptor 45 2 2
MIRT640437 ERVMER34-1 endogenous retrovirus group MER34 member 1, envelope 2 2
MIRT643006 ZNF829 zinc finger protein 829 2 2
MIRT644233 SLC35E3 solute carrier family 35 member E3 2 2
MIRT644661 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT644957 ATP6AP1L ATPase H+ transporting accessory protein 1 like 2 2
MIRT645086 SLC35E2B solute carrier family 35 member E2B 2 2
MIRT645256 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT645861 GBP6 guanylate binding protein family member 6 2 2
MIRT645987 ACP6 acid phosphatase 6, lysophosphatidic 2 2
MIRT646502 FAM217B family with sequence similarity 217 member B 2 2
MIRT646811 COX19 COX19, cytochrome c oxidase assembly factor 2 2
MIRT647706 NFX1 nuclear transcription factor, X-box binding 1 2 2
MIRT649657 TEP1 telomerase associated protein 1 2 2
MIRT650550 YIPF4 Yip1 domain family member 4 2 2
MIRT650785 GSR glutathione-disulfide reductase 2 2
MIRT651461 XIAP X-linked inhibitor of apoptosis 2 2
MIRT652098 TRUB2 TruB pseudouridine synthase family member 2 2 2
MIRT654117 RPS6KA5 ribosomal protein S6 kinase A5 2 2
MIRT658901 DPY19L4 dpy-19 like 4 2 2
MIRT659370 CREG2 cellular repressor of E1A stimulated genes 2 2 2
MIRT662537 MTAP methylthioadenosine phosphorylase 2 2
MIRT662617 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 2
MIRT663491 IYD iodotyrosine deiodinase 2 2
MIRT663899 MRI1 methylthioribose-1-phosphate isomerase 1 2 2
MIRT664552 MKI67IP nucleolar protein interacting with the FHA domain of MKI67 1 1
MIRT664582 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT664953 PTCD3 pentatricopeptide repeat domain 3 2 2
MIRT665193 ESF1 ESF1 nucleolar pre-rRNA processing protein homolog 2 2
MIRT665446 WDR17 WD repeat domain 17 2 2
MIRT665894 TCEANC2 transcription elongation factor A N-terminal and central domain containing 2 2 2
MIRT666480 SBNO1 strawberry notch homolog 1 2 2
MIRT666514 RNF170 ring finger protein 170 2 2
MIRT666692 RBM23 RNA binding motif protein 23 2 2
MIRT666791 PSMD1 proteasome 26S subunit, non-ATPase 1 2 2
MIRT667453 MAPK14 mitogen-activated protein kinase 14 2 2
MIRT667553 LRAT lecithin retinol acyltransferase 2 4
MIRT667744 KDELR1 KDEL endoplasmic reticulum protein retention receptor 1 2 2
MIRT668080 GMEB1 glucocorticoid modulatory element binding protein 1 2 2
MIRT668114 GK5 glycerol kinase 5 (putative) 2 2
MIRT668501 ESYT2 extended synaptotagmin 2 2 2
MIRT668942 CNKSR3 CNKSR family member 3 2 2
MIRT670408 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT671134 CD226 CD226 molecule 2 2
MIRT671919 PLEKHS1 pleckstrin homology domain containing S1 2 4
MIRT672287 GP2 glycoprotein 2 2 2
MIRT672427 POLR2D RNA polymerase II subunit D 2 2
MIRT672762 UBE2V2 ubiquitin conjugating enzyme E2 V2 2 2
MIRT672923 LRRC2 leucine rich repeat containing 2 2 2
MIRT673150 C1orf50 chromosome 1 open reading frame 50 2 2
MIRT673309 UBE2G2 ubiquitin conjugating enzyme E2 G2 2 2
MIRT673560 PLA2G16 phospholipase A2 group XVI 2 2
MIRT673895 DCTN6 dynactin subunit 6 2 2
MIRT674513 PRR23A proline rich 23A 2 2
MIRT674614 RBBP4 RB binding protein 4, chromatin remodeling factor 2 2
MIRT674747 SLC16A1 solute carrier family 16 member 1 2 2
MIRT675693 PIWIL1 piwi like RNA-mediated gene silencing 1 2 2
MIRT675890 SNAP29 synaptosome associated protein 29 2 2
MIRT685271 KIAA1143 KIAA1143 2 2
MIRT686057 KCNA7 potassium voltage-gated channel subfamily A member 7 2 2
MIRT693886 C3orf62 chromosome 3 open reading frame 62 2 2
MIRT695594 TMEM199 transmembrane protein 199 2 2
MIRT696592 ORMDL2 ORMDL sphingolipid biosynthesis regulator 2 2 2
MIRT698041 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT699907 RUNDC1 RUN domain containing 1 2 2
MIRT706608 CYB5B cytochrome b5 type B 2 2
MIRT706628 PNPT1 polyribonucleotide nucleotidyltransferase 1 2 2
MIRT706640 NCBP2 nuclear cap binding protein subunit 2 2 2
MIRT706676 COL13A1 collagen type XIII alpha 1 chain 2 2
MIRT706723 RFK riboflavin kinase 2 2
MIRT706857 MAFF MAF bZIP transcription factor F 2 2
MIRT706891 ST3GAL1 ST3 beta-galactoside alpha-2,3-sialyltransferase 1 2 2
MIRT706958 FANCC Fanconi anemia complementation group C 2 2
MIRT706976 XPO5 exportin 5 2 2
MIRT707010 RRP36 ribosomal RNA processing 36 2 2
MIRT707028 ACTR5 ARP5 actin related protein 5 homolog 2 2
MIRT707068 MED29 mediator complex subunit 29 2 2
MIRT713253 ZFP30 ZFP30 zinc finger protein 2 2
MIRT719130 NR2F6 nuclear receptor subfamily 2 group F member 6 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-6501 Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-mir-6501 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-miR-6501-5p Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-6501-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-6501-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-6501-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-6501-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-6501-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (451Lu)
hsa-miR-6501-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-6501-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-6501-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-6501-5p Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)

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