miRTarBase - #MIRT456846


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pre-miRNA Information
pre-miRNA hsa-mir-6888   
Genomic Coordinates chr2: 159186835 - 159186901
Description Homo sapiens miR-6888 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6888-5p
Sequence 6| AAGGAGAUGCUCAGGCAGAU |25
Evidence Experimental
Experiments Meta-analysis
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs766276740 4 dbSNP
rs1348014091 6 dbSNP
rs755543842 16 dbSNP
rs1224830578 19 dbSNP
Putative Targets

Gene Information
Gene Symbol ZNF460   
Synonyms HZF8, ZNF272
Description zinc finger protein 460
Transcript NM_006635   
Expression
Putative miRNA Targets on ZNF460
3'UTR of ZNF460
(miRNA target sites are highlighted)		 
>ZNF460|NM_006635|3'UTR
   1 CAGATGTGGAAAGACTTTTTACGTACACTTCAGTCAACATCCAAGAATTCCTATTAGCGAAATAGTTTTTTAATATAACC
  81 ACTGAAGAAAATCTGTGGTGAGAGGAAACATCTTACCATCTGGTCATTCATACTGAAGAGAAACTCCATAAGTATCATCT
 161 CTGTGGGAAAACCTGTTTTAGATCATCATTTGTCATCTAAACAATTATGTTAGAAATTGACACAGCCAAGAGTCTTATTC
 241 TACATCTGATAATTCACCCATGAAAGAGACCCAGTGGTTACTGTGCACTTAGGAAAACCTTCAGCCACATCTTTCTTATT
 321 AGTTTACAGTGAAATGTTATCTCAGGGACATTCAAACAAAGGAGGAGGAGTCATAGGGAAGAGAAAGAAATGGAAGCACA
 401 GCTTCTTTCAGACTTCCCTGACAAGCCCATGGCAATTTGTCATCCCCTCCTTATTTTATTTGGGAGAGGGAAATGTTTCA
 481 GAAACAAAAGGGCCTCATCCCCTTTATTTTCCCTGTGTATACATTCACTGCTGTCCAGTGCTGTAGACAAACGGTTTGTT
 561 TGAAAACATTTTGTGAAAGCCTGCTTTGTTCCACAGCATTGTCTCCACTCTTGAGGAGCAGAAGCATATATCTTTATGAG
 641 AAAGATGGAGGCTTGAGTTATGAAATACTTTTACATTTAAGGAGATAAAGGATGTACATATGAATGGGCACATTTTACTG
 721 CACACTTCAGACGCTTTGACTTTTTTAAAAAAATTGTTTCTCCGTGTGTCTTTAACCACCCAGTACCATACTTTTTTCTT
 801 GATCTGGATCTACTTGTCAATTTCTTCTTTATTTTTCTGTAGGATGGAGATGATATTGTAGCTGTTTGTACATAATGTAA
 881 TCCAGGGAGTCCTAATTCTTCCCTCTGATTGTGGTTTCTCAGCTTTTTTACTGCTCTTTAGAGAGAGTAAATAGTTCAAA
 961 ATTCACCTCAACAATTTTCTAGAGGTCAATTTGGAACCAAAAATGAAATAAGACATGTAGCTAAAGTAAGTTAAAAGATT
1041 ATGATAAACTCAGAAAATAAACACAGAGAAGGAATCTCATTTTTCAGTCTTACAGAAGATTGTGTGAAGGCTGACTATAC
1121 ATAAAGTGACTGGAATTTTAACAGGTGAACCTGCATATGTATATGCAGGTAGTTGTCACCATGGATTGAGTCCAGTCGTA
1201 GTAATTAATATGTTTAATCAGAATATTTTGGAATTTCTCTTTTGGTATTCTTTTTGTTTCTTTTATTGTTTTTAATTGAC
1281 AATGTTTATGGGGTTTGGTGTGATATTTCAATACATGTGTGCTAAGAGTAATGATCAAATCAGGGTAATTAGCATATCCA
1361 TCTCAATCATTTATCATTTCTTTGTGTTTAGAAACATTCACAGTCTGCTTTTCTAGCTATTTGAAAATATAAAATGTATT
