pre-miRNA Information
pre-miRNA hsa-mir-4747   
Genomic Coordinates chr19: 4932687 - 4932740
Description Homo sapiens miR-4747 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4747-5p
Sequence 1| AGGGAAGGAGGCUUGGUCUUAG |22
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs560927363 4 dbSNP
rs1471226927 10 dbSNP
rs763137545 12 dbSNP
rs767337154 15 dbSNP
rs775298039 16 dbSNP
rs760472311 19 dbSNP
rs1207950315 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol BHLHB9   
Synonyms GASP3, p60TRP
Description basic helix-loop-helix family member b9
Transcript NM_001142524   
Other Transcripts NM_001142525 , NM_001142526 , NM_001142527 , NM_001142528 , NM_001142529 , NM_001142530 , NM_030639   
Expression
Putative miRNA Targets on BHLHB9
3'UTR of BHLHB9
(miRNA target sites are highlighted)
>BHLHB9|NM_001142524|3'UTR
   1 AATGAGCCAGAGATAGAACATTTTAAGCCATCTTCAAACTCTAGCAGGCTGTACATTACAGTGTACACATTATACACTGC
  81 ATCTTTAACACAGAGTCACCTGTGACAGGCTCTAGGTTTGAGCTAGACTATTTTGGGGGTATCAAATGAATATTATACCT
 161 TGGGCTGAAAATGTTTGATTTTTATCTTGTCTAGATTGGCATATTTTTAACATTTTACTTAAGATAGCAAACCAGTTCGT
 241 TTTAAGTAAGCTAACTTGTTCATTAGTATCTGTGGCTTAAAATGGCAAAAAAGAAAATATCCTTGAGTTTGTAATCTAGT
 321 TACAGAAGTAAGGCATACACACACACAAAGATAACAGTACCTAGAGAGAGAGTGTGTGTGAGTGTGCGTGTCTCTGTGTG
 401 TGCACGTGCACGCTCATGGCCAAATGTGCGCACTCTACATAAAGGAGGCAGGAGTTCCTATAGGCTATTTAATGTAAGAG
 481 AAACTATTTTTCTCCTGTTCCAGCTGTATCAGATACTCGTTCCGCAACACAGAAATGACTCAGAATCTCAGACAAAATGT
 561 ATTATTTGTTCAATTTTAATTTTGCTACTACATTCATAACTCTTAAATTGTTAGGCTGTTTCATTTACATCAAAGTTATC
 641 TCACAAAAGAGAAGGCAGGAAACGTTTTGTGAGTGCCTATTCTATGTCAAACACTGTGTTGGCACCATATTTTACAAGTT
 721 TTTTTCCTCTTCTCACAGTGATCTTGTGAGTTAGTTACTTATATTTTTATTAGAACTCATTATTCTGGGTACCCTCCAAT
 801 GAGAATTAGAGAGGTTAAATACCTTTTCCTAGATTCCCACAGCAGGAAGGTGGCATAGCTGTTTTGTCTGACACCAGAAC
 881 CCATCTCACCACACTGCTTTACAGTCTTCCTGAAGGACATTTTGAGGTGGGGGGGCCTTCAAAGCTCAGAGACTGGTTTG
 961 AATGGTTTAATTTTGCAATGGATCATGTCCATGCCAGGTGTTACAATTCTTAACTTCCTCCAAATTCGTGTGTCCATTAG
1041 ACATTTGGCTACATCTGGCTGGAGGTCAGGAGAAAATTCTGAGGTAAATAGATGGATTTTATCTGGCAGTGTCGAAAATA
1121 GTAGGAGCCTAAAACTTTGTTCAATGAGTAAGATGTAGATTTGGAGTCATCAGCAGGGGAAACTTGTTAGATGTCCTTTG
1201 TATCTTTTTCTATCCATTTGTATTTTTTCTTTCCCAAAGAGCTGAAATCATTTTATACCCTGAATTTAAAAGGTAATTGC
1281 TTTTTTCCTCCTTGCGAAATCATACCTTAATTTTTTTTTTTTTTTTTTTTACCATTTATGATTTATTCTCCTATGTGTCA
1361 TATGAAAGGCCAAGGGGCTTTATCTTTTACTAGTAGGCAAGCCTGGGCATTTCTGCATTTGTGCCAGCTAACACTACAAA
1441 ATAGACTTAATTAGAGAAATTTAGACCCAGAATTGCAGCTTCAACAACACAAAACAGGAAAGCTAGAAGAGGTTGCTGTG
1521 TCAACCTACAAGATAGTGATTCTTGGAAGTTGGTATGGACCAGAAAGCATTCCCAGGACATTTAGGCTATGGCTGAGTTC
1601 TCTAAGACTCAGGGTGGGAATTATAATCCCTGGTCTAAGCTGATATGAAAGTTTCTATGTGTGAAAATATGGAGTTATAT
1681 GCTTTGAGATTTTCTGCCAGTTAAACTAAAACAAGATCATACTGTAAATGTTTGTAACTTGCTTCCCCCCACTGTATACT
1761 GTAAACATCTTTGCATGTCAATAAATATGCCTCTACAACATAAAAAAAAAAAAAAA
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' gauucugguucGGAGGAAGGGa 5'
                     ::||:||||| 
Target 5' catttgtatttTTTCTTTCCCa 3'
1215 - 1236 131.00 -10.90
2
miRNA  3' gaUUCUGGUUCGGAGGAAGGGa 5'
            :||:::|| :  |:||:|| 
Target 5' gaGAGGTTAAATACCTTTTCCt 3'
809 - 830 124.00 -13.40
3
miRNA  3' gauUCUGGUUCGGAGGAAGGGa 5'
             :|||||:    | ||||| 
Target 5' tatGGACCAGAAAGCATTCCCa 3'
