miRTarBase - #MIRT286224


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pre-miRNA Information
pre-miRNA hsa-mir-8067   
Genomic Coordinates chr15: 62304658 - 62304734
Description Homo sapiens miR-8067 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-8067
Sequence 11| CCUAGAAACUGUAAACUUAGUC |32
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1439702395 3 dbSNP
rs973468045 19 dbSNP
rs1474855764 20 dbSNP
rs183845458 20 dbSNP
Putative Targets

Gene Information
Gene Symbol TMEM97   
Synonyms MAC30
Description transmembrane protein 97
Transcript NM_014573   
Expression
Putative miRNA Targets on TMEM97
3'UTR of TMEM97
(miRNA target sites are highlighted)		 
>TMEM97|NM_014573|3'UTR
   1 AGGAAACAACCACTGGCCCAGGGTAGAGATGCCTACAGGGTGGTTGCTTGTTGGATACAATACAAGGAACACTGCTCAGA
  81 ACCCACGTCTTCAGCAGCATTTGAAACACTGGCAGCAATGCACAAGAGCAAGATGGTGTCAGGAACCATGTCAAACCCTC
 161 ACCTTCTTCCATTTTTTTTTTTTTTTTAAGACAGTCTCACTCTGTTGCCCAGGCTGGAGTAAAGGGCAGTGGCATGATCT
 241 CGGCTCACTGCAACCTCCGCCTCCTGGGCTCAAGCCATCTTCCTTAGCCTCCCAAGTAGCTAGAACTACAGGTGTGTACC
 321 AACACGTATGGCTAATTTGTTTTGTTTTTTTTGTGTGTGTGGAGACAGGGTTTTGCCATGTTGCCCAGGTTGGTCTCGAA
 401 CGCCTAGGCTCAAGTGATCTGCCCACCTCAGTCTCCCTAAGTGCTGGGATTACAGACGTGAACCACTGGGCCCAGCCCAA
 481 ACCTTCACCTTCTAAGGGCACTGGGATGAACAGACCGATCGGCTTGAGGGTGGGCAAAGGGGTGTGGGCTAGGTTATAAG
 561 GAAGTGGTACCAAATAACTGTGTGCCTGAGTTCCACCGCAAGATTACTAAAAGCAGGACCAGACCAGAAACTGCTAAAGA
 641 ACATGGCCTGTTTGACATGTTCATGAGTCACCTGACCCACAGCATATATGCTTATGACTAAACCCTCCACTCCTGATTCT
 721 CAAGAGTGTATCACCTGTCAGCAAAATGAATAGTGGGATATTTTGGGCCATTTTAAATGTGAAATTTTGCCTCTTTAATG
 801 TTAATTCAAAACTATATCAATGTTTTCTTGTTCCCACCTCTAACCCAAGGAAAAAAGAGAAAACATACTATGCAAAGGAA
 881 GTTTAAACTTAAGTTTTCCTTAAGGGTCAGCCCAACAATGACTTTCAGTCAAATGGATTAAACTGGAAAATGTTTTTGTT
 961 TCTGTTGTAAACAGATCATCCTAGGCGAAAGTTTTTTTTGTTTGTTTGCTTTTAAATTAGTTTATTTCTAAATCTTAGTC
1041 TTCCACATTTCTAGAGGCCACCTGACACAAGTCCCTGTATCTGAAGTCTAGCATCTCAAGGCTGATCTGGAAGTGTGCTA
1121 GTATGCTCCCTAGTGGATAACTTAATCTTTTAATACAGTTCCGTCATTCCCATCTTGTTTTCAGAAGAGAAGGTGGCTAC
1201 AGCCAGGCATAACATATCCACTGTGTGCATAGAGGGTCTCTTCACGTTGATGCTTGGCATTCCATCAGCTTTCTCTAAGT
1281 CTTTGCTCAAGTTCAACCTTAAAATGATGTTAGACAACAGGTCCCAGTCAGTTCCCTCTATTTTCACCCATTTTGCTCAC
1361 AAGCCATATTGGCCCGATTAGTGGTACTGTCTGACTCACGTGTGTGATCCAAATAAAGGTAGCTGCTGACCACTGCCTGG
1441 TTTGTTTTGTGGACTAGGGGATAGAGAATCCAGGGTTCTCTCATGAGGAGTTAAACATATTTCAAGAGCAACAGGAAAAA
1521 AGGTACATCAAGCCATTTGAAAACAAAAATTTATTGCTTCTCCTTCCAAAGCTTTGTGAATTTACAAAAAAAAGGATGAA
1601 AGTTTACAAACTGCTTAGTTCCAACTAAGCATAAGAGGTGAGAACGTACACTGCAGGGCCACCAGCAGCAGCTGTGCACT
1681 GATGTTAAAACTGGCTCCCCCAGACTTGTAGTGCTGTCTTCAGGGGGCTGCATTCCTTACACGCCACCTCTTGTGACATA