1441 ATTGCCAATTGTACTCATTCTGCAGTGCCACAGAACACTACAACTTATTCAAATGGAATCTTACTTGCTGTAATTTTGTA
1521 TTTGTTAACCAATCTCTATCTGCCTCTCTGCTGTCCTTCCCAGCCTCTGGTTACCACCATTCTCAACCTTTTATGCTTGC
1601 ATATGAGTAGAAACATGGAGTATTTCTCTTTCTGTGTCTAGCTTATTTCACTTAATGTCTTTCAAGCTCATTCATGTTGC
1681 TGTGAATGACAGGTTTATTTTTCATGGCTGAGTAGTATTCCATTGTGTATATATGCCATGTTTTCTTTCTTCATTCATCT
1761 GATAATGGACACTTAGACTGATTTCTTAGCTATTATGAATAGTGCTTCAATAAACATAGGAGTGTAGATCTCTCTTTG
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' uaGACGGACU---CGUAGAGGAa 5'
            :| |:|||   | |||| || 
Target 5' ttTTTCTTGATCTGGATCTACTt 3'
 793 - 815 122.00 -8.30
2 
miRNA  3' uagaCGGACUCGUAGAGGAa 5'
              ||||   |||| ||| 
Target 5' aaggGCCT---CATCCCCTt 3'
 488 - 504 121.00 -12.40
3 
miRNA  3' uagacGGACUCG-UAGAGGAa 5'
               ||| | | ||:|:|| 
Target 5' attcaCCTCAACAATTTTCTa 3'
 961 - 981 119.00 -6.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30127773 23 COSMIC
COSN30502690 30 COSMIC
COSN30159005 40 COSMIC
COSN31504480 42 COSMIC
COSN1219331 47 COSMIC
COSN30503878 52 COSMIC
COSN13839101 59 COSMIC
COSN30186342 60 COSMIC
COSN31581063 60 COSMIC
COSN30466227 130 COSMIC
COSN30034020 149 COSMIC
COSN31525900 207 COSMIC
COSN1772774 230 COSMIC
COSN30760325 251 COSMIC
COSN26613283 329 COSMIC
COSN2470390 334 COSMIC
COSN25563036 506 COSMIC
COSN20116148 747 COSMIC
COSN21622466 754 COSMIC
COSN28949731 1109 COSMIC
rs12459174 1122 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1475052438 1 dbSNP
rs761316193 3 dbSNP
rs770139856 4 dbSNP
rs574950289 6 dbSNP
rs1456622314 7 dbSNP
rs772580736 13 dbSNP
rs1195151043 15 dbSNP
rs1237380583 16 dbSNP
rs1444969034 18 dbSNP
rs765913872 19 dbSNP
rs774325083 23 dbSNP
rs146064837 24 dbSNP
rs374914464 28 dbSNP
rs1165003524 29 dbSNP
rs758964592 30 dbSNP
rs1463762877 32 dbSNP
rs932156767 33 dbSNP
rs1268782266 35 dbSNP
rs1383039931 40 dbSNP
rs45618338 47 dbSNP
rs1311025169 50 dbSNP
rs532687232 54 dbSNP
rs112083299 59 dbSNP
rs551171680 60 dbSNP
rs185214458 64 dbSNP
rs902204594 65 dbSNP
rs1395767534 67 dbSNP
rs777079185 72 dbSNP
rs755518939 76 dbSNP
rs1309559949 77 dbSNP
rs562451571 94 dbSNP
rs986838350 96 dbSNP
rs908524019 111 dbSNP
rs1032689237 117 dbSNP
rs531449454 124 dbSNP
rs865801458 131 dbSNP
rs971980690 138 dbSNP
rs920511295 144 dbSNP
rs1203287947 154 dbSNP
rs930500077 159 dbSNP
rs1310493045 160 dbSNP