1554 - 1575 123.00 -14.60
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1203930338 2 dbSNP
rs1340893100 11 dbSNP
rs1264671702 14 dbSNP
rs1456150822 15 dbSNP
rs757072249 19 dbSNP
rs1326265112 30 dbSNP
rs1251616881 39 dbSNP
rs1421401640 42 dbSNP
rs370688868 43 dbSNP
rs746115931 47 dbSNP
rs755975511 56 dbSNP
rs1486822278 75 dbSNP
rs943062425 80 dbSNP
rs1375482843 85 dbSNP
rs1053443198 95 dbSNP
rs1477964347 100 dbSNP
rs111321025 112 dbSNP
rs180743593 113 dbSNP
rs1191985228 121 dbSNP
rs1486919226 124 dbSNP
rs1480469151 125 dbSNP
rs1201215907 126 dbSNP
rs915502665 129 dbSNP
rs1418907511 131 dbSNP
rs945649512 146 dbSNP
rs1277288693 154 dbSNP
rs1397917936 156 dbSNP
rs1334724627 172 dbSNP
rs769319639 191 dbSNP
rs114554907 196 dbSNP
rs1172249360 198 dbSNP
rs1465778869 200 dbSNP
rs749163604 212 dbSNP
rs1003626202 219 dbSNP
rs1168900637 221 dbSNP
rs1347278505 228 dbSNP
rs1476400475 235 dbSNP
rs1055658824 239 dbSNP
rs762418386 240 dbSNP
rs1441233701 254 dbSNP
rs1252730356 266 dbSNP
rs1199384955 271 dbSNP
rs895225759 271 dbSNP
rs1256413883 277 dbSNP
rs759392397 279 dbSNP
rs1366337809 290 dbSNP
rs1406843703 303 dbSNP
rs1284605471 305 dbSNP
rs765839353 313 dbSNP
rs774298335 321 dbSNP
rs1243944849 329 dbSNP
rs759336904 349 dbSNP
rs778824972 353 dbSNP
rs752235859 363 dbSNP
rs1332748603 364 dbSNP
rs1446893490 367 dbSNP
rs1328857177 372 dbSNP
rs1399026052 372 dbSNP
rs1406804131 389 dbSNP
rs1016920056 406 dbSNP
rs961344444 426 dbSNP
rs1472072781 430 dbSNP
rs993427582 431 dbSNP
rs1026203404 443 dbSNP
rs767352254 451 dbSNP
rs1439148214 461 dbSNP
rs954530554 477 dbSNP
rs752428029 489 dbSNP
rs1290935712 509 dbSNP
rs1490381378 511 dbSNP
rs756414215 514 dbSNP
rs1224038138 515 dbSNP
rs1354092775 519 dbSNP
rs772236107 520 dbSNP
rs186358056 524 dbSNP
rs1230626746 525 dbSNP
rs1306507853 534 dbSNP
rs1480124392 552 dbSNP
rs1177355848 553 dbSNP
rs1410636729 554 dbSNP
rs754007467 569 dbSNP
rs563121227 579 dbSNP
rs1350133379 582 dbSNP
rs1323228650 597 dbSNP
rs1403967115 611 dbSNP
rs1443151276 625 dbSNP
rs779085614 626 dbSNP
rs773438527 637 dbSNP
rs1419662691 639 dbSNP
rs1378525390 650 dbSNP
rs17342421 660 dbSNP
rs914919529 664 dbSNP
rs945007630 665 dbSNP
rs758762585 672 dbSNP
rs1426680392 679 dbSNP
rs1326961268 686 dbSNP
rs138296423 694 dbSNP
rs1287981579 695 dbSNP
rs928215419 703 dbSNP
rs1352959666 708 dbSNP
rs939557964 709 dbSNP
rs1220457391 715 dbSNP
rs1367799257 720 dbSNP
rs1273865900 728 dbSNP
rs1433935682 738 dbSNP
rs1459610529 740 dbSNP
rs1299242333 741 dbSNP
rs1055288312 749 dbSNP
rs1359215760 750 dbSNP
rs1178248023 755 dbSNP
rs1415125328 770 dbSNP
rs771283747 788 dbSNP
rs1171035199 795 dbSNP
rs895247675 815 dbSNP
rs1265035236 817 dbSNP
rs551595463 854 dbSNP
rs1300059028 858 dbSNP
rs530664709 862 dbSNP
rs1450144102 865 dbSNP
rs1240296256 880 dbSNP
rs769476307 882 dbSNP
rs1312258427 914 dbSNP
rs772887043 929 dbSNP
rs548794192 936 dbSNP
rs1217090798 949 dbSNP
rs1314350720 958 dbSNP
rs1319580170 961 dbSNP
rs60286630 976 dbSNP
rs1360095594 979 dbSNP
rs1248029269 986 dbSNP
rs1270278152 1005 dbSNP
rs189437364 1012 dbSNP
rs1449493946 1019 dbSNP
rs1332332360 1028 dbSNP
rs1358619136 1028 dbSNP
rs1306353133 1029 dbSNP
rs1424646597 1037 dbSNP
rs1171051253 1059 dbSNP
