pre-miRNA Information
pre-miRNA hsa-mir-1303   
Genomic Coordinates chr5: 154685776 - 154685861
Synonyms MIRN1303, hsa-mir-1303, MIR1303
Description Homo sapiens miR-1303 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-1303
Sequence 52| UUUAGAGACGGGGUCUUGCUCU |73
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 4 5 + 154685830 23291724, 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs370437195 6 dbSNP
rs1195001383 7 dbSNP
rs546614687 8 dbSNP
rs762579883 9 dbSNP
rs766041486 10 dbSNP
rs751079975 12 dbSNP
rs888516744 13 dbSNP
rs566454487 14 dbSNP
rs766973220 15 dbSNP
rs1474274822 17 dbSNP
rs753222192 18 dbSNP
rs1230907999 19 dbSNP
rs756552638 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TWF1   
Synonyms A6, PTK9
Description twinfilin actin binding protein 1
Transcript NM_002822   
Expression
Putative miRNA Targets on TWF1
3'UTR of TWF1
(miRNA target sites are highlighted)
>TWF1|NM_002822|3'UTR
   1 AGTCATCACATTAAACATTGTAATACTAGTTTTTTAAAAGTCCAGCTTTTAGTACAGGAGAACTGAAATCATTCCATGTT
  81 GATATAAAGTAGGGAAAAAAATTGTACTTTTTGGAAAATAGCACTTTTCACTTCTGTGTGTTTTTAAAATTAATGTTATA
 161 GAAGACTCATGATTTCTATTTTTGAGTTAAAGCTAGAAAAGGGTTCAACATAATGTTTAATTTTGTCACACTGTTTTCAT
 241 AGCGTTGATTCCACACTTCAAATACTTCTTAAAATTTTATACAGTTGGGCCAGTTCTAGAAAGTCTGATGTCTCAAAGGG
 321 TAAACTTACTACTTTCTTGTGGGACAGAAAGACCTTAAAATATTCATATTACTTAATGAATATGTTAAGGACCAGGCTAG
 401 AGTATTTTCTAAGCTGGAAACTTAGTGTGCCTTGGAAAAGGCCGCAAGTTGCTTACTCCGAGTAGCTGTGCTAGCTCTGT
 481 CAGACTGTAGGATCATGTCTGCAACTTTTAGAAATAGTGCTTTATATTGCAGCAGTCTTTTATATTTGACTTTTTTTTAA
 561 TAGCATTAAAATTGCAGATCAGCTCACTCTGAAACTTTAAGGGTACCAGATATTTTCTATACTGCAGGATTTCTGATGAC
 641 ATTGAAAGACTTTAAACAGCCTTAGTAAATTATCTTTCTAATGCTCTGTGAGGCCAAACATTTATGTTCAGATTGAAATT
 721 TAAATTAATATCATTCAAAAGGAAACAAAAAATGTTGAGTTTTAAAAATCAGGATTGACTTTTTTCTCCAAAACCATACA
 801 TTTATGGGCAAATTGTGTTCTTTATCACTTCCGAGCAAATACTCAGATTTAAAATTACTTTAAAGTCCTGGTACTTAACA
 881 GGCTAACGTAGATAAACACCTTAATAATCTCAGTTAATACTGTATTTCAAAACACATTTAACTGTTTTCTAATGCTTTGC
 961 ATTATCAGTTACAACCTAGAGAGATTTTGAGCCTCATATTTCTTTGATACTTGAAATAGAGGGAGCTAGAACACTTAATG
1041 TTTAATCTGTTAAACCTGCTGCAAGAGCCATAACTTTGAGGCATTTTCTAAATGAACTGTGGGGATCCAGGATTTGTAAT
1121 TTCTTGATCTAAACTTTATGCTGCATAAATCACTTATCGGAAATGCACATTTCATAGTGTGAAGCACTCATTTCTAAACC
1201 TTATTATCTAAGGTAATATATGCACCTTTCAGAAATTTGTGTTCGAGTAAGTAAAGCATATTAGAATAATTGTGGGTTGA
1281 CAGATTTTTAAAATAGAATTTAGAGTATTTGGGGTTTTGTTTGTTTACAAATAATCAGACTATAATATTTAAACATGCAA
1361 AATAACTGACAATAATGTTGCACTTGTTTACTAAAGATATAAGTTGTTCCATGGGTGTACACGTAGACAGACACACATAC
1441 ACCCAAATTATTGCATTAAGAATCCTGGAGCAGACCATAGCTGAAGCTGTTATTTTCAGTCAGGAAGACTACCTGTCATG
1521 AAGGTATAAAATAATTTAGAAGTGAATGTTTTTCTGTACCATCTATGTGCAATTATACTCTAAATTCCACTACACTACAT
1601 TAAAGTAAATGGACATTCCAGAATATAGATGTGATTATAGTCTTAAACTAATTATTATTAAACCAATGATTGCTGAAAAT
1681 CAGTGATGCATTTGTTATAGAGTATAACTCATCGTTTACAGTATGTTTTAGTTGGCAGTATCATACCTAGATGGTGAATA
1761 ACATATTCCCAGTAAATTTATATAGCAGTGAAGAATTACATGCCTTCTGGTGGACATTTTATAAGTGCATTTTATATCAC
1841 AATAAAAATTTTTTCTCTTTAAAAAAAAAAAAAAAAAAA
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' ucucgUUCUGGGGCAGAGAUUu 5'
               |||  |:| |:||||| 
Target 5' gtgtgAAGCACTCATTTCTAAa 3'
1177 - 1198 141.00 -10.50
2
miRNA  3' ucUCGUUCUGGGGCAGAGAUUu 5'
            ||:|| |:: : |:||||| 
Target 5' ttAGTAA-ATTATCTTTCTAAt 3'
662 - 682 139.00 -7.20
3
miRNA  3' ucUCGUUCUGGGGCAGAGAUUu 5'
            :|| ||| : : |:||||| 
Target 5' caGGCTAGAGTAT-TTTCTAAg 3'
393 - 413 135.00 -9.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30190011 4 COSMIC
COSN30106752 7 COSMIC
COSN30458841 9 COSMIC
COSN31519715 29 COSMIC
COSN13395521 60 COSMIC
COSN30157197 74 COSMIC
COSN30138502 91 COSMIC