1761 GGTCATTGGTCAAGCCGCTGGAATGCTACAGAGGTTTTTTTGGTTTTGAGAGGCTTTTTTTTGTTTTGCCTTCCTACTAT
1841 AAAAGCGAAATTTTCAGTTCATTTCTGAAAAATAAATTGGTCAATAAATTCAAAAAAAAAAAAAAAAAA
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' cuGAUUCA-AA--UGUCAAAGAUCc 5'
            || ||| ||  ||| ||||||| 
Target 5' atCTTAGTCTTCCACA-TTTCTAGa 3'
 1032 - 1055 161.00 -8.00
2 
miRNA  3' cuGAUUCAAAUGUC----AAAGAUcc 5'
            | || ||| |||    |||||:  
Target 5' agCGAAATTTTCAGTTCATTTCTGaa 3'
 1844 - 1869 126.00 -5.40
3 
miRNA  3' cugaUUCAAAUGUCAAAGAUcc 5'
              | |||| : ||||||:  
Target 5' gaaaATGTTT-TTGTTTCTGtt 3'
 946 - 966 121.00 -6.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30472359 3 COSMIC
COSN30139228 55 COSMIC
COSN30115899 75 COSMIC
COSN30452246 80 COSMIC
COSN30514006 112 COSMIC
COSN31507850 141 COSMIC
COSN19614302 162 COSMIC
COSN20113718 188 COSMIC
COSN31598058 260 COSMIC
COSN28819316 1173 COSMIC
COSN28205154 1280 COSMIC
COSN26641703 1411 COSMIC
COSN20888689 1467 COSMIC
COSN21231873 1504 COSMIC
COSN31547721 1552 COSMIC
COSN28706527 1631 COSMIC
COSN26441743 1677 COSMIC
COSN30673859 1727 COSMIC
COSN20078892 1744 COSMIC
COSN30634323 1778 COSMIC
COSN31507459 1797 COSMIC
COSN19372586 1807 COSMIC
COSN30113262 1822 COSMIC
COSN30593096 1823 COSMIC
COSN31523768 1823 COSMIC
COSN31515612 1848 COSMIC
COSM9339747 1883 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs782393067 2 dbSNP
rs781990299 3 dbSNP
rs782229931 5 dbSNP
rs782346870 8 dbSNP
rs781942359 9 dbSNP
rs782060032 13 dbSNP
rs1450282722 16 dbSNP
rs1268771255 17 dbSNP
rs1223974353 19 dbSNP
rs1362229079 20 dbSNP
rs183839374 27 dbSNP
rs1283903240 32 dbSNP
rs782013597 37 dbSNP
rs375640398 39 dbSNP
rs371150467 41 dbSNP
rs1444087838 44 dbSNP
rs1329187826 48 dbSNP
rs1302462642 49 dbSNP
rs1405407605 51 dbSNP
rs1367381854 55 dbSNP
rs545935776 58 dbSNP
rs1295756901 61 dbSNP
rs533998233 70 dbSNP
rs782786530 72 dbSNP
rs1408223993 87 dbSNP
rs1159989661 88 dbSNP
rs782559996 92 dbSNP
rs564087171 104 dbSNP
rs1200618744 108 dbSNP
rs1490970557 110 dbSNP
rs1261698907 124 dbSNP
rs1215123407 141 dbSNP
rs189252817 142 dbSNP
rs1286598502 148 dbSNP
rs375015302 149 dbSNP
rs1217754342 153 dbSNP
rs762648614 159 dbSNP
rs1282331068 161 dbSNP
rs1347277033 163 dbSNP
rs549805184 163 dbSNP
rs1268383097 169 dbSNP
rs1429385081 170 dbSNP
rs1319722620 172 dbSNP
rs1345328194 172 dbSNP
rs782224492 172 dbSNP
rs1177554648 188 dbSNP
rs1061480 189 dbSNP
rs1422084833 192 dbSNP
rs1186508609 197 dbSNP
rs1475777790 203 dbSNP
rs1243847724 208 dbSNP
rs1208123801 216 dbSNP
rs1460998938 217 dbSNP
rs1264021082 222 dbSNP
rs1204025235 225 dbSNP
