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 GFER   
Synonyms ALR, ERV1, HERV1, HPO, HPO1, HPO2, HSS
Description growth factor, augmenter of liver regeneration
Transcript NM_005262   
Expression
Putative miRNA Targets on GFER
3'UTR of GFER
(miRNA target sites are highlighted)
>GFER|NM_005262|3'UTR
   1 AGGGTGGTCAGCCAGAGCTCATGGGACAGCTAGCCAGGCATGGTTGGATAGGGGCAGGGCACTCATTAAAGTGCATCACA
  81 GCCAGAGCCTGTTGTGTCTCAGTTGGGTGGTCCCCAGGACACTGCCTGTGGGGACCTGCCCTGCCCCTCTTAGGTTTGGA
 161 GCAGAAGTGGAGGTGCCCACAGCAGGTACCCACTGGCCCCCTCCTCAGTGGAGACCCCAAGGAGCTGCAGCTGAACTGCA
 241 GGGGAGGGAAGGAGGAGCAGCCTGGGCTGCCCCTTGACATTCAGGATGTAGCTTCCTGCCCACCGCATACCCTGGCGCCT
 321 CACTCCTCACACGGGAAGACAGCGGGCCTGGCTGGGCATCCCTGTGCCTGTCCCTGGCGGCCAGGCCATTGCCTTCCCAC
 401 TATGCAGCCAGGGATGCCCCTGCCCCCCATGGCTCTGTGCTGCTCACTTTAGGGGGCTCAATTCTCCACTCTGCTCAGTC
 481 CCTACAGGGAAAGCTCAGGTCGGGTCTTTCTGAGGGTCCACCAGCCATCCTACCCTCTCCCTGCCTGGCACATGCCTGCC
 561 AGCGTTGTGTCATGCCTGTCCACAGGGGATTCGTGGGGCTCACTTCATCAGAGTTTGAAGCCCAAATGAAACGCTGAAGT
 641 GACTGAGAACCTGGCTTCAGTATATTTTCTGCTGGGGCTTAATAAAGCAGTAGACAGGGCTTGTTCCATCCCTCTGTGCT
 721 CAGCTGCATTTCCTGCTGGGGTCCTGGTTCCTCAGGAGAGAGAGACCACAGGGTGAGAGTGAGCCAGGAACAGCAAGGAC
 801 GTTGATTGGTTGGGGCAGGGGGGCCAGAGTAGCTGATGTAGGAGTACTGGGAGGCCAGACGGCACGAGGTCTCCAAGGCC
 881 CCAGCAAAGCCATGGCTTCTACCCCTAGTTCCCCTGACAGGAAGTTCTTGGCGGGTTTGGAGCCAGGGGATGGCATGGAG
 961 TGATGTGGCTTTGAAGGGTCCTCTGGCTGCTGAGCTGGGATGAGGCAGGTAAGGGTGGAACAGGAGGGGTGGGGAGGAAG
1041 CCGGGGCAGTCACCGAGTGACCACCAAGAGGAAGACCCACCCCACGGCGGGGACAGATGCGGGGTACGTTAAAGGGAGAG
1121 CCAGAGAACTCATGGGGTGAGGATGGAGTCCGAGGAGACTGCTGGGAGCCGCCGTGTGGGTCAGAGATGGAGAAGGCTGA
1201 GTGCAGCAAGGTGGGGGGTGACTGGGACCCAGCCTTTGGGCCTCCCCAGCCAGAGCAGCCCAGCAACAGTGTGTCCTGTG
1281 GTCATAAAACTCCAGGGACCTCTATCCTCCAGGAGTCTCAGCCTTTCCCTGGGCGCAGGCCCACCTTGGCATGGCCGCCT
1361 CAGGCCTCCATGGAGGGAGCTGCTATGTCCCCACCAGATTGGCCCCGTGCGGCTGCTGGCTTCTGTAGAGGCTGCCCAGA
1441 GGGGCCAGGTGGCACAAATAAGAGAGGGGAGATGGGGGGCAGCCAGGAGAGGAGGTGTCCCTTCCTCGCCCAGACACAGC
1521 GCGCTTCTCTCTGGCCTTTCCCGAGGCCTGTGAGTGCCTCAGGAAGCAGCTGGGCCCTCTGGGAAGGCTGTGTTCAGCTT
1601 AGGAACATACCGCCTGTATCTGCTGTCCCTCCCCTGCCCCCCTGCCCCCCCCACCGCCTTCCCTTTTTCCCTGTCTTCCT
1681 TAAAGTTTCACTCCTGAATAAAACTTCACTTTGCCTTAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' gauuCUGGUUCGG--A-GGAAGGGa 5'
              |:|||:|||  | ||||||| 