COSN31649450 114 COSMIC
COSN30102996 125 COSMIC
COSN31539475 274 COSMIC
COSN17075960 364 COSMIC
COSN16908104 397 COSMIC
COSN21733823 709 COSMIC
COSN21176674 764 COSMIC
COSN31533958 984 COSMIC
COSN31531525 1184 COSMIC
COSN24304391 1278 COSMIC
COSN20626814 1323 COSMIC
COSN29338484 1331 COSMIC
COSN24853546 1423 COSMIC
COSN31527660 1530 COSMIC
COSN30174441 1700 COSMIC
COSN31486368 1713 COSMIC
COSN31513624 1729 COSMIC
COSN22460466 1785 COSMIC
COSN24304390 1796 COSMIC
COSN1573890 1836 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs773643762 4 dbSNP
rs921443984 7 dbSNP
rs768039861 9 dbSNP
rs761332163 16 dbSNP
rs373297018 17 dbSNP
rs768298154 18 dbSNP
rs1392156692 19 dbSNP
rs749004245 21 dbSNP
rs1453747641 25 dbSNP
rs1253486655 28 dbSNP
rs1194963696 29 dbSNP
rs1463214370 40 dbSNP
rs1266925514 42 dbSNP
rs369394985 45 dbSNP
rs1352360642 50 dbSNP
rs1306807968 76 dbSNP
rs1334345879 77 dbSNP
rs765571809 78 dbSNP
rs1225672480 79 dbSNP
rs1264331454 84 dbSNP
rs1284254541 89 dbSNP
rs569070697 95 dbSNP
rs745965976 99 dbSNP
rs944295063 102 dbSNP
rs1252535789 105 dbSNP
rs912850201 106 dbSNP
rs1176266124 111 dbSNP
rs988206856 112 dbSNP
rs1339186222 118 dbSNP
rs1434697951 127 dbSNP
rs1199813886 151 dbSNP
rs1309793072 159 dbSNP
rs1428549139 161 dbSNP
rs1468134917 168 dbSNP
rs935042095 172 dbSNP
rs192639904 178 dbSNP
rs979197043 184 dbSNP
rs1297835891 186 dbSNP
rs1023481675 196 dbSNP
rs992038931 201 dbSNP
rs111381081 202 dbSNP
rs184208840 210 dbSNP
rs1426756638 227 dbSNP
rs1391783164 239 dbSNP
rs535312216 243 dbSNP
rs1026998124 244 dbSNP
rs574183025 252 dbSNP
rs546580839 254 dbSNP
rs1802561 259 dbSNP
rs1420057414 261 dbSNP
rs866306708 261 dbSNP
rs1250792861 262 dbSNP
rs1169780653 281 dbSNP
rs1371595472 290 dbSNP
rs115917962 299 dbSNP
rs1304195895 302 dbSNP
rs944243097 306 dbSNP
rs891361041 307 dbSNP
rs1291161190 314 dbSNP
rs1490724788 318 dbSNP
rs1363206056 321 dbSNP
rs567330513 329 dbSNP
rs1292776265 336 dbSNP
rs1361211191 340 dbSNP
rs1246240780 341 dbSNP
rs1290846184 345 dbSNP
rs1489799449 351 dbSNP
rs934970361 371 dbSNP
rs191959992 372 dbSNP
rs1353665246 375 dbSNP
rs1186055053 383 dbSNP
rs531002149 389 dbSNP
rs924986156 400 dbSNP
rs749390153 412 dbSNP
rs1384785024 415 dbSNP
rs1403973485 416 dbSNP
rs866833538 419 dbSNP
rs61933173 420 dbSNP
rs1161680766 421 dbSNP
rs1346343264 425 dbSNP
rs1430612273 428 dbSNP
rs1237153154 429 dbSNP
rs866490724 433 dbSNP
rs563952739 443 dbSNP
rs545274303 444 dbSNP
rs1313940148 455 dbSNP
rs1331855444 459 dbSNP
rs916373710 460 dbSNP
rs1284667354 461 dbSNP
rs1316327870 462 dbSNP
rs1213557328 464 dbSNP
rs1244829588 484 dbSNP
rs991979455 486 dbSNP
rs187670930 495 dbSNP
rs1242794440 499 dbSNP
rs1471914081 505 dbSNP
rs1179365582 506 dbSNP
rs1400705760 508 dbSNP
rs1157595352 509 dbSNP
rs1408864793 510 dbSNP
rs11834357 511 dbSNP
rs1469898329 514 dbSNP
rs1335457295 523 dbSNP
rs1160081732 525 dbSNP
rs1380187355 531 dbSNP
rs1443908093 535 dbSNP
rs1015232341 537 dbSNP
rs1372357267 538 dbSNP
rs777830001 540 dbSNP
rs754917999 542 dbSNP
rs1264954668 545 dbSNP
rs150162165 555 dbSNP
rs1204426948 559 dbSNP
rs951422472 561 dbSNP
rs540995868 562 dbSNP
rs1440962838 564 dbSNP
rs995505054 565 dbSNP
rs1233599264 572 dbSNP
rs1478889403 585 dbSNP
rs1246870827 591 dbSNP
rs746894867 596 dbSNP
rs899918180 598 dbSNP
rs1432135577 604 dbSNP
rs1018344342 607 dbSNP
rs1175161903 610 dbSNP
rs1399429319 626 dbSNP
rs140904391 630 dbSNP
rs183330154 635 dbSNP
rs1329149229 642 dbSNP
rs1353514277 647 dbSNP
rs1208865333 648 dbSNP
rs1329018704 651 dbSNP
rs1407802019 652 dbSNP
rs1284924314 659 dbSNP
rs1346124804 664 dbSNP
rs555427981 672 dbSNP