rs1343255044 162 dbSNP
rs1303146139 169 dbSNP
rs1232276894 176 dbSNP
rs894941104 180 dbSNP
rs1373546316 182 dbSNP
rs1045260163 186 dbSNP
rs763841073 197 dbSNP
rs1352655510 200 dbSNP
rs1330767424 202 dbSNP
rs1235590141 204 dbSNP
rs1430361553 205 dbSNP
rs753496374 213 dbSNP
rs548279744 228 dbSNP
rs758853200 233 dbSNP
rs375866255 251 dbSNP
rs1012094674 262 dbSNP
rs1425502007 263 dbSNP
rs1176100870 265 dbSNP
rs1479348805 266 dbSNP
rs1234136650 267 dbSNP
rs1056203424 270 dbSNP
rs567720216 271 dbSNP
rs892159635 273 dbSNP
rs1257096294 275 dbSNP
rs1280057367 276 dbSNP
rs1024846671 277 dbSNP
rs1341995401 282 dbSNP
rs1209248115 289 dbSNP
rs970798389 297 dbSNP
rs983971467 310 dbSNP
rs374138644 320 dbSNP
rs1410290894 322 dbSNP
rs904072469 322 dbSNP
rs1374848771 327 dbSNP
rs1310834495 328 dbSNP
rs997028012 329 dbSNP
rs1157852643 331 dbSNP
rs1416953507 334 dbSNP
rs1028887311 335 dbSNP
rs1182353853 337 dbSNP
rs780542871 343 dbSNP
rs963727237 346 dbSNP
rs973642785 354 dbSNP
rs922197971 356 dbSNP
rs1008759819 358 dbSNP
rs1015616128 362 dbSNP
rs1434390343 379 dbSNP
rs932271923 388 dbSNP
rs536956090 391 dbSNP
rs1427686341 402 dbSNP
rs1354716829 408 dbSNP
rs1170443606 414 dbSNP
rs1239746025 418 dbSNP
rs1370901526 422 dbSNP
rs920513034 423 dbSNP
rs952030152 428 dbSNP
rs1293148921 429 dbSNP
rs980641168 430 dbSNP
rs926478178 438 dbSNP
rs1159227773 439 dbSNP
rs1388751427 445 dbSNP
rs561733969 450 dbSNP
rs527437530 452 dbSNP
rs939180411 454 dbSNP
rs547264452 461 dbSNP
rs570770908 467 dbSNP
rs913644446 475 dbSNP
rs368889986 482 dbSNP
rs1307476454 489 dbSNP
rs1257225219 494 dbSNP
rs1262459807 498 dbSNP
rs912087859 500 dbSNP
rs747510641 503 dbSNP
rs868089089 512 dbSNP
rs138081768 517 dbSNP
rs79840013 520 dbSNP
rs936334827 522 dbSNP
rs568880816 525 dbSNP
rs904123374 526 dbSNP
rs1343294725 529 dbSNP
rs1053675523 536 dbSNP
rs570329452 538 dbSNP
rs1221377419 544 dbSNP
rs1264051849 549 dbSNP
rs1380360529 553 dbSNP
rs537973698 554 dbSNP
rs1320759087 555 dbSNP
rs1439732168 562 dbSNP
rs895055698 572 dbSNP
rs1166478401 574 dbSNP
rs1459897641 579 dbSNP
rs1369609235 582 dbSNP
rs142673301 599 dbSNP
rs891313848 608 dbSNP
rs1392452387 622 dbSNP
rs1189389790 627 dbSNP
rs1024794188 629 dbSNP
rs1210082430 646 dbSNP
rs1246832887 655 dbSNP
rs553750243 662 dbSNP
rs1190408117 670 dbSNP
rs1390771231 672 dbSNP