rs1477365050 1063 dbSNP
rs1417207742 1085 dbSNP
rs1183492693 1087 dbSNP
rs897167091 1088 dbSNP
rs770445238 1096 dbSNP
rs1204849516 1104 dbSNP
rs1236330162 1113 dbSNP
rs1234254176 1115 dbSNP
rs367916377 1120 dbSNP
rs1026276559 1125 dbSNP
rs181846203 1126 dbSNP
rs16984147 1131 dbSNP
rs1315326613 1139 dbSNP
rs767340688 1140 dbSNP
rs1183345357 1142 dbSNP
rs1244077781 1144 dbSNP
rs571510576 1145 dbSNP
rs1449097086 1146 dbSNP
rs777112521 1151 dbSNP
rs1009170220 1153 dbSNP
rs1166600410 1154 dbSNP
rs567311633 1171 dbSNP
rs1352522187 1176 dbSNP
rs1166677265 1193 dbSNP
rs1424281590 1198 dbSNP
rs1412978090 1221 dbSNP
rs919528936 1239 dbSNP
rs989250116 1246 dbSNP
rs1238333509 1257 dbSNP
rs1418915672 1263 dbSNP
rs1479483415 1264 dbSNP
rs914950747 1272 dbSNP
rs1410596558 1274 dbSNP
rs1321574455 1281 dbSNP
rs1313538609 1291 dbSNP
rs1243036342 1296 dbSNP
rs6652880 1297 dbSNP
rs1444770212 1303 dbSNP
rs1177492332 1311 dbSNP
rs1370035156 1311 dbSNP
rs1416898167 1311 dbSNP
rs201112932 1311 dbSNP
rs57962077 1311 dbSNP
rs796837048 1311 dbSNP
rs879026240 1311 dbSNP
rs1269029414 1313 dbSNP
rs1192081631 1325 dbSNP
rs1404151969 1330 dbSNP
rs1290089806 1331 dbSNP
rs1488356233 1331 dbSNP
rs1452124323 1332 dbSNP
rs1335874906 1334 dbSNP
rs1383167285 1337 dbSNP
rs931871409 1339 dbSNP
rs1268330894 1340 dbSNP
rs1360747139 1341 dbSNP
rs966386239 1342 dbSNP
rs113117345 1343 dbSNP
rs1259645288 1346 dbSNP
rs1320999351 1349 dbSNP
rs1202599467 1351 dbSNP
rs1264152705 1352 dbSNP
rs780278724 1354 dbSNP
rs866635853 1355 dbSNP
rs1043080 1360 dbSNP
rs1462890911 1363 dbSNP
rs1191744354 1371 dbSNP
rs1242010311 1390 dbSNP
rs1475809596 1394 dbSNP
rs1386492390 1398 dbSNP
rs1344604615 1407 dbSNP
rs1188378545 1419 dbSNP
rs1050535865 1422 dbSNP
rs1427238055 1434 dbSNP
rs1301120863 1448 dbSNP
rs754134405 1467 dbSNP
rs762067806 1479 dbSNP
rs1469486472 1495 dbSNP
rs1177344910 1502 dbSNP
rs977720867 1510 dbSNP
rs1406618925 1519 dbSNP
rs1157462824 1546 dbSNP
rs1451014012 1553 dbSNP
rs1176293343 1573 dbSNP
rs372347126 1598 dbSNP
rs1267151256 1599 dbSNP
rs939601150 1601 dbSNP
rs991456175 1611 dbSNP
rs916769960 1614 dbSNP
rs1203950985 1615 dbSNP
rs941493566 1616 dbSNP
rs1038459079 1619 dbSNP
rs897243013 1625 dbSNP
rs1321705717 1629 dbSNP
rs1281098474 1639 dbSNP
rs1220241678 1641 dbSNP
rs929988335 1647 dbSNP
rs750457961 1652 dbSNP
rs1380497233 1656 dbSNP
rs891105988 1658 dbSNP
rs1302943120 1660 dbSNP
rs1465197082 1671 dbSNP
rs1431328439 1678 dbSNP
rs1279578903 1697 dbSNP
rs1478344103 1700 dbSNP
rs1008825983 1703 dbSNP
rs1017904614 1708 dbSNP
rs900336193 1721 dbSNP
rs759937999 1722 dbSNP
rs1283514351 1723 dbSNP
rs1260253505 1750 dbSNP
rs1347667431 1751 dbSNP
rs1199571939 1752 dbSNP
rs1318296498 1754 dbSNP
rs1022033128 1755 dbSNP
rs12388886 1767 dbSNP
rs966420605 1770 dbSNP
rs1312722123 1801 dbSNP
rs1283936502 1809 dbSNP
rs191389379 1819 dbSNP
rs891346831 1820 dbSNP
rs1403335089 1822 dbSNP
rs1004404416 1824 dbSNP
rs1465856366 1826 dbSNP
rs1396199972 1828 dbSNP
rs181400264 1830 dbSNP
rs1474038915 1833 dbSNP
rs898652303 1843 dbSNP
rs55962884 1854 dbSNP
rs149350761 1866 dbSNP
rs1186859722 1868 dbSNP
rs1027405036 1884 dbSNP
rs144138382 1888 dbSNP
rs991081775 1890 dbSNP
rs1181950959 1899 dbSNP
rs991097110 1914 dbSNP