rs1282798268 684 dbSNP
rs1342966935 699 dbSNP
rs1197571793 701 dbSNP
rs1274000165 703 dbSNP
rs1437432474 713 dbSNP
rs1203514930 714 dbSNP
rs1266812352 731 dbSNP
rs891315001 736 dbSNP
rs1053088506 738 dbSNP
rs1490675840 744 dbSNP
rs1479822888 755 dbSNP
rs1376375158 757 dbSNP
rs1225658288 772 dbSNP
rs999789978 774 dbSNP
rs867587318 779 dbSNP
rs1167953251 796 dbSNP
rs761630803 797 dbSNP
rs1274690590 804 dbSNP
rs3990369 806 dbSNP
rs116442992 810 dbSNP
rs1304788982 816 dbSNP
rs1365955856 819 dbSNP
rs758165588 827 dbSNP
rs866944834 832 dbSNP
rs1328078613 833 dbSNP
rs1321273905 837 dbSNP
rs1270824167 842 dbSNP
rs1339046795 845 dbSNP
rs1226457962 846 dbSNP
rs1294140852 851 dbSNP
rs947736210 863 dbSNP
rs916314561 870 dbSNP
rs1056242962 879 dbSNP
rs11556066 881 dbSNP
rs907708788 882 dbSNP
rs1447352096 883 dbSNP
rs192434354 887 dbSNP
rs1385408148 888 dbSNP
rs538466561 891 dbSNP
rs1416161998 892 dbSNP
rs1161199929 900 dbSNP
rs1425607126 901 dbSNP
rs1211507017 902 dbSNP
rs1387098184 903 dbSNP
rs1382698718 918 dbSNP
rs571532912 919 dbSNP
rs1364555489 921 dbSNP
rs920544153 922 dbSNP
rs1432920013 931 dbSNP
rs546938203 934 dbSNP
rs1360394820 937 dbSNP
rs1391652970 939 dbSNP
rs1244571765 945 dbSNP
rs1264021370 954 dbSNP
rs867247117 955 dbSNP
rs1353540600 960 dbSNP
rs1206232666 967 dbSNP
rs1284098466 974 dbSNP
rs534584912 978 dbSNP
rs567310677 985 dbSNP
rs1243409853 996 dbSNP
rs1018291976 998 dbSNP
rs1246663044 1000 dbSNP
rs1008326981 1006 dbSNP
rs1365320714 1011 dbSNP
rs1454062818 1022 dbSNP
rs1157943546 1025 dbSNP
rs1386305950 1033 dbSNP
rs549095021 1035 dbSNP
rs1443563743 1039 dbSNP
rs1338751358 1062 dbSNP
rs1278322703 1067 dbSNP
rs1199146645 1070 dbSNP
rs1395653564 1072 dbSNP
rs1311106696 1073 dbSNP
rs1341688736 1074 dbSNP
rs1337903831 1077 dbSNP
rs1298615024 1081 dbSNP
rs1240131377 1083 dbSNP
rs1288293584 1095 dbSNP
rs530579560 1101 dbSNP
rs1227688611 1110 dbSNP
rs1263193961 1111 dbSNP
rs1031172728 1112 dbSNP
rs1363102976 1113 dbSNP
rs563244850 1125 dbSNP
rs1450092703 1138 dbSNP
rs551916006 1153 dbSNP
rs1000142159 1154 dbSNP
rs1333209082 1156 dbSNP
rs1412573370 1158 dbSNP
rs904098587 1159 dbSNP
rs1178743725 1169 dbSNP
rs1406911927 1179 dbSNP
rs1044024200 1196 dbSNP
rs1168848834 1201 dbSNP
rs1448558359 1207 dbSNP
rs533380255 1212 dbSNP
rs1392364590 1213 dbSNP
rs1288080596 1219 dbSNP
rs1349234343 1223 dbSNP
rs1225883415 1225 dbSNP
rs559593970 1244 dbSNP
rs1011895475 1250 dbSNP
rs894826448 1253 dbSNP
rs1311119735 1259 dbSNP
rs1387777408 1264 dbSNP
rs552168065 1268 dbSNP
rs939115244 1286 dbSNP
rs1204245051 1293 dbSNP
rs907653835 1317 dbSNP
rs1490838242 1319 dbSNP
rs1200062335 1324 dbSNP
rs764238770 1327 dbSNP
rs1432693011 1329 dbSNP
rs1173991706 1343 dbSNP
rs1375040770 1346 dbSNP
rs1462667663 1351 dbSNP
rs1047547515 1356 dbSNP
rs930499777 1358 dbSNP
rs1208377250 1370 dbSNP
rs920495188 1373 dbSNP
rs1275872311 1383 dbSNP
rs1384613793 1387 dbSNP
rs1297075339 1392 dbSNP
rs1204701009 1394 dbSNP
rs1307776751 1397 dbSNP
rs1227199952 1399 dbSNP
rs573691871 1403 dbSNP
rs974651256 1406 dbSNP
rs561794574 1409 dbSNP
rs963986902 1411 dbSNP
rs543458117 1412 dbSNP
rs911232431 1415 dbSNP
rs1228989541 1422 dbSNP
rs576442302 1423 dbSNP
rs1426984838 1425 dbSNP
rs1164575620 1428 dbSNP
rs1031539579 1433 dbSNP
rs1434931538 1436 dbSNP
rs1445463676 1437 dbSNP
rs1433631654 1440 dbSNP
rs999687583 1443 dbSNP
rs557988233 1447 dbSNP
rs1022524279 1452 dbSNP
rs1246490410 1472 dbSNP
rs538798597 1477 dbSNP
rs1012510665 1479 dbSNP
rs894774125 1481 dbSNP
rs1217858651 1501 dbSNP
rs1261179276 1506 dbSNP
rs1465418736 1523 dbSNP
rs1187960948 1529 dbSNP
rs1308478462 1530 dbSNP