rs1423026295 674 dbSNP
rs1162353309 685 dbSNP
rs574943649 687 dbSNP
rs1488752594 691 dbSNP
rs1250726768 692 dbSNP
rs769826328 699 dbSNP
rs1225187314 701 dbSNP
rs1308981911 706 dbSNP
rs534446153 718 dbSNP
rs1233029840 722 dbSNP
rs963379471 728 dbSNP
rs1368423090 733 dbSNP
rs973805895 734 dbSNP
rs995483820 739 dbSNP
rs3833289 741 dbSNP
rs796375650 741 dbSNP
rs1298066924 742 dbSNP
rs1169698295 747 dbSNP
rs1372723688 747 dbSNP
rs76980960 747 dbSNP
rs1028990990 748 dbSNP
rs981120583 754 dbSNP
rs190061263 756 dbSNP
rs773444792 757 dbSNP
rs960856073 761 dbSNP
rs1249932579 763 dbSNP
rs1193940556 764 dbSNP
rs3746228 765 dbSNP
rs912030106 774 dbSNP
rs946223421 778 dbSNP
rs913657379 788 dbSNP
rs1276291331 791 dbSNP
rs1334611333 793 dbSNP
rs977826753 795 dbSNP
rs1300434001 796 dbSNP
rs182083810 799 dbSNP
rs145996487 808 dbSNP
rs1228263327 809 dbSNP
rs752267814 813 dbSNP
rs1308993265 820 dbSNP
rs774130763 821 dbSNP
rs1245026121 822 dbSNP
rs1267155787 825 dbSNP
rs894836341 827 dbSNP
rs947923527 828 dbSNP
rs141412974 832 dbSNP
rs1050472070 838 dbSNP
rs891372032 845 dbSNP
rs1046366284 847 dbSNP
rs1252515096 851 dbSNP
rs906325789 854 dbSNP
rs576060460 855 dbSNP
rs1036235067 856 dbSNP
rs995575736 857 dbSNP
rs1027008113 859 dbSNP
rs1349588507 862 dbSNP
rs905898302 872 dbSNP
rs541952302 877 dbSNP
rs1001534395 878 dbSNP
rs561859684 881 dbSNP
rs1352833581 882 dbSNP
rs1289477255 888 dbSNP
rs1414733585 897 dbSNP
rs1034020547 898 dbSNP
rs1248113522 905 dbSNP
rs1336559000 906 dbSNP
rs1396825402 910 dbSNP
rs3746227 927 dbSNP
rs1156873516 935 dbSNP
rs139943011 938 dbSNP
rs994955884 951 dbSNP
rs1412836452 954 dbSNP
rs1180069810 962 dbSNP
rs1474193095 963 dbSNP
rs1028939988 964 dbSNP
rs1238922116 970 dbSNP
rs992012724 972 dbSNP
rs1446041146 973 dbSNP
rs564112339 980 dbSNP
rs1210241276 985 dbSNP
rs966521670 1004 dbSNP
rs1009078441 1010 dbSNP
rs11666061 1013 dbSNP
rs1233134652 1014 dbSNP
rs566120492 1016 dbSNP
rs186412310 1025 dbSNP
rs1318741254 1027 dbSNP
rs1455845660 1027 dbSNP
rs1437579290 1034 dbSNP
rs1389395302 1035 dbSNP
rs1322566859 1039 dbSNP
rs1325307065 1044 dbSNP
rs1459795314 1047 dbSNP
rs1415935922 1050 dbSNP
rs1345879520 1059 dbSNP
rs767499803 1064 dbSNP
rs1371148211 1065 dbSNP
rs1190038601 1066 dbSNP
rs1465068312 1067 dbSNP
rs1251826649 1076 dbSNP
rs775221021 1080 dbSNP
rs912823050 1080 dbSNP