rs1024177938 1915 dbSNP
rs1193861111 1940 dbSNP
rs1431678294 1942 dbSNP
rs1265941376 1948 dbSNP
rs1245236076 1954 dbSNP
rs1379897372 1955 dbSNP
rs1310881664 1956 dbSNP
rs1447003590 1958 dbSNP
rs1334840133 1959 dbSNP
rs1327196657 1960 dbSNP
rs1478915294 1965 dbSNP
rs1407451194 1967 dbSNP
rs767210687 1975 dbSNP
rs1156619280 1977 dbSNP
rs1423348129 1991 dbSNP
rs1383921063 2021 dbSNP
rs1179371617 2026 dbSNP
rs1469758990 2047 dbSNP
rs977293058 2051 dbSNP
rs186206586 2056 dbSNP
rs1401225361 2063 dbSNP
rs1453107740 2072 dbSNP
rs1267840210 2079 dbSNP
rs924467646 2092 dbSNP
rs1299900194 2101 dbSNP
rs916780619 2110 dbSNP
rs1240253065 2118 dbSNP
rs1349435125 2119 dbSNP
rs941579632 2123 dbSNP
rs1363239198 2127 dbSNP
rs903534900 2131 dbSNP
rs781481977 2134 dbSNP
rs1303429075 2140 dbSNP
rs918696796 2140 dbSNP
rs1332480915 2144 dbSNP
rs1403593340 2144 dbSNP
rs1159268105 2148 dbSNP
rs2485253 2150 dbSNP
rs112555071 2154 dbSNP
rs1405963566 2154 dbSNP
rs750095082 2157 dbSNP
rs755887652 2159 dbSNP
rs1290211526 2168 dbSNP
rs1051150462 2182 dbSNP
rs1217324937 2192 dbSNP
rs778541206 2193 dbSNP
rs942656934 2196 dbSNP
rs921339299 2200 dbSNP
rs191109427 2201 dbSNP
rs779688711 2204 dbSNP
rs1181277636 2205 dbSNP
rs1342835476 2222 dbSNP
rs753702294 2232 dbSNP
rs1363027439 2241 dbSNP
rs1022067282 2242 dbSNP
rs1336273639 2251 dbSNP
rs1160456857 2260 dbSNP
rs1415220739 2268 dbSNP
rs891399114 2271 dbSNP
rs1034700146 2272 dbSNP
rs528174124 2278 dbSNP
rs1479326166 2289 dbSNP
rs1037268643 2292 dbSNP
rs898699426 2293 dbSNP
rs1163697704 2297 dbSNP
rs1211621125 2298 dbSNP
rs1239820625 2298 dbSNP
rs1392174170 2310 dbSNP
rs995682373 2311 dbSNP
rs1320409417 2312 dbSNP
rs1327749167 2317 dbSNP
rs1336792698 2319 dbSNP
rs990891600 2336 dbSNP
rs1449423003 2337 dbSNP
rs1313618208 2341 dbSNP
rs1285965488 2345 dbSNP
rs1448871586 2356 dbSNP
rs1405520921 2360 dbSNP
rs182382176 2368 dbSNP
rs1467418686 2371 dbSNP
rs1027824493 2377 dbSNP
rs1247302086 2395 dbSNP
rs1170917439 2412 dbSNP
rs894189329 2424 dbSNP
rs1012555008 2425 dbSNP
rs775317274 2430 dbSNP
rs1242027889 2435 dbSNP
rs1181342773 2444 dbSNP
rs1410271200 2452 dbSNP
rs971023255 2455 dbSNP
rs1458829292 2461 dbSNP
rs1252212402 2462 dbSNP
rs1204277063 2472 dbSNP
rs367812438 2479 dbSNP
rs1031583129 2483 dbSNP
rs760640492 2487 dbSNP
rs989963188 2490 dbSNP
rs1382087791 2495 dbSNP
rs1313074156 2496 dbSNP
rs112056317 2501 dbSNP
rs768584440 2508 dbSNP
rs942749591 2510 dbSNP
rs186723569 2517 dbSNP
rs1461283135 2524 dbSNP
rs986871871 2526 dbSNP
rs1165320503 2535 dbSNP
rs1352614415 2544 dbSNP
rs762190467 2563 dbSNP
rs1425272277 2566 dbSNP
rs1384022810 2567 dbSNP
rs912592618 2570 dbSNP
rs1040096673 2579 dbSNP
rs940035317 2585 dbSNP
rs1441088686 2588 dbSNP
rs1250815464 2591 dbSNP
rs1460019955 2597 dbSNP
rs1176325724 2601 dbSNP
rs1479860590 2604 dbSNP
rs921896987 2608 dbSNP
rs1037723921 2621 dbSNP
rs1167005394 2659 dbSNP
rs898713076 2662 dbSNP
rs1289636033 2699 dbSNP
rs778929483 2714 dbSNP
rs931474827 2731 dbSNP
rs1242419754 2747 dbSNP
rs748170573 2751 dbSNP
rs1306551610 2754 dbSNP
rs894241635 2762 dbSNP
rs1389929646 2770 dbSNP
rs144389445 2777 dbSNP
rs1295091807 2782 dbSNP
rs1405437588 2785 dbSNP
rs375405354 2795 dbSNP
rs906915045 2806 dbSNP