rs1428669199 1531 dbSNP
rs577941422 1536 dbSNP
rs1368369117 1538 dbSNP
rs775501218 1539 dbSNP
rs1166225532 1556 dbSNP
rs1446648627 1560 dbSNP
rs1034685988 1564 dbSNP
rs1003652744 1566 dbSNP
rs1405450239 1567 dbSNP
rs1413633743 1570 dbSNP
rs375367040 1590 dbSNP
rs1161927817 1593 dbSNP
rs1473896991 1600 dbSNP
rs1456276216 1603 dbSNP
rs1252956179 1605 dbSNP
rs1181972855 1634 dbSNP
rs1452897185 1637 dbSNP
rs1047957156 1649 dbSNP
rs1376718989 1651 dbSNP
rs1225211340 1655 dbSNP
rs1307658324 1661 dbSNP
rs534962974 1663 dbSNP
rs1328352275 1666 dbSNP
rs1208243726 1667 dbSNP
rs1248709566 1675 dbSNP
rs1222307849 1686 dbSNP
rs1321206924 1687 dbSNP
rs930456585 1690 dbSNP
rs1237058664 1694 dbSNP
rs1300510957 1698 dbSNP
rs1179275267 1700 dbSNP
rs1389466909 1700 dbSNP
rs1413393176 1701 dbSNP
rs1331190286 1710 dbSNP
rs899018176 1713 dbSNP
rs1409011612 1714 dbSNP
rs1430780075 1715 dbSNP
rs1414476146 1716 dbSNP
rs567569462 1720 dbSNP
rs943295401 1721 dbSNP
rs1298516199 1725 dbSNP
rs1436827932 1733 dbSNP
rs1226496666 1749 dbSNP
rs1285047182 1765 dbSNP
rs1219832748 1766 dbSNP
rs911837637 1784 dbSNP
rs986812199 1794 dbSNP
rs1440876091 1814 dbSNP
rs934015032 1817 dbSNP
rs1252971818 1821 dbSNP
rs781171026 1823 dbSNP
rs1483053596 1830 dbSNP
rs372167070 1834 dbSNP
rs978593968 1836 dbSNP
rs968174484 1842 dbSNP
rs1022473925 1844 dbSNP
rs1422684972 1847 dbSNP
rs1348792136 1848 dbSNP
rs1169060431 1850 dbSNP
rs1369728452 1860 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 GSM545212. RNA binding protein: AGO1. Condition:Control ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ucucguucuggggcaGAGAUUu 5'
                         |||||| 
Target 5' -------caauuauaCUCUAAa 3'
1 - 15
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 C8166
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- 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' ucucguucuggggcaGAGAUUu 5'
                         |||||| 
Target 5' -------caauuauaCUCUAAa 3'
1 - 15
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM545212
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / Control
Location of target site ENST00000552521.1 | 3UTR | CAAUUAUACUCUAAAUUCCACUACACUACAUU
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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000552521.1 | 3UTR | CAAUUAUACUCUAAAUUCCACUACACUACAUUAAAG
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
GSE28544 Breast cancer -0.528 4.0e-3 -0.572 1.7e-3 24 Click to see details
GSE42095 Differentiated embryonic stem cells -0.5 7.6e-3 -0.467 1.2e-2 23 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.285 8.4e-2 0.108 3.0e-1 25 Click to see details
GSE32688 Pancreatic cancer -0.144 2.2e-1 -0.078 3.4e-1 32 Click to see details
GSE38226 Liver fibrosis -0.128 2.9e-1 -0.053 4.1e-1 21 Click to see details
GSE28260 Renal cortex and medulla 0.075 4.0e-1 -0.110 3.6e-1 13 Click to see details
GSE26953 Aortic valvular endothelial cells -0.017 4.7e-1 -0.043 4.2e-1 24 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
186 hsa-miR-1303 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT035871 SOAT1 sterol O-acyltransferase 1 1 1
MIRT035872 FHOD3 formin homology 2 domain containing 3 1 1
MIRT035873 RPL7A ribosomal protein L7a 1 1
MIRT035874 NCAPD2 non-SMC condensin I complex subunit D2 1 1
MIRT035875 RPS8 ribosomal protein S8 1 1
MIRT035876 AHNAK AHNAK nucleoprotein 1 1
MIRT035877 ACTB actin beta 1 1
MIRT035878 DEF8 differentially expressed in FDCP 8 homolog 1 1
MIRT035879 MET MET proto-oncogene, receptor tyrosine kinase 1 1
MIRT035880 MED13 mediator complex subunit 13 1 1
MIRT035881 FAT3 FAT atypical cadherin 3 1 1