rs1381767611 1112 dbSNP
rs1292695715 1115 dbSNP
rs367813986 1118 dbSNP
rs12459174 1122 dbSNP
rs1230802321 1124 dbSNP
rs1366283952 1128 dbSNP
rs548281230 1133 dbSNP
rs1326563261 1136 dbSNP
rs377052027 1144 dbSNP
rs1048990261 1148 dbSNP
rs1268153815 1150 dbSNP
rs1351717554 1152 dbSNP
rs188417331 1160 dbSNP
rs180783809 1161 dbSNP
rs1035672793 1164 dbSNP
rs756939099 1166 dbSNP
rs1449688462 1173 dbSNP
rs940659332 1176 dbSNP
rs1478703684 1177 dbSNP
rs371488109 1177 dbSNP
rs1246807533 1186 dbSNP
rs1222878429 1191 dbSNP
rs1036587722 1194 dbSNP
rs1013537760 1196 dbSNP
rs899028651 1198 dbSNP
rs185199828 1199 dbSNP
rs1369741459 1202 dbSNP
rs979254333 1203 dbSNP
rs751938489 1205 dbSNP
rs35677391 1206 dbSNP
rs889073730 1206 dbSNP
rs1008859043 1208 dbSNP
rs1018934558 1209 dbSNP
rs1032515777 1214 dbSNP
rs1414026855 1226 dbSNP
rs968032531 1234 dbSNP
rs557121148 1240 dbSNP
rs142101923 1243 dbSNP
rs1425177727 1257 dbSNP
rs912257395 1260 dbSNP
rs943686589 1264 dbSNP
rs1250296068 1267 dbSNP
rs972998668 1269 dbSNP
rs1483558142 1281 dbSNP
rs573797462 1281 dbSNP
rs1208196617 1283 dbSNP
rs910609857 1283 dbSNP
rs957580252 1294 dbSNP
rs559787367 1297 dbSNP
rs1279403399 1299 dbSNP
rs1048515922 1301 dbSNP
rs540140136 1304 dbSNP
rs1290099120 1305 dbSNP
rs1366266829 1308 dbSNP
rs1217030979 1309 dbSNP
rs1280648414 1315 dbSNP
rs781739088 1319 dbSNP
rs1312640819 1325 dbSNP
rs1449770983 1329 dbSNP
rs1359442585 1334 dbSNP
rs1157694880 1342 dbSNP
rs1455148851 1349 dbSNP
rs1413559552 1350 dbSNP
rs778953571 1363 dbSNP
rs1204373216 1368 dbSNP
rs1161929431 1371 dbSNP
rs1388472179 1373 dbSNP
rs916341001 1374 dbSNP
rs1255893831 1381 dbSNP
rs1180533809 1385 dbSNP
rs1484344975 1388 dbSNP
rs373292664 1391 dbSNP
rs1215378879 1395 dbSNP
rs969162155 1396 dbSNP
rs753096493 1397 dbSNP
rs1233721999 1402 dbSNP
rs1477736393 1415 dbSNP
rs927678208 1437 dbSNP
rs1228861804 1446 dbSNP
rs940591422 1449 dbSNP
rs756235755 1451 dbSNP
rs1427374002 1452 dbSNP
rs1010241351 1454 dbSNP
rs1229871476 1455 dbSNP
rs1036297128 1460 dbSNP
rs1379661067 1465 dbSNP
rs920397982 1470 dbSNP
rs1042364322 1482 dbSNP
rs930478080 1483 dbSNP
rs1390113578 1484 dbSNP
rs1050435052 1488 dbSNP
rs150753616 1489 dbSNP
rs944830911 1492 dbSNP
rs370169338 1493 dbSNP
rs1432073526 1508 dbSNP
rs1368443776 1510 dbSNP
rs964713100 1515 dbSNP
rs1040333361 1518 dbSNP