rs1325481047 238 dbSNP
rs782032935 242 dbSNP
rs557035057 243 dbSNP
rs1362589340 260 dbSNP
rs1271383249 261 dbSNP
rs1449875289 266 dbSNP
rs1381549846 269 dbSNP
rs1337043659 274 dbSNP
rs1471155199 278 dbSNP
rs1398649171 282 dbSNP
rs1170189827 285 dbSNP
rs1410959913 299 dbSNP
rs1422296816 300 dbSNP
rs562056352 304 dbSNP
rs1180147495 309 dbSNP
rs191347455 316 dbSNP
rs1243949429 326 dbSNP
rs1185721363 327 dbSNP
rs1462483924 332 dbSNP
rs1249345120 336 dbSNP
rs1203588668 341 dbSNP
rs1307966569 343 dbSNP
rs1275081521 344 dbSNP
rs1243113148 345 dbSNP
rs1315309556 345 dbSNP
rs548208727 345 dbSNP
rs782044387 346 dbSNP
rs566551257 350 dbSNP
rs1370738098 351 dbSNP
rs1356753666 352 dbSNP
rs1443421585 352 dbSNP
rs183657898 352 dbSNP
rs1162277413 353 dbSNP
rs1424084684 354 dbSNP
rs1386013348 355 dbSNP
rs781819894 356 dbSNP
rs1165563205 357 dbSNP
rs1438008000 360 dbSNP
rs1250116223 368 dbSNP
rs1176378232 370 dbSNP
rs1480863116 381 dbSNP
rs1234516213 383 dbSNP
rs552648373 385 dbSNP
rs1220247035 391 dbSNP
rs1490166184 396 dbSNP
rs1291801615 398 dbSNP
rs1247568450 399 dbSNP
rs368511557 402 dbSNP
rs1305903087 403 dbSNP
rs1224665598 409 dbSNP
rs1376059830 413 dbSNP
rs1301831534 416 dbSNP
rs1404806738 423 dbSNP
rs1366758182 428 dbSNP
rs1304990126 429 dbSNP
rs1451770570 432 dbSNP
rs1363414756 442 dbSNP
rs782120485 456 dbSNP
rs1419445698 457 dbSNP
rs188363234 458 dbSNP
rs1490153275 459 dbSNP
rs1269562495 467 dbSNP
rs542218565 468 dbSNP
rs1224034101 471 dbSNP
rs1484636351 483 dbSNP
rs781888426 488 dbSNP
rs1259770788 491 dbSNP
rs1216148703 492 dbSNP
rs1318359477 494 dbSNP
rs1281720657 496 dbSNP
rs1223311314 501 dbSNP
rs1346660929 502 dbSNP
rs1285803888 518 dbSNP
rs782553660 521 dbSNP
rs538476433 533 dbSNP
rs1289524777 536 dbSNP
rs1455484957 542 dbSNP
rs1404219844 543 dbSNP
rs1173945132 559 dbSNP
rs1480012165 561 dbSNP
rs1429883181 562 dbSNP
rs1200989000 566 dbSNP
rs1426216112 567 dbSNP
rs1260353511 583 dbSNP
rs1186607096 589 dbSNP
rs1486620649 594 dbSNP
rs1260910185 598 dbSNP
rs1203408566 599 dbSNP
rs558969201 602 dbSNP
rs1324787654 603 dbSNP
rs1265535832 605 dbSNP
rs1225788782 608 dbSNP
rs782567779 618 dbSNP
rs1296322790 620 dbSNP
rs781810899 621 dbSNP
rs1380823020 622 dbSNP
rs1336380748 627 dbSNP
rs1469091233 635 dbSNP
rs1174111063 637 dbSNP
rs556567668 637 dbSNP
rs139090480 648 dbSNP
rs1460350829 654 dbSNP
rs1372463648 655 dbSNP
rs1193234614 657 dbSNP
rs1450844849 662 dbSNP
rs1240868904 663 dbSNP
rs1182666496 664 dbSNP
rs1461491787 675 dbSNP
rs1258629054 678 dbSNP
rs1194457543 682 dbSNP
rs1339264205 685 dbSNP
rs577491390 690 dbSNP
rs1229679251 696 dbSNP