rs191203876 2807 dbSNP
rs1032012427 2811 dbSNP
rs1363944762 2814 dbSNP
rs902363949 2815 dbSNP
rs999277994 2828 dbSNP
rs1416992882 2853 dbSNP
rs1427643960 2858 dbSNP
rs777899987 2865 dbSNP
rs957289722 2873 dbSNP
rs766436893 2874 dbSNP
rs1454000438 2876 dbSNP
rs1028190522 2879 dbSNP
rs896218177 2888 dbSNP
rs1011945351 2894 dbSNP
rs112188145 2899 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' gauucugGUUCG-GAGGAAGGGa 5'
                 ||| | || |||||| 
Target 5' cccacugCAACCUCUGCUUCCCa 3'
10 - 32
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 SRX1760630. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_A ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gauucugGUUCG-GAGGAAGGGa 5'
                 ||| | || |||||| 
Target 5' cccacugCAACCUCUGCUUCCCa 3'
8 - 30
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 ENST00000372735.1 | 3UTR | CAAUCUCGGCCCACUGCAACCUCUGCUUCCCAG
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
215 hsa-miR-4747-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT061689 BTG2 BTG anti-proliferation factor 2 2 2
MIRT062834 BCL7A BCL tumor suppressor 7A 2 2
MIRT079371 CCDC137 coiled-coil domain containing 137 2 2
MIRT081190 MIDN midnolin 2 4
MIRT081724 ZNF507 zinc finger protein 507 2 2
MIRT110565 ZMYND11 zinc finger MYND-type containing 11 2 2
MIRT133724 SKI SKI proto-oncogene 2 4
MIRT146689 MINK1 misshapen like kinase 1 2 2
MIRT150676 SLC27A1 solute carrier family 27 member 1 2 2
MIRT159196 NRBP1 nuclear receptor binding protein 1 2 2
MIRT180865 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT190659 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT196111 MPRIP myosin phosphatase Rho interacting protein 2 2
MIRT232390 SP1 Sp1 transcription factor 2 2
MIRT331070 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT338632 SHMT2 serine hydroxymethyltransferase 2 2 2
MIRT407441 CTDSP1 CTD small phosphatase 1 2 2
MIRT444276 NKX6-1 NK6 homeobox 1 2 2
MIRT444834 PDE6D phosphodiesterase 6D 2 2
MIRT445452 EXT1 exostosin glycosyltransferase 1 2 2
MIRT445644 NPY4R neuropeptide Y receptor Y4 2 2
MIRT446157 RPL12 ribosomal protein L12 2 2
MIRT446608 HIP1 huntingtin interacting protein 1 2 2
MIRT447108 CLPX caseinolytic mitochondrial matrix peptidase chaperone subunit 2 2
MIRT449314 MRO maestro 2 2
MIRT450305 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT451245 ZNF444 zinc finger protein 444 2 2
MIRT451714 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT451908 ILK integrin linked kinase 2 2
MIRT452183 KIAA1456 KIAA1456 2 2
MIRT452610 REPIN1 replication initiator 1 2 2
MIRT453422 GLG1 golgi glycoprotein 1 2 2
MIRT454006 ALKBH5 alkB homolog 5, RNA demethylase 2 2
MIRT455072 ARHGAP39 Rho GTPase activating protein 39 2 2
MIRT455319 TTLL9 tubulin tyrosine ligase like 9 2 2
MIRT455357 KDM5C lysine demethylase 5C 2 2
MIRT455589 TAF12 TATA-box binding protein associated factor 12 2 2
MIRT455711 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT455860 TMEM254 transmembrane protein 254 2 2
MIRT455919 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT455946 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT456935 LRP10 LDL receptor related protein 10 2 2