rs1330224331 1521 dbSNP
rs1425885734 1521 dbSNP
rs191240759 1530 dbSNP
rs1276056861 1532 dbSNP
rs1249977019 1533 dbSNP
rs903212697 1533 dbSNP
rs999484250 1536 dbSNP
rs140146115 1537 dbSNP
rs1488105218 1539 dbSNP
rs1263562754 1546 dbSNP
rs1344023170 1547 dbSNP
rs1033269251 1560 dbSNP
rs575218019 1580 dbSNP
rs1322038367 1589 dbSNP
rs1294590165 1597 dbSNP
rs1225719968 1598 dbSNP
rs139099620 1603 dbSNP
rs1297665508 1604 dbSNP
rs1439569811 1610 dbSNP
rs1387991792 1611 dbSNP
rs1292245560 1613 dbSNP
rs1013082996 1615 dbSNP
rs1006662301 1618 dbSNP
rs1350766821 1625 dbSNP
rs542401887 1627 dbSNP
rs1447874638 1638 dbSNP
rs1392312933 1650 dbSNP
rs1189265155 1651 dbSNP
rs1451191791 1655 dbSNP
rs1265374750 1660 dbSNP
rs1192782075 1662 dbSNP
rs1019778391 1671 dbSNP
rs1273629151 1681 dbSNP
rs1219676627 1685 dbSNP
rs1248490251 1694 dbSNP
rs969110059 1694 dbSNP
rs981888582 1698 dbSNP
rs965048895 1706 dbSNP
rs749583259 1710 dbSNP
rs1302778944 1713 dbSNP
rs961753736 1714 dbSNP
rs1389030986 1722 dbSNP
rs1368990993 1723 dbSNP
rs1307786319 1724 dbSNP
rs771132097 1726 dbSNP
rs972349731 1728 dbSNP
rs972338494 1730 dbSNP
rs183098993 1733 dbSNP
rs1372818120 1735 dbSNP
rs1169399158 1739 dbSNP
rs1465734696 1741 dbSNP
rs920530116 1763 dbSNP
rs930594155 1768 dbSNP
rs1462383228 1770 dbSNP
rs79658377 1779 dbSNP
rs528351037 1784 dbSNP
rs1433675938 1788 dbSNP
rs952940793 1789 dbSNP
rs1179961456 1790 dbSNP
rs1451717253 1796 dbSNP
rs1483887520 1797 dbSNP
rs1252294000 1801 dbSNP
rs369320121 1810 dbSNP
rs1342526560 1816 dbSNP
rs944780053 1818 dbSNP
rs1233402819 1819 dbSNP
rs1324857677 1827 dbSNP
rs1288229996 1831 dbSNP
rs1325571525 1833 dbSNP
rs1350570499 1835 dbSNP
rs937488405 1835 dbSNP
rs1395656824 1837 dbSNP
rs1400390860 1838 dbSNP
rs1390490883 1840 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' uaGACGGACUCGUAGAGGAa 5'
            ||  ||| | ||||||| 
Target 5' auCUUGCUGUG-AUCUCCUu 3'
 		17 - 35
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions Prostate Tissue
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 SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148 PAR-CLIP data was present in SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A ...

- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.).

Article - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al.
- Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000360338.3 | 3UTR | UUUUCUUUUAUUUUUAAUCUUGCUGUGAUCUCCUUAG
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
110 hsa-miR-6888-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100971 CENPQ centromere protein Q 2 4
MIRT177381 WAC WW domain containing adaptor with coiled-coil 2 4
MIRT215237 NPM1 nucleophosmin 1 2 4
MIRT264969 TMEM136 transmembrane protein 136 2 2
MIRT306298 KLHL24 kelch like family member 24 2 2
MIRT319712 UBN2 ubinuclein 2 2 2
MIRT332866 TXNIP thioredoxin interacting protein 2 2
MIRT444384 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT445270 CPPED1 calcineurin like phosphoesterase domain containing 1 2 2
MIRT447185 PGRMC2 progesterone receptor membrane component 2 2 2
MIRT448763 HDX highly divergent homeobox 2 2
MIRT451468 HSD11B1L hydroxysteroid 11-beta dehydrogenase 1 like 2 2
MIRT452754 U2AF2 U2 small nuclear RNA auxiliary factor 2 2 2
MIRT455325 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT456846 ZNF460 zinc finger protein 460 2 2
MIRT457372 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT460352 ARL14EP ADP ribosylation factor like GTPase 14 effector protein 2 2
MIRT462004 SNRNP27 small nuclear ribonucleoprotein U4/U6.U5 subunit 27 2 2
MIRT462104 TMEM214 transmembrane protein 214 2 2
MIRT465309 TRAM2 translocation associated membrane protein 2 2 2
MIRT468841 RRM2 ribonucleotide reductase regulatory subunit M2 2 4
MIRT469635 RAD21 RAD21 cohesin complex component 2 6
MIRT470181 PSMD11 proteasome 26S subunit, non-ATPase 11 2 4
MIRT471782 NUP153 nucleoporin 153 2 2
MIRT472261 NFIC nuclear factor I C 2 2
MIRT473731 MAPK1 mitogen-activated protein kinase 1 2 2
MIRT477728 EEF1A1 eukaryotic translation elongation factor 1 alpha 1 2 2
MIRT479358 CEP97 centrosomal protein 97 2 2
MIRT481063 BASP1 brain abundant membrane attached signal protein 1 2 2
MIRT482044 AMER1 APC membrane recruitment protein 1 2 2
MIRT482892 IAH1 isoamyl acetate-hydrolyzing esterase 1 homolog 2 4
MIRT485773 B4GALT5 beta-1,4-galactosyltransferase 5 2 2
MIRT492646 PLEKHM3 pleckstrin homology domain containing M3 2 2
MIRT501915 MBD4 methyl-CpG binding domain 4, DNA glycosylase 2 4
MIRT503022 CAND1 cullin associated and neddylation dissociated 1 2 2
MIRT503247 ZFP36 ZFP36 ring finger protein 2 4
MIRT504591 FAM103A1 family with sequence similarity 103 member A1 2 6
MIRT507346 FAM168A family with sequence similarity 168 member A 2 2
MIRT508274 DYNLL2 dynein light chain LC8-type 2 2 4
MIRT508414 C1orf210 chromosome 1 open reading frame 210 2 6
MIRT508956 SNRPB small nuclear ribonucleoprotein polypeptides B and B1 2 4
MIRT514698 SOD2 superoxide dismutase 2 2 2
MIRT515837 MCM8 minichromosome maintenance 8 homologous recombination repair factor 2 4
MIRT516095 ZBTB8OS zinc finger and BTB domain containing 8 opposite strand 2 4
MIRT516420 ADAMTS4 ADAM metallopeptidase with thrombospondin type 1 motif 4 2 2
MIRT516863 TYW5 tRNA-yW synthesizing protein 5 2 2
MIRT516940 MRRF mitochondrial ribosome recycling factor 2 2
MIRT518122 RNMTL1 mitochondrial rRNA methyltransferase 3 2 4
MIRT522745 LNPEP leucyl and cystinyl aminopeptidase 2 2
MIRT523816 FAM179A TOG array regulator of axonemal microtubules 2 2 2
MIRT524107 DNA2 DNA replication helicase/nuclease 2 2 2
MIRT526722 RPS9 ribosomal protein S9 2 2
MIRT527047 ISY1-RAB43 ISY1-RAB43 readthrough 2 2
MIRT534174 SLC8A1 solute carrier family 8 member A1 2 2