Target 5' tggcGGCCAGGCCATTGCCTTCCCa 3'
375 - 399 164.00 -25.80
2
miRNA  3' gauucuGGUUCGGAGGAAGGGa 5'
                |||  || ||||||| 
Target 5' ccccccCCA--CCGCCTTCCCt 3'
1645 - 1664 152.00 -18.40
3
miRNA  3' gaUUCUGGUUCGGAGGAAGGGa 5'
            |:||:  |||:|||| ||| 
Target 5' tcAGGATGTAGCTTCCTGCCCa 3'
281 - 302 140.00 -19.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
381072 4 ClinVar
1192012 89 ClinVar
COSN30497295 10 COSMIC
COSN31562088 17 COSMIC
COSN18739698 20 COSMIC
COSN26557684 30 COSMIC
COSN13656627 35 COSMIC
COSN30169048 98 COSMIC
COSN19618239 114 COSMIC
COSN25012280 134 COSMIC
COSN8494318 176 COSMIC
COSN20112533 457 COSMIC
COSN8494321 529 COSMIC
COSN21336395 917 COSMIC
COSN20112537 1065 COSMIC
COSN32150189 1158 COSMIC
COSN26872828 1357 COSMIC
COSN6644726 1567 COSMIC
COSN22864208 1706 COSMIC
rs1046495 20 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs755761266 3 dbSNP
rs779641464 4 dbSNP
rs754482090 8 dbSNP
rs899235039 12 dbSNP
rs778574653 13 dbSNP
rs1442803954 15 dbSNP
rs1046494 16 dbSNP
rs920759135 18 dbSNP
rs747482644 19 dbSNP
rs1046495 20 dbSNP
rs1468762317 21 dbSNP
rs1204175194 26 dbSNP
rs1048242618 30 dbSNP
rs886530247 31 dbSNP
rs781585682 36 dbSNP
rs1378439235 37 dbSNP
rs746282425 39 dbSNP
rs1008831385 44 dbSNP
rs1243349626 49 dbSNP
rs376347462 51 dbSNP
rs970630629 52 dbSNP
rs1040367770 54 dbSNP
rs572404227 58 dbSNP
rs997162482 62 dbSNP
rs143512788 63 dbSNP
rs1028273100 72 dbSNP
rs150953401 75 dbSNP
rs112914759 76 dbSNP
rs1371580520 78 dbSNP
rs1469376855 88 dbSNP
rs61729107 89 dbSNP
rs1252240299 101 dbSNP
rs1031401127 102 dbSNP
rs1165550801 104 dbSNP
rs1425708219 106 dbSNP
rs955787166 110 dbSNP
rs562561911 117 dbSNP
rs978008484 120 dbSNP
rs768826382 123 dbSNP
rs113398284 126 dbSNP
rs916900973 146 dbSNP
rs575994898 155 dbSNP
rs1487962336 169 dbSNP
rs980754598 181 dbSNP
rs1265724197 185 dbSNP
rs61729106 188 dbSNP
rs565205569 198 dbSNP
rs1386585355 200 dbSNP
rs527565190 201 dbSNP
rs1286946074 214 dbSNP
rs1047912757 216 dbSNP
rs889363387 228 dbSNP
rs1351413928 233 dbSNP
rs1327179427 240 dbSNP
rs1385506589 245 dbSNP
rs1370890131 248 dbSNP
rs1390288681 267 dbSNP
rs907938377 277 dbSNP
rs1294386926 282 dbSNP
rs547677664 283 dbSNP
rs748598076 286 dbSNP
rs1459491518 296 dbSNP
rs944781909 297 dbSNP