MIRT457223 AP3D1 adaptor related protein complex 3 delta 1 subunit 2 2
MIRT457431 NOL10 nucleolar protein 10 2 2
MIRT457470 SLC35F6 solute carrier family 35 member F6 2 2
MIRT457907 ZNF212 zinc finger protein 212 2 2
MIRT458046 TSEN54 tRNA splicing endonuclease subunit 54 2 2
MIRT458073 RNLS renalase, FAD dependent amine oxidase 2 2
MIRT458234 NXPH3 neurexophilin 3 2 2
MIRT458307 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458378 ITM2C integral membrane protein 2C 2 2
MIRT458967 ZNF436 zinc finger protein 436 2 2
MIRT459099 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT459446 TMEM37 transmembrane protein 37 2 2
MIRT459671 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT460727 ASXL3 additional sex combs like 3, transcriptional regulator 2 2
MIRT460744 SRP14 signal recognition particle 14 2 2
MIRT461531 C14orf1 ergosterol biosynthesis 28 homolog 2 2
MIRT461752 DDX11 DEAD/H-box helicase 11 2 2
MIRT461837 F2RL3 F2R like thrombin or trypsin receptor 3 2 2
MIRT462019 RIF1 replication timing regulatory factor 1 2 2
MIRT462631 PHF5A PHD finger protein 5A 2 2
MIRT462772 ZNF8 zinc finger protein 8 2 2
MIRT463032 ZNF689 zinc finger protein 689 2 2
MIRT463886 WNT7B Wnt family member 7B 2 2
MIRT463995 WDTC1 WD and tetratricopeptide repeats 1 2 2
MIRT464371 URM1 ubiquitin related modifier 1 2 2
MIRT465342 TPM3 tropomyosin 3 2 4
MIRT465515 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465602 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT465697 TNPO2 transportin 2 2 10
MIRT466988 SSRP1 structure specific recognition protein 1 2 4
MIRT467630 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468132 SH3PXD2A SH3 and PX domains 2A 2 2
MIRT468322 SF3B3 splicing factor 3b subunit 3 2 2
MIRT468502 SESN2 sestrin 2 2 2
MIRT468881 RREB1 ras responsive element binding protein 1 2 2
MIRT469322 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT469562 RARA retinoic acid receptor alpha 2 2
MIRT469898 PTRF caveolae associated protein 1 2 2
MIRT470045 PTGFRN prostaglandin F2 receptor inhibitor 2 2
MIRT470068 PTGES2 prostaglandin E synthase 2 2 2
MIRT470238 PRRC2A proline rich coiled-coil 2A 2 2
MIRT470390 PPP1R16B protein phosphatase 1 regulatory subunit 16B 2 2
MIRT470500 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT470689 POLR2D RNA polymerase II subunit D 2 2
MIRT470704 POGK pogo transposable element derived with KRAB domain 2 2
MIRT471083 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta 2 2
MIRT472482 NACC2 NACC family member 2 2 2
MIRT473583 MAT2A methionine adenosyltransferase 2A 2 2
MIRT474554 KLHDC3 kelch domain containing 3 2 2
MIRT474651 KLF13 Kruppel like factor 13 2 2
MIRT474843 KHSRP KH-type splicing regulatory protein 2 2
MIRT474934 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475573 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 2
MIRT476045 GRSF1 G-rich RNA sequence binding factor 1 2 2
MIRT476080 GRB2 growth factor receptor bound protein 2 2 2
MIRT476440 GBA2 glucosylceramidase beta 2 2 2
MIRT476764 FOSL2 FOS like 2, AP-1 transcription factor subunit 2 2
MIRT478785 CRTC2 CREB regulated transcription coactivator 2 2 2
MIRT479287 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 2 2
MIRT479505 CDH6 cadherin 6 2 2