rs1357450885 697 dbSNP
rs1314628715 705 dbSNP
rs1453569723 706 dbSNP
rs1385281286 707 dbSNP
rs782468820 714 dbSNP
rs1389501205 720 dbSNP
rs1395655927 722 dbSNP
rs1168480962 729 dbSNP
rs1431098611 732 dbSNP
rs535419437 735 dbSNP
rs782629325 737 dbSNP
rs1162389038 748 dbSNP
rs1444809731 750 dbSNP
rs114830246 754 dbSNP
rs1437669310 758 dbSNP
rs149888615 760 dbSNP
rs1291058611 765 dbSNP
rs1490004893 765 dbSNP
rs1246835460 766 dbSNP
rs1361820901 780 dbSNP
rs1278050708 782 dbSNP
rs145926849 790 dbSNP
rs1236594090 807 dbSNP
rs1335016954 808 dbSNP
rs572494753 815 dbSNP
rs1411519672 817 dbSNP
rs576148737 819 dbSNP
rs1363658276 820 dbSNP
rs1301943058 821 dbSNP
rs1424796182 822 dbSNP
rs1415487884 829 dbSNP
rs782241622 834 dbSNP
rs1469947172 835 dbSNP
rs1364675178 838 dbSNP
rs782385831 845 dbSNP
rs1479714863 851 dbSNP
rs1268839436 856 dbSNP
rs1223288905 869 dbSNP
rs1453457545 872 dbSNP
rs545326890 879 dbSNP
rs1204703845 882 dbSNP
rs1351685979 883 dbSNP
rs1288693137 900 dbSNP
rs1230031908 905 dbSNP
rs561815761 907 dbSNP
rs1343528291 909 dbSNP
rs1282620630 911 dbSNP
rs1405020387 917 dbSNP
rs1351186142 928 dbSNP
rs140182368 934 dbSNP
rs191616621 937 dbSNP
rs1399700865 945 dbSNP
rs1385251771 963 dbSNP
rs1161778255 973 dbSNP
rs1468613967 977 dbSNP
rs560072938 987 dbSNP
rs1200859651 988 dbSNP
rs1479291791 989 dbSNP
rs1192587446 992 dbSNP
rs1240368789 992 dbSNP
rs1447754510 992 dbSNP
rs1270293103 993 dbSNP
rs1210340491 995 dbSNP
rs1262432004 997 dbSNP
rs1321234093 997 dbSNP
rs74586350 1000 dbSNP
rs1219671672 1005 dbSNP
rs1369657722 1009 dbSNP
rs1267850470 1010 dbSNP
rs1429453263 1012 dbSNP
rs1365435962 1016 dbSNP
rs527680824 1020 dbSNP
rs1468560943 1026 dbSNP
rs1405723715 1038 dbSNP
rs1177616392 1045 dbSNP
rs1416605058 1048 dbSNP
rs1418027504 1051 dbSNP
rs1167371005 1075 dbSNP
rs1250123893 1077 dbSNP
rs751076541 1081 dbSNP
rs552384028 1096 dbSNP
rs1242247473 1109 dbSNP
rs1210586383 1116 dbSNP
rs782305313 1122 dbSNP
rs1270845219 1127 dbSNP
rs1213461696 1143 dbSNP
rs184912091 1149 dbSNP
rs1299179072 1171 dbSNP
rs1449937929 1172 dbSNP
rs11554038 1173 dbSNP
rs1303747863 1175 dbSNP
rs1450679242 1177 dbSNP
rs1353242021 1194 dbSNP
rs549995523 1196 dbSNP
rs1392032304 1201 dbSNP
rs1161766921 1206 dbSNP
rs1444185484 1210 dbSNP
rs1386129571 1215 dbSNP
rs200476960 1216 dbSNP
rs536121098 1218 dbSNP
rs1203654443 1219 dbSNP
rs1243175522 1231 dbSNP
rs782373121 1235 dbSNP
rs1358242836 1239 dbSNP
rs189946605 1241 dbSNP
rs1371719320 1242 dbSNP
rs79867449 1246 dbSNP
rs539461497 1247 dbSNP
rs182181876 1253 dbSNP
rs782152751 1256 dbSNP
rs1350665827 1265 dbSNP
rs1167253605 1268 dbSNP