rs1040473056 299 dbSNP
rs1037688658 305 dbSNP
rs770576776 306 dbSNP
rs1197001011 311 dbSNP
rs183744268 312 dbSNP
rs996197837 313 dbSNP
rs529853737 317 dbSNP
rs1026111045 318 dbSNP
rs540801496 319 dbSNP
rs146752626 333 dbSNP
rs563965614 334 dbSNP
rs959303649 335 dbSNP
rs1302188318 344 dbSNP
rs989571142 344 dbSNP
rs1000407179 345 dbSNP
rs139351234 348 dbSNP
rs533040694 352 dbSNP
rs1336328569 360 dbSNP
rs1170798125 361 dbSNP
rs977830044 364 dbSNP
rs1267266033 365 dbSNP
rs1467062426 373 dbSNP
rs752447835 376 dbSNP
rs1426380642 379 dbSNP
rs186856814 380 dbSNP
rs987623925 382 dbSNP
rs1176841741 390 dbSNP
rs762340954 392 dbSNP
rs943608528 393 dbSNP
rs1199268822 394 dbSNP
rs550086806 400 dbSNP
rs1256959796 401 dbSNP
rs566067616 403 dbSNP
rs1235622676 409 dbSNP
rs1038119047 415 dbSNP
rs563527259 422 dbSNP
rs1394444139 423 dbSNP
rs1435875625 423 dbSNP
rs929382458 423 dbSNP
rs1047839428 424 dbSNP
rs529239322 426 dbSNP
rs376238901 429 dbSNP
rs983699491 431 dbSNP
rs1003357467 432 dbSNP
rs1054862824 433 dbSNP
rs1382889999 434 dbSNP
rs908035078 446 dbSNP
rs1185969720 447 dbSNP
rs1442366025 448 dbSNP
rs11864543 451 dbSNP
rs3833071 452 dbSNP
rs1356973954 453 dbSNP
rs757794171 458 dbSNP
rs922041028 465 dbSNP
rs1344324096 467 dbSNP
rs931950764 470 dbSNP
rs1282513371 472 dbSNP
rs1244224959 478 dbSNP
rs1043745168 488 dbSNP
rs903880389 492 dbSNP
rs935915379 497 dbSNP
rs868196153 499 dbSNP
rs1369746369 502 dbSNP
rs1308220044 520 dbSNP
rs1431262523 523 dbSNP
rs1273543778 527 dbSNP
rs891626763 528 dbSNP
rs1437031066 536 dbSNP
rs1387880388 541 dbSNP
rs1162115350 545 dbSNP
rs1014105251 552 dbSNP
rs1472879272 553 dbSNP
rs556029488 555 dbSNP
rs118144645 564 dbSNP
rs905633030 565 dbSNP
rs1471791872 566 dbSNP
rs545053910 568 dbSNP
rs1206064120 576 dbSNP
rs1484150127 585 dbSNP
rs143272026 591 dbSNP
rs1209280588 593 dbSNP
rs756276578 594 dbSNP
rs987656550 599 dbSNP
rs910692090 600 dbSNP
rs1226534761 601 dbSNP
rs572045152 602 dbSNP
rs17135743 603 dbSNP
rs1397825433 604 dbSNP
rs1411495982 607 dbSNP
rs1328995712 613 dbSNP
rs973639649 624 dbSNP
rs920840373 626 dbSNP
rs929355903 629 dbSNP
rs1047704018 634 dbSNP
rs11859464 635 dbSNP
rs1411948988 640 dbSNP
rs939412168 641 dbSNP
rs1471381712 654 dbSNP
rs1376952981 655 dbSNP
rs983668337 660 dbSNP
rs1198456242 674 dbSNP