MIRT479732 CCND1 cyclin D1 2 6
MIRT480352 C5orf24 chromosome 5 open reading frame 24 2 2
MIRT480407 C19orf47 chromosome 19 open reading frame 47 2 2
MIRT480859 BHLHB9 basic helix-loop-helix family member b9 2 2
MIRT481445 ARRB2 arrestin beta 2 2 2
MIRT481732 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT481824 AP2M1 adaptor related protein complex 2 mu 1 subunit 2 2
MIRT482566 ABHD2 abhydrolase domain containing 2 2 2
MIRT482607 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483144 SYCE1L synaptonemal complex central element protein 1 like 2 2
MIRT483214 APOA1 apolipoprotein A1 2 6
MIRT483878 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483917 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483939 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484420 SNX19 sorting nexin 19 2 2
MIRT484489 SLC9A1 solute carrier family 9 member A1 2 2
MIRT484612 SIX3 SIX homeobox 3 2 6
MIRT484705 RNF11 ring finger protein 11 2 2
MIRT485107 SHISA6 shisa family member 6 2 2
MIRT485354 MYO1C myosin IC 2 4
MIRT485609 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT487311 GLTSCR1 BRD4 interacting chromatin remodeling complex associated protein 2 2
MIRT487417 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT487695 CDK14 cyclin dependent kinase 14 2 2
MIRT487791 GPR20 G protein-coupled receptor 20 2 4
MIRT488042 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 2
MIRT488058 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 2
MIRT488237 DNLZ DNL-type zinc finger 2 4
MIRT488764 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT489401 TUBB2A tubulin beta 2A class IIa 2 2
MIRT489777 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490099 FN3K fructosamine 3 kinase 2 2
MIRT490290 ISL2 ISL LIM homeobox 2 2 2
MIRT490378 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT491329 GFER growth factor, augmenter of liver regeneration 2 2
MIRT491435 MSX2 msh homeobox 2 2 2
MIRT491769 ZNF385A zinc finger protein 385A 2 2
MIRT491922 WNK2 WNK lysine deficient protein kinase 2 2 2
MIRT491983 UNK unkempt family zinc finger 2 2
MIRT492228 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492404 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT492767 PDGFB platelet derived growth factor subunit B 2 2
MIRT492966 NCS1 neuronal calcium sensor 1 2 2
MIRT493295 LLGL2 LLGL2, scribble cell polarity complex component 2 2
MIRT493650 HDLBP high density lipoprotein binding protein 2 2
MIRT493913 FAM127B retrotransposon Gag like 8A 2 4
MIRT495601 NKX2-5 NK2 homeobox 5 2 2
MIRT496875 AHCYL2 adenosylhomocysteinase like 2 2 2
MIRT498514 MYH14 myosin heavy chain 14 2 2
MIRT499178 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT502143 KIF5B kinesin family member 5B 2 8
MIRT502692 CSNK1G1 casein kinase 1 gamma 1 2 4
MIRT508460 HOXB6 homeobox B6 2 4
MIRT510430 ZNF207 zinc finger protein 207 2 6
MIRT511837 GPATCH8 G-patch domain containing 8 2 4
MIRT512368 CPM carboxypeptidase M 2 2
MIRT512506 BTBD19 BTB domain containing 19 2 2
MIRT513065 ANKRD45 ankyrin repeat domain 45 2 2
MIRT513267 SCUBE1 signal peptide, CUB domain and EGF like domain containing 1 2 4
MIRT513575 EVX1 even-skipped homeobox 1 2 2