rs574941448 1275 dbSNP
rs1405448484 1276 dbSNP
rs576117402 1277 dbSNP
rs1472852746 1279 dbSNP
rs1253936033 1289 dbSNP
rs543177986 1290 dbSNP
rs1490059388 1291 dbSNP
rs1265662892 1292 dbSNP
rs1223230071 1305 dbSNP
rs1314783053 1311 dbSNP
rs561440618 1316 dbSNP
rs1229432130 1320 dbSNP
rs781801532 1328 dbSNP
rs1404399624 1331 dbSNP
rs1368308745 1341 dbSNP
rs1295373395 1343 dbSNP
rs11554037 1349 dbSNP
rs1158099629 1351 dbSNP
rs1457613079 1355 dbSNP
rs1414071051 1360 dbSNP
rs1197267160 1363 dbSNP
rs1432531657 1365 dbSNP
rs1267371747 1367 dbSNP
rs1192453848 1368 dbSNP
rs1484668037 1372 dbSNP
rs1259826189 1376 dbSNP
rs1209727631 1377 dbSNP
rs1261665320 1385 dbSNP
rs1223368468 1392 dbSNP
rs1313319769 1398 dbSNP
rs1303447586 1400 dbSNP
rs1361497680 1403 dbSNP
rs1321535156 1422 dbSNP
rs143873183 1438 dbSNP
rs1174012004 1443 dbSNP
rs1465445260 1444 dbSNP
rs1378168534 1447 dbSNP
rs1177567000 1448 dbSNP
rs1426270276 1459 dbSNP
rs1247020989 1460 dbSNP
rs1188882414 1463 dbSNP
rs1465985512 1484 dbSNP
rs992300012 1490 dbSNP
rs1043172 1499 dbSNP
rs559267485 1500 dbSNP
rs1203466867 1503 dbSNP
rs1346289479 1513 dbSNP
rs782071620 1515 dbSNP
rs527666837 1518 dbSNP
rs1258336307 1521 dbSNP
rs1225313835 1526 dbSNP
rs1307057634 1533 dbSNP
rs1298424916 1537 dbSNP
rs1230816773 1545 dbSNP
rs1380886181 1545 dbSNP
rs1334407704 1552 dbSNP
rs1395285030 1560 dbSNP
rs1402797348 1564 dbSNP
rs1304573047 1573 dbSNP
rs1460023626 1575 dbSNP
rs948236851 1578 dbSNP
rs1168698087 1579 dbSNP
rs1450901431 1586 dbSNP
rs76925317 1587 dbSNP
rs980840468 1588 dbSNP
rs1187250405 1591 dbSNP
rs1443407777 1597 dbSNP
rs778167334 1607 dbSNP
rs1194512863 1609 dbSNP
rs1483024940 1613 dbSNP
rs1275384717 1616 dbSNP
rs782750781 1619 dbSNP
rs931280624 1627 dbSNP
rs114585959 1629 dbSNP
rs1243780246 1633 dbSNP
rs886326350 1646 dbSNP
rs564402815 1647 dbSNP
rs1369904888 1654 dbSNP
rs1308081093 1662 dbSNP
rs940599232 1664 dbSNP
rs1431155861 1666 dbSNP
rs1162348225 1698 dbSNP
rs1040324533 1699 dbSNP
rs901669979 1711 dbSNP
rs531803268 1724 dbSNP
rs1370502107 1727 dbSNP
rs995988970 1741 dbSNP
rs116558075 1743 dbSNP
rs1253223643 1748 dbSNP
rs1207359816 1749 dbSNP
rs903625774 1756 dbSNP
rs1210590980 1758 dbSNP
rs1289425576 1758 dbSNP
rs187102473 1760 dbSNP
rs1031088053 1764 dbSNP
rs956438084 1770 dbSNP
rs1236664525 1771 dbSNP
rs1014247359 1774 dbSNP
rs1349775451 1774 dbSNP
rs529560028 1777 dbSNP
rs548101265 1778 dbSNP
rs1322318926 1788 dbSNP
rs1405544385 1790 dbSNP
rs1392474226 1791 dbSNP
rs35381358 1795 dbSNP
rs1157165418 1796 dbSNP
rs1457093564 1802 dbSNP
rs566411616 1803 dbSNP
rs781834356 1814 dbSNP