rs1415045298 674 dbSNP
rs1328380852 681 dbSNP
rs1054894193 699 dbSNP
rs768610681 701 dbSNP
rs1206682615 711 dbSNP
rs1292250377 719 dbSNP
rs1328376684 720 dbSNP
rs1268767760 723 dbSNP
rs779066500 724 dbSNP
rs1365290201 725 dbSNP
rs1011154308 728 dbSNP
rs1436754226 736 dbSNP
rs1338198690 747 dbSNP
rs17135745 752 dbSNP
rs182688114 756 dbSNP
rs921988924 757 dbSNP
rs1338662721 765 dbSNP
rs1202809290 767 dbSNP
rs1160613908 768 dbSNP
rs932068022 769 dbSNP
rs999213825 771 dbSNP
rs367990056 780 dbSNP
rs1485846945 781 dbSNP
rs979953478 784 dbSNP
rs1006610304 789 dbSNP
rs1186752630 792 dbSNP
rs1464533357 798 dbSNP
rs1255646558 801 dbSNP
rs925300071 807 dbSNP
rs187140560 810 dbSNP
rs1052984067 811 dbSNP
rs891724332 813 dbSNP
rs111960608 814 dbSNP
rs1346678191 818 dbSNP
rs1294994637 820 dbSNP
rs1365318866 822 dbSNP
rs150407325 822 dbSNP
rs1321760568 824 dbSNP
rs950946101 825 dbSNP
rs1433512460 826 dbSNP
rs983431097 828 dbSNP
rs571912027 833 dbSNP
rs552218964 840 dbSNP
rs1027848983 841 dbSNP
rs887413936 848 dbSNP
rs1004515353 850 dbSNP
rs1399591900 855 dbSNP
rs1383481300 857 dbSNP
rs1015102518 861 dbSNP
rs565739180 866 dbSNP
rs976328603 867 dbSNP
rs528428688 871 dbSNP
rs537341501 873 dbSNP
rs1210517210 877 dbSNP
rs1029150013 895 dbSNP
rs1486555490 896 dbSNP
rs1043932634 904 dbSNP
rs902446090 905 dbSNP
rs11542302 907 dbSNP
rs11859311 909 dbSNP
rs1226180545 914 dbSNP
rs537273406 919 dbSNP
rs925362341 924 dbSNP
rs1284168484 925 dbSNP
rs890753769 929 dbSNP
rs1006556728 930 dbSNP
rs1306366059 931 dbSNP
rs535397549 933 dbSNP
rs898223937 934 dbSNP
rs916849770 937 dbSNP
rs1172616542 939 dbSNP
rs988152005 948 dbSNP
rs1412945165 950 dbSNP
rs1028209844 955 dbSNP
rs1207025541 975 dbSNP
rs1476040744 975 dbSNP
rs1262548632 978 dbSNP
rs1249352214 981 dbSNP
rs1203929631 984 dbSNP
rs913127877 992 dbSNP
rs1483173814 1011 dbSNP
rs950978243 1013 dbSNP
rs1464468428 1014 dbSNP
rs1187236486 1016 dbSNP
rs948278495 1017 dbSNP
rs1289733027 1024 dbSNP
rs1234476013 1027 dbSNP
rs949928277 1028 dbSNP
rs1046088162 1030 dbSNP
rs1409672474 1034 dbSNP
rs1351305989 1037 dbSNP
rs1300162107 1038 dbSNP
rs927138495 1043 dbSNP
rs557513682 1044 dbSNP
rs1409744355 1045 dbSNP
rs1181188773 1046 dbSNP
rs1048771635 1048 dbSNP
rs1252204064 1050 dbSNP
rs1375614269 1055 dbSNP
rs991215723 1056 dbSNP