MIRT537151 GJA1 gap junction protein alpha 1 2 2
MIRT544174 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT544558 CSNK2A1 casein kinase 2 alpha 1 2 2
MIRT544569 POLDIP3 DNA polymerase delta interacting protein 3 2 2
MIRT545174 SPATA18 spermatogenesis associated 18 2 2
MIRT545478 TRIM37 tripartite motif containing 37 2 2
MIRT549771 ZNF611 zinc finger protein 611 2 4
MIRT550733 PMPCA peptidase, mitochondrial processing alpha subunit 2 4
MIRT550864 SNAP47 synaptosome associated protein 47 2 4
MIRT551297 MCF2L2 MCF.2 cell line derived transforming sequence-like 2 2 6
MIRT551325 GSG2 histone H3 associated protein kinase 2 6
MIRT552807 XIAP X-linked inhibitor of apoptosis 2 4
MIRT555345 PPP1R3B protein phosphatase 1 regulatory subunit 3B 2 4
MIRT558137 ENPP4 ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative) 2 2
MIRT560877 SULT1B1 sulfotransferase family 1B member 1 2 2
MIRT561906 SMCR7L mitochondrial elongation factor 1 1 1
MIRT564414 EMILIN2 elastin microfibril interfacer 2 2 4
MIRT568716 TMEM30B transmembrane protein 30B 2 2
MIRT573284 NCAPH non-SMC condensin I complex subunit H 2 2
MIRT573685 HES6 hes family bHLH transcription factor 6 2 2
MIRT618161 CHCHD5 coiled-coil-helix-coiled-coil-helix domain containing 5 2 2
MIRT622840 PDZD4 PDZ domain containing 4 2 2
MIRT624355 CHRM3 cholinergic receptor muscarinic 3 2 2
MIRT642273 SMIM17 small integral membrane protein 17 2 2
MIRT652967 SVEP1 sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 2 2
MIRT666642 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT680851 ARL8B ADP ribosylation factor like GTPase 8B 2 2
MIRT681368 BRI3BP BRI3 binding protein 2 2
MIRT681551 ZNF738 zinc finger protein 738 2 2
MIRT681667 DTX3L deltex E3 ubiquitin ligase 3L 2 2
MIRT681808 EIF4A3 eukaryotic translation initiation factor 4A3 2 2
MIRT681955 SLC19A3 solute carrier family 19 member 3 2 2
MIRT682192 SLC38A7 solute carrier family 38 member 7 2 2
MIRT682249 SAR1A secretion associated Ras related GTPase 1A 2 2
MIRT682396 PHACTR4 phosphatase and actin regulator 4 2 2
MIRT685160 DTWD2 DTW domain containing 2 2 2
MIRT687030 RNF24 ring finger protein 24 2 2
MIRT688377 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 2 2
MIRT690383 ZSWIM7 zinc finger SWIM-type containing 7 2 2
MIRT691949 DNAJC28 DnaJ heat shock protein family (Hsp40) member C28 2 2
MIRT693036 MB21D1 Mab-21 domain containing 1 2 2
MIRT693110 SCNM1 sodium channel modifier 1 2 2
MIRT694481 LRTOMT leucine rich transmembrane and O-methyltransferase domain containing 2 2
MIRT694898 ZNF417 zinc finger protein 417 2 2
MIRT696667 AGXT2 alanine--glyoxylate aminotransferase 2 2 2
MIRT698663 TERF2 telomeric repeat binding factor 2 2 2
MIRT700157 RNF115 ring finger protein 115 2 2
MIRT700984 PDE4D phosphodiesterase 4D 2 2
MIRT702139 MAPKAPK5 mitogen-activated protein kinase-activated protein kinase 5 2 2
MIRT702207 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT702496 KIAA1328 KIAA1328 2 2
MIRT704932 CCDC36 coiled-coil domain containing 36 2 2
MIRT705778 ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 2 2
MIRT707795 TTYH3 tweety family member 3 2 2
MIRT711479 MYH15 myosin heavy chain 15 2 2
MIRT713188 ERO1L endoplasmic reticulum oxidoreductase 1 alpha 1 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-6888-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-6888-5p Tamoxifen+Fulvestrant sensitive cell line (LCC9)

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