rs781854530 1815 dbSNP
rs782766251 1815 dbSNP
rs782462955 1818 dbSNP
rs782726537 1820 dbSNP
rs781790398 1823 dbSNP
rs749520845 1824 dbSNP
rs782536935 1827 dbSNP
rs563673798 1828 dbSNP
rs782249628 1829 dbSNP
rs782500870 1834 dbSNP
rs782598200 1838 dbSNP
rs1206573759 1841 dbSNP
rs1328295224 1843 dbSNP
rs782200326 1847 dbSNP
rs782312110 1848 dbSNP
rs782041220 1851 dbSNP
rs1342809215 1857 dbSNP
rs1273691506 1864 dbSNP
rs952917251 1878 dbSNP
rs982925150 1883 dbSNP
rs782273317 1886 dbSNP
rs1332445735 1887 dbSNP
rs11871371 1890 dbSNP
rs1434820731 1891 dbSNP
rs944080087 1892 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.

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 HEK293
Disease 27346.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 "PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cuGAUUCA-AA--UGUCAAAGAUCc 5'
            || ||| ||  ||| ||||||| 
Target 5' auCUUAGUCUUCCACA-UUUCUAG- 3'
 		11 - 33
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
CLIP-seq Support 1 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000226230.6 | 3UTR | UUUAUUUCUAAAUCUUAGUCUUCCACAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000226230.6 | 3UTR | UUUAUUUCUAAAUCUUAGUCUUCCACAUUUCUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000226230.6 | 3UTR | UUAUUUCUAAAUCUUAGUCUUCCACAUUUCUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
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
68 hsa-miR-8067 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT084581 BCL2L11 BCL2 like 11 2 4
MIRT088215 NUP50 nucleoporin 50 2 2
MIRT092085 ABHD5 abhydrolase domain containing 5 2 2
MIRT135269 TMBIM6 transmembrane BAX inhibitor motif containing 6 2 8
MIRT175259 PSAT1 phosphoserine aminotransferase 1 2 6
MIRT182508 KLHL20 kelch like family member 20 2 2
MIRT286224 TMEM97 transmembrane protein 97 2 4
MIRT301718 TEF TEF, PAR bZIP transcription factor 2 2
MIRT329381 CCNG1 cyclin G1 2 2
MIRT362146 MTRNR2L6 MT-RNR2-like 6 2 4
MIRT366561 EIF2S3 eukaryotic translation initiation factor 2 subunit gamma 2 2
MIRT442002 NDUFV3 NADH:ubiquinone oxidoreductase subunit V3 2 2
MIRT442039 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT443045 HPS4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 2 2
MIRT446861 SAMD9L sterile alpha motif domain containing 9 like 2 2
MIRT450346 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT454306 ZNF134 zinc finger protein 134 2 2
MIRT481951 ANKRD11 ankyrin repeat domain 11 2 2
MIRT484816 ZNFX1 zinc finger NFX1-type containing 1 2 2
MIRT497596 EBAG9 estrogen receptor binding site associated, antigen, 9 2 2