MIRT035882 HUWE1 HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase 1 1
MIRT035883 RPS16 ribosomal protein S16 1 1
MIRT035884 CDK6 cyclin dependent kinase 6 1 1
MIRT035885 GEMIN5 gem nuclear organelle associated protein 5 1 1
MIRT035886 PITRM1 pitrilysin metallopeptidase 1 1 1
MIRT035887 PRRC2A proline rich coiled-coil 2A 1 1
MIRT035888 KIAA0226 RUN and cysteine rich domain containing beclin 1 interacting protein 1 1
MIRT035889 MLLT6 MLLT6, PHD finger containing 1 1
MIRT035890 EIF3I eukaryotic translation initiation factor 3 subunit I 1 1
MIRT035891 FASN fatty acid synthase 1 1
MIRT035892 LEPREL4 prolyl 3-hydroxylase family member 4 (non-enzymatic) 1 1
MIRT035893 HSCB HscB mitochondrial iron-sulfur cluster cochaperone 1 1
MIRT035894 PSME4 proteasome activator subunit 4 1 1
MIRT035895 FRS2 fibroblast growth factor receptor substrate 2 1 1
MIRT035896 ZNF264 zinc finger protein 264 1 1
MIRT035897 HYLS1 HYLS1, centriolar and ciliogenesis associated 1 1
MIRT035898 USP54 ubiquitin specific peptidase 54 1 1
MIRT035899 L1TD1 LINE1 type transposase domain containing 1 1 1
MIRT035900 OR51E2 olfactory receptor family 51 subfamily E member 2 1 1
MIRT053762 CLDN18 claudin 18 3 1
MIRT060730 RPS3 ribosomal protein S3 2 2
MIRT083986 RAB22A RAB22A, member RAS oncogene family 2 2
MIRT098550 TBPL1 TATA-box binding protein like 1 2 6
MIRT134983 TWF1 twinfilin actin binding protein 1 2 4
MIRT136956 FNDC3A fibronectin type III domain containing 3A 2 2
MIRT222065 PURB purine rich element binding protein B 2 2
MIRT239574 UBN2 ubinuclein 2 2 4
MIRT261820 BUB3 BUB3, mitotic checkpoint protein 2 2
MIRT264698 C11ORF57 chromosome 11 open reading frame 57 2 4
MIRT308476 GXYLT2 glucoside xylosyltransferase 2 2 2
MIRT377481 NDUFB5 NADH:ubiquinone oxidoreductase subunit B5 2 2
MIRT442304 NEU3 neuraminidase 3 2 2
MIRT446083 SLC30A10 solute carrier family 30 member 10 2 2
MIRT449606 PRPF4 pre-mRNA processing factor 4 2 2
MIRT453767 NUCB1 nucleobindin 1 2 10
MIRT455603 SRSF3 serine and arginine rich splicing factor 3 2 2
MIRT455913 KIF2C kinesin family member 2C 2 2
MIRT460091 ZYG11B zyg-11 family member B, cell cycle regulator 2 4
MIRT460866 UBE2S ubiquitin conjugating enzyme E2 S 2 2
MIRT461339 NUP133 nucleoporin 133 2 2
MIRT463769 YOD1 YOD1 deubiquitinase 2 2
MIRT466368 THAP1 THAP domain containing 1 2 4
MIRT467168 SPTY2D1 SPT2 chromatin protein domain containing 1 2 2
MIRT468703 SDHD succinate dehydrogenase complex subunit D 2 2
MIRT469122 RNF126 ring finger protein 126 2 2
MIRT472426 NCBP2 nuclear cap binding protein subunit 2 2 4
MIRT479420 CDKN1B cyclin dependent kinase inhibitor 1B 2 8
MIRT484260 FAM177A1 family with sequence similarity 177 member A1 2 2
MIRT485468 IL6ST interleukin 6 signal transducer 2 10
MIRT490237 H2AFZ H2A histone family member Z 2 6
MIRT491002 ATF7IP activating transcription factor 7 interacting protein 2 2
MIRT492127 SUMO2 small ubiquitin-like modifier 2 2 2
MIRT499169 RBPJL recombination signal binding protein for immunoglobulin kappa J region like 2 2
MIRT499825 PCSK9 proprotein convertase subtilisin/kexin type 9 2 8
MIRT501794 NRAS NRAS proto-oncogene, GTPase 2 2
MIRT503441 GINS4 GINS complex subunit 4 2 4
MIRT503688 MAVS mitochondrial antiviral signaling protein 2 5
MIRT506926 IGDCC4 immunoglobulin superfamily DCC subclass member 4 2 6
MIRT511430 HOXA10 homeobox A10 2 6
MIRT512415 LAYN layilin 2 4
MIRT513791 NIPAL3 NIPA like domain containing 3 2 4
MIRT516163 NTMT1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 2 4
MIRT516513 PARK2 parkin RBR E3 ubiquitin protein ligase 2 2