rs146344112 1060 dbSNP
rs58000767 1060 dbSNP
rs201766530 1065 dbSNP
rs887542722 1071 dbSNP
rs1337577201 1078 dbSNP
rs570919437 1079 dbSNP
rs12924762 1080 dbSNP
rs558642302 1082 dbSNP
rs1309367181 1086 dbSNP
rs1385309967 1087 dbSNP
rs901547156 1087 dbSNP
rs1366924424 1089 dbSNP
rs572082575 1090 dbSNP
rs541020575 1101 dbSNP
rs1029698097 1102 dbSNP
rs554616847 1105 dbSNP
rs928106112 1106 dbSNP
rs953533156 1108 dbSNP
rs1001448390 1109 dbSNP
rs1173438431 1111 dbSNP
rs34284279 1111 dbSNP
rs1032397557 1112 dbSNP
rs539285000 1117 dbSNP
rs1439952347 1119 dbSNP
rs1051045846 1122 dbSNP
rs751749930 1124 dbSNP
rs762726229 1135 dbSNP
rs1320179627 1137 dbSNP
rs891038697 1142 dbSNP
rs1318457472 1146 dbSNP
rs988246623 1147 dbSNP
rs1262877624 1150 dbSNP
rs917909022 1152 dbSNP
rs970749415 1153 dbSNP
rs1304502441 1155 dbSNP
rs1039756692 1162 dbSNP
rs981376448 1165 dbSNP
rs927213219 1169 dbSNP
rs543288469 1171 dbSNP
rs1382715961 1172 dbSNP
rs1386796738 1174 dbSNP
rs1027828386 1175 dbSNP
rs1465393828 1176 dbSNP
rs563514338 1188 dbSNP
rs1395286610 1191 dbSNP
rs886649974 1204 dbSNP
rs1175150861 1206 dbSNP
rs1447084162 1211 dbSNP
rs370041352 1214 dbSNP
rs1035264486 1215 dbSNP
rs192980891 1216 dbSNP
rs1281245745 1217 dbSNP
rs909075309 1219 dbSNP
rs1191028638 1220 dbSNP
rs1213330443 1221 dbSNP
rs1265734058 1222 dbSNP
rs990855044 1224 dbSNP
rs1182083673 1226 dbSNP
rs1410689671 1229 dbSNP
rs763453834 1234 dbSNP
rs1228329770 1247 dbSNP
rs1036105667 1251 dbSNP
rs901514599 1255 dbSNP
rs1310546709 1257 dbSNP
rs968167182 1259 dbSNP
rs1375865217 1260 dbSNP
rs751083603 1267 dbSNP
rs762185905 1268 dbSNP
rs938487241 1269 dbSNP
rs545901614 1270 dbSNP
rs986616882 1272 dbSNP
rs768034389 1276 dbSNP
rs1375268900 1278 dbSNP
rs1375264186 1285 dbSNP
rs74333711 1286 dbSNP
rs1032491993 1294 dbSNP
rs111672367 1303 dbSNP
rs548154709 1308 dbSNP
rs1196430669 1317 dbSNP
rs1341588881 1323 dbSNP
rs930993737 1326 dbSNP
rs1243977611 1331 dbSNP
rs1047286888 1332 dbSNP
rs1025101124 1335 dbSNP
rs1295181218 1343 dbSNP
rs1407836310 1346 dbSNP
rs970685450 1357 dbSNP
rs11860243 1364 dbSNP
rs1034249224 1370 dbSNP
rs958854853 1371 dbSNP
rs984755715 1372 dbSNP
rs557516955 1383 dbSNP
rs1161907397 1384 dbSNP
rs531250292 1394 dbSNP
rs909042796 1395 dbSNP
rs940568578 1397 dbSNP