MIRT498620 MTRNR2L10 MT-RNR2-like 10 2 12
MIRT501852 MTRNR2L8 MT-RNR2-like 8 2 15
MIRT502628 DDX3X DEAD-box helicase 3, X-linked 2 8
MIRT503298 GTF2A1 general transcription factor IIA subunit 1 2 6
MIRT506789 KLHL15 kelch like family member 15 2 6
MIRT515069 PLA2G2C phospholipase A2 group IIC 2 2
MIRT521334 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT523692 FHL2 four and a half LIM domains 2 2 4
MIRT524416 CNOT6L CCR4-NOT transcription complex subunit 6 like 2 4
MIRT525526 FSIP2 fibrous sheath interacting protein 2 2 2
MIRT525771 SOD2 superoxide dismutase 2 2 2
MIRT526262 CCDC169 coiled-coil domain containing 169 2 2
MIRT526545 MDM2 MDM2 proto-oncogene 2 2
MIRT527522 CD59 CD59 molecule (CD59 blood group) 2 2
MIRT530875 TRUB1 TruB pseudouridine synthase family member 1 2 4
MIRT532991 ZKSCAN8 zinc finger with KRAB and SCAN domains 8 2 2
MIRT535581 NUP35 nucleoporin 35 2 2
MIRT536922 HEPHL1 hephaestin like 1 2 2
MIRT540004 NT5DC3 5'-nucleotidase domain containing 3 2 2
MIRT540779 SCO1 SCO1, cytochrome c oxidase assembly protein 2 2
MIRT541006 ZNF136 zinc finger protein 136 2 2
MIRT542072 ASS1 argininosuccinate synthase 1 2 6
MIRT544103 IPMK inositol polyphosphate multikinase 2 2
MIRT547669 KPNA1 karyopherin subunit alpha 1 2 4
MIRT549914 MRPS30 mitochondrial ribosomal protein S30 2 2
MIRT551741 HIST1H2BD histone cluster 1 H2B family member d 2 2
MIRT556374 LUZP1 leucine zipper protein 1 2 2
MIRT557320 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT561442 TOB2 transducer of ERBB2, 2 2 2
MIRT563938 TAF7 TATA-box binding protein associated factor 7 2 2
MIRT622315 SEH1L SEH1 like nucleoporin 2 2
MIRT622334 SEC63 SEC63 homolog, protein translocation regulator 2 2
MIRT627928 KANSL1 KAT8 regulatory NSL complex subunit 1 2 2
MIRT636122 YPEL1 yippee like 1 2 2
MIRT644871 C2orf48 chromosome 2 open reading frame 48 2 2
MIRT645105 LANCL3 LanC like 3 2 2
MIRT650430 BBS9 Bardet-Biedl syndrome 9 2 2
MIRT653330 SMIM18 small integral membrane protein 18 2 2
MIRT658101 FOXN3 forkhead box N3 2 2
MIRT690032 CCDC90B coiled-coil domain containing 90B 2 2
MIRT697283 ZNF800 zinc finger protein 800 2 2
MIRT700266 RAP2B RAP2B, member of RAS oncogene family 2 2
MIRT700310 RABGEF1 RAB guanine nucleotide exchange factor 1 2 2
MIRT705431 ATP11A ATPase phospholipid transporting 11A 2 2
MIRT706193 MED24 mediator complex subunit 24 2 2
MIRT707928 PPP1R3D protein phosphatase 1 regulatory subunit 3D 2 2
MIRT716123 RPL24 ribosomal protein L24 2 2
MIRT720940 PPP1R3E protein phosphatase 1 regulatory subunit 3E 2 2

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