MIRT516915 HINFP histone H4 transcription factor 2 2
MIRT517102 NDUFV3 NADH:ubiquinone oxidoreductase subunit V3 2 2
MIRT517350 NLRP9 NLR family pyrin domain containing 9 2 2
MIRT518019 ABHD15 abhydrolase domain containing 15 2 2
MIRT520945 SRSF10 serine and arginine rich splicing factor 10 2 2
MIRT525250 RNF213 ring finger protein 213 2 2
MIRT530634 PPIC peptidylprolyl isomerase C 2 4
MIRT530671 CHRNB1 cholinergic receptor nicotinic beta 1 subunit 2 4
MIRT531563 ILDR1 immunoglobulin like domain containing receptor 1 2 2
MIRT538205 CYR61 cysteine rich angiogenic inducer 61 2 2
MIRT538419 COLEC10 collectin subfamily member 10 2 2
MIRT541964 ZNF485 zinc finger protein 485 2 2
MIRT543088 KNSTRN kinetochore localized astrin/SPAG5 binding protein 2 2
MIRT543257 ZNF662 zinc finger protein 662 2 2
MIRT543589 KIAA1549 KIAA1549 2 2
MIRT543955 RNF20 ring finger protein 20 2 2
MIRT544043 C9orf64 chromosome 9 open reading frame 64 2 4
MIRT548064 GIGYF1 GRB10 interacting GYF protein 1 2 2
MIRT548240 FBXW7 F-box and WD repeat domain containing 7 2 2
MIRT548442 EIF1AX eukaryotic translation initiation factor 1A, X-linked 2 2
MIRT548623 DAZAP1 DAZ associated protein 1 2 4
MIRT548770 COLEC12 collectin subfamily member 12 2 2
MIRT549506 HDDC2 HD domain containing 2 2 4
MIRT551924 AKAP8 A-kinase anchoring protein 8 2 4
MIRT555656 PGRMC1 progesterone receptor membrane component 1 2 2
MIRT556286 MAP3K5 mitogen-activated protein kinase kinase kinase 5 2 2
MIRT557012 HOXD13 homeobox D13 2 4
MIRT563907 CLSPN claspin 2 2
MIRT565527 SON SON DNA binding protein 2 2
MIRT568000 COMMD2 COMM domain containing 2 2 2
MIRT569831 PLA2G16 phospholipase A2 group XVI 2 4
MIRT573905 PARP1 poly(ADP-ribose) polymerase 1 2 2
MIRT616589 KLHL9 kelch like family member 9 2 2
MIRT617137 ZNF556 zinc finger protein 556 2 2
MIRT617400 API5 apoptosis inhibitor 5 2 2
MIRT617455 CCS copper chaperone for superoxide dismutase 2 2
MIRT617799 ZNF793 zinc finger protein 793 2 2
MIRT618190 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT618303 GNE glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase 2 2
MIRT618329 ZNF813 zinc finger protein 813 2 2
MIRT618820 PHF20 PHD finger protein 20 2 2
MIRT619153 PPDPF pancreatic progenitor cell differentiation and proliferation factor 2 2
MIRT619530 ZNF708 zinc finger protein 708 2 2
MIRT619849 KIR3DX1 killer cell immunoglobulin like receptor, three Ig domains X1 2 2
MIRT620806 SLC26A2 solute carrier family 26 member 2 2 2
MIRT621312 YIPF4 Yip1 domain family member 4 2 2
MIRT621358 GUCA1B guanylate cyclase activator 1B 2 2
MIRT621366 ART4 ADP-ribosyltransferase 4 (Dombrock blood group) 2 2
MIRT621547 ZMYM1 zinc finger MYM-type containing 1 2 2
MIRT621883 TAOK1 TAO kinase 1 2 2
MIRT622451 RNF19B ring finger protein 19B 2 2
MIRT623404 KREMEN1 kringle containing transmembrane protein 1 2 2
MIRT623587 IPO9 importin 9 2 2
MIRT623974 FAM63A MINDY lysine 48 deubiquitinase 1 2 2
MIRT624086 DPP8 dipeptidyl peptidase 8 2 2
MIRT624108 DNAH10OS dynein axonemal heavy chain 10 opposite strand 2 2
MIRT632486 RNF8 ring finger protein 8 2 2
MIRT634057 PLIN3 perilipin 3 2 2
MIRT634657 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT640682 MCUR1 mitochondrial calcium uniporter regulator 1 2 2
MIRT641242 CENPN centromere protein N 2 2
MIRT642260 ZNF677 zinc finger protein 677 2 2
MIRT642954 RELA RELA proto-oncogene, NF-kB subunit 2 2
MIRT644326 IPP intracisternal A particle-promoted polypeptide 2 2
MIRT644632 ICA1L islet cell autoantigen 1 like 2 2
MIRT645721 POLR3A RNA polymerase III subunit A 2 2
MIRT647850 LYPLA1 lysophospholipase I 2 2
MIRT649281 NEK8 NIMA related kinase 8 2 2