MIRT515051 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515790 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT521657 PRKD3 protein kinase D3 2 2
MIRT522679 LUZP1 leucine zipper protein 1 2 6
MIRT528845 RAB32 RAB32, member RAS oncogene family 2 2
MIRT533569 TOR1AIP1 torsin 1A interacting protein 1 2 2
MIRT543738 DHCR7 7-dehydrocholesterol reductase 2 2
MIRT544295 TSPYL1 TSPY like 1 2 2
MIRT544857 MYH2 myosin heavy chain 2 2 4
MIRT557323 HIATL1 major facilitator superfamily domain containing 14B 2 4
MIRT560522 TMEM98 transmembrane protein 98 2 2
MIRT561565 SLC6A9 solute carrier family 6 member 9 2 2
MIRT562374 ERI2 ERI1 exoribonuclease family member 2 2 2
MIRT565780 SEMA6D semaphorin 6D 2 2
MIRT569548 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT569944 PRRT2 proline rich transmembrane protein 2 2 2
MIRT570016 COL1A2 collagen type I alpha 2 chain 2 2
MIRT572163 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT572322 HSPB6 heat shock protein family B (small) member 6 2 2
MIRT573495 IQSEC3 IQ motif and Sec7 domain 3 2 2
MIRT574139 MARVELD1 MARVEL domain containing 1 2 2
MIRT609449 CCDC149 coiled-coil domain containing 149 2 2
MIRT610619 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT623355 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT629854 ACOX1 acyl-CoA oxidase 1 2 2
MIRT630516 CDC73 cell division cycle 73 2 2
MIRT632535 PSMB2 proteasome subunit beta 2 2 2
MIRT633975 SLC35E2 solute carrier family 35 member E2 2 2
MIRT636408 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 2 2
MIRT641722 LTBR lymphotoxin beta receptor 2 2
MIRT642661 RGS6 regulator of G protein signaling 6 2 2
MIRT649649 MAST3 microtubule associated serine/threonine kinase 3 2 2
MIRT650367 MOCS3 molybdenum cofactor synthesis 3 2 2
MIRT651355 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT664840 HUS1 HUS1 checkpoint clamp component 2 2
MIRT667322 MYH9 myosin heavy chain 9 2 2
MIRT670680 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 2 2
MIRT674922 TRPM6 transient receptor potential cation channel subfamily M member 6 2 2
MIRT675919 CYP51A1 cytochrome P450 family 51 subfamily A member 1 2 2
MIRT676493 GJD3 gap junction protein delta 3 2 2
MIRT680162 ZDHHC20 zinc finger DHHC-type containing 20 2 2
MIRT688008 GSN gelsolin 2 2
MIRT688997 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT700337 RAB4A RAB4A, member RAS oncogene family 2 2
MIRT701344 NR4A3 nuclear receptor subfamily 4 group A member 3 2 2
MIRT703519 FKBP15 FK506 binding protein 15 2 2
MIRT703901 EPT1 selenoprotein I 2 2
MIRT705565 ARHGEF18 Rho/Rac guanine nucleotide exchange factor 18 2 2
MIRT709709 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT713108 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT718426 ZNF85 zinc finger protein 85 2 2
MIRT719236 CYSLTR2 cysteinyl leukotriene receptor 2 2 2
MIRT719326 STAC SH3 and cysteine rich domain 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4747 Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4747-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4747-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4747-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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