MIRT650038 VHL von Hippel-Lindau tumor suppressor 2 2
MIRT650354 RRP36 ribosomal RNA processing 36 2 2
MIRT651144 ZNF384 zinc finger protein 384 2 2
MIRT651778 UTP6 UTP6, small subunit processome component 2 2
MIRT652576 TLCD2 TLC domain containing 2 2 2
MIRT654621 PTPRJ protein tyrosine phosphatase, receptor type J 2 2
MIRT656023 MYO5A myosin VA 2 2
MIRT656105 MSRB3 methionine sulfoxide reductase B3 2 2
MIRT657749 GMEB1 glucocorticoid modulatory element binding protein 1 2 2
MIRT657924 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT658848 DUSP19 dual specificity phosphatase 19 2 2
MIRT659100 DENND6A DENN domain containing 6A 2 2
MIRT659153 DCX doublecortin 2 2
MIRT660870 ADRBK2 G protein-coupled receptor kinase 3 2 2
MIRT661941 FAHD1 fumarylacetoacetate hydrolase domain containing 1 2 2
MIRT663577 C10orf32 BLOC-1 related complex subunit 7 2 2
MIRT664625 WDPCP WD repeat containing planar cell polarity effector 2 4
MIRT666562 RHOBTB3 Rho related BTB domain containing 3 2 2
MIRT669992 GPR156 G protein-coupled receptor 156 2 4
MIRT670445 RSBN1L round spermatid basic protein 1 like 2 2
MIRT670853 IFNAR1 interferon alpha and beta receptor subunit 1 2 4
MIRT671942 SPPL3 signal peptide peptidase like 3 2 2
MIRT674269 LMOD3 leiomodin 3 2 2
MIRT674424 MIOX myo-inositol oxygenase 2 4
MIRT674982 ATP5G1 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C1 (subunit 9) 2 2
MIRT675038 BACE2 beta-site APP-cleaving enzyme 2 2 4
MIRT675309 C2orf68 chromosome 2 open reading frame 68 2 2
MIRT675641 TTPAL alpha tocopherol transfer protein like 2 2
MIRT688688 CPS1 carbamoyl-phosphate synthase 1 2 2
MIRT689369 ZNF101 zinc finger protein 101 2 2
MIRT689605 AKAP6 A-kinase anchoring protein 6 2 2
MIRT691715 LARS leucyl-tRNA synthetase 2 2
MIRT695473 TRAT1 T-cell receptor associated transmembrane adaptor 1 2 2
MIRT695530 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 2 2
MIRT695878 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT696586 ORMDL2 ORMDL sphingolipid biosynthesis regulator 2 2 2
MIRT703007 HEATR5A HEAT repeat containing 5A 2 2
MIRT707942 PHKA1 phosphorylase kinase regulatory subunit alpha 1 2 2
MIRT709765 GPR183 G protein-coupled receptor 183 2 2
MIRT710332 ZNF669 zinc finger protein 669 2 2
MIRT713249 ZFP30 ZFP30 zinc finger protein 2 2
MIRT716613 RBM18 RNA binding motif protein 18 2 2
MIRT733414 BAG2 BCL2 associated athanogene 2 2 0
MIRT756135 THSD7A thrombospondin type 1 domain containing 7A 3 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-1 Anthocyanin NULL 145858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Caffeic acid NULL 689043 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Catechin approved 9064 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Curcumin NULL 969516 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Ferulic acid NULL 445858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Quercetin NULL 5280343 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Galactose NULL 6036 Quantitative real-time PCR lens 22736950 2012 up-regulated
miR-1 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Quantitative real-time PCR myocardial differentiation of mouse ES cells 19521018 2009 down-regulated
miR-1 Sulfonyl-hydrazone-1 (SHZ) NULL NULL Quantitative real-time PCR Murine broblast-derived Induced pluripotent stem cells 21445862 2011 up-regulated
miR-1 Cocaine NULL 446220 Next-generation sequencing ventral striatum 21708909 2011 up-regulated
miR-1 Atorvastatin approved 60823 Quantitative real-time PCR Cardiomyocyte 23860036 2013 down-regualted
miR-1 Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-1 Docosahexaenoic acid NULL 445580 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 Palmitic acid approved 985 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miR-1 Essential amino acids (EAA) NULL NULL Quantitative real-time PCR skeletal muscle of young adults 19828686 2009 up-regulated
miR-1 Hydrogen peroxide (H2O2) NULL 784 Quantitative real-time PCR Human umbilical vein endothelial cells 21527937 2011 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Microarray apoptosis-resistant breast cancer cells 21971930 2011 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR acute promyelocytic leukemia 22072212 2012 up-regulated
miR-1 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-1 Bicalutamide approved 2375 Microarray prostate 22674191 2012 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR cardia 22889704 2012 up-regulated
miR-1 Perfluorooctane sulfonate NULL 74483 Microarray zebrafish embryos 20878907 2011 up-regulated
miR-1 Quinidine approved 441074 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 up-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 down-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR post-infarction rat cardiomyocytes 21220930 2011 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 down-regulated
miR-1 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-1303 Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (RKO)
hsa-miR-1303 Oxaliplatin 6857599 NSC266046 approved resistant High Colorectal Cancer cell line (HT-29)
hsa-miR-1303 Imatinib 5291 NSC743414 approved sensitive High Gastrointestinal Stromal Tumor cell line (882R-NC, 882R-OE, 882R-KD)
hsa-miR-1303 Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-1303 Rituximab sensitive High Diffuse Large B-Cell Lymphoma cell line (DB, NU-DHL-1, NU-DUL-1, MC-116, SU-DHL-4, SU-DHL-5, FARAGE, HBL-1, OCI-Ly3, OCI-Ly7, OCI-Ly8, OCI-Ly19, RIVA, SU-DHL-8, U2932)
hsa-miR-1303 Etoposide 36462 NSC141540 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-1303 Doxorubicin 31703 NSC123127 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-1303 Vinorelbine 44424639 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-1303 Vincristine 5978 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-1303 Paclitaxel 36314 NSC125973 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-mir-1303 Dabrafenib 44462760 NSC764134 approved sensitive cell line (A375)
hsa-mir-1303 Cisplatin 5460033 NSC119875 approved resistant cell line (W1)
hsa-mir-1303 Topotecan 60699 NSC609699 approved resistant cell line (W1)
hsa-mir-1303 Androstenedione+Letrozole resistant cell line (MCF-7)
hsa-miR-1303 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-1303 Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-1303 Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-1303 Vemurafenib 42611257 NSC761431 approved resistant cell line (451Lu)
hsa-miR-1303 Palbociclib 5330286 NSC758247 approved resistant tissue (breast cancer)
hsa-miR-1303 Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-1303 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-1303 Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-miR-1303 Doxorubicin 31703 NSC123127 approved resistant cell line (HS578T)
hsa-miR-1303 Cisplatin 5460033 NSC119875 approved resistant cell line (CP20)
hsa-miR-1303 Cisplatin 5460033 NSC119875 approved sensitive cell line (MGC-803)
hsa-miR-1303 Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-1303 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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