rs1481830276 1400 dbSNP
rs563543697 1405 dbSNP
rs756435800 1407 dbSNP
rs1471395294 1408 dbSNP
rs550962998 1411 dbSNP
rs932972077 1412 dbSNP
rs1335385541 1420 dbSNP
rs1050532374 1429 dbSNP
rs1275019722 1436 dbSNP
rs748558180 1438 dbSNP
rs1226325914 1443 dbSNP
rs367907676 1445 dbSNP
rs1328252032 1452 dbSNP
rs968493536 1454 dbSNP
rs1162616801 1456 dbSNP
rs766093278 1461 dbSNP
rs888810852 1463 dbSNP
rs1322294376 1464 dbSNP
rs1441093175 1474 dbSNP
rs936905252 1475 dbSNP
rs1395826740 1479 dbSNP
rs1356194476 1480 dbSNP
rs571030170 1483 dbSNP
rs1307145220 1489 dbSNP
rs1159305857 1492 dbSNP
rs892634252 1495 dbSNP
rs1376203817 1503 dbSNP
rs1193050159 1508 dbSNP
rs1009739225 1509 dbSNP
rs956756205 1510 dbSNP
rs986648458 1512 dbSNP
rs1208022784 1517 dbSNP
rs1408256272 1520 dbSNP
rs1025037451 1521 dbSNP
rs113173128 1522 dbSNP
rs539999840 1523 dbSNP
rs552344160 1526 dbSNP
rs1273928987 1527 dbSNP
rs557549168 1533 dbSNP
rs952777192 1543 dbSNP
rs1228679926 1544 dbSNP
rs931002479 1546 dbSNP
rs114584528 1548 dbSNP
rs1482257231 1549 dbSNP
rs1212587313 1554 dbSNP
rs1319383778 1555 dbSNP
rs1402845860 1556 dbSNP
rs1400310592 1558 dbSNP
rs1016138291 1564 dbSNP
rs1173273990 1566 dbSNP
rs11860328 1567 dbSNP
rs1186537131 1570 dbSNP
rs372580678 1572 dbSNP
rs971884285 1575 dbSNP
rs1482677713 1593 dbSNP
rs1440504954 1606 dbSNP
rs1056564160 1612 dbSNP
rs1211159003 1613 dbSNP
rs554534173 1617 dbSNP
rs1294749130 1618 dbSNP
rs1012413387 1622 dbSNP
rs1045761457 1625 dbSNP
rs1271333278 1631 dbSNP
rs1433268598 1631 dbSNP
rs1357819977 1632 dbSNP
rs1312432208 1635 dbSNP
rs1167830724 1636 dbSNP
rs574318592 1638 dbSNP
rs933046668 1642 dbSNP
rs1388120999 1643 dbSNP
rs985926290 1643 dbSNP
rs866207172 1644 dbSNP
rs1409497850 1645 dbSNP
rs372788926 1645 dbSNP
rs1471647621 1646 dbSNP
rs1256552330 1647 dbSNP
rs1188463703 1648 dbSNP
rs1315019727 1650 dbSNP
rs904090048 1651 dbSNP
rs1447473275 1653 dbSNP
rs910200851 1653 dbSNP
rs1301130813 1654 dbSNP
rs936387756 1657 dbSNP
rs1436509436 1660 dbSNP
rs1297432463 1661 dbSNP
rs1340499933 1665 dbSNP
rs1053999987 1667 dbSNP
rs1415857387 1670 dbSNP
rs1236939962 1671 dbSNP
rs1306460432 1674 dbSNP
rs1441513887 1675 dbSNP
rs1355187499 1680 dbSNP
rs1172369790 1682 dbSNP
rs892737568 1687 dbSNP
rs1311221118 1700 dbSNP
rs3177440 1709 dbSNP
rs945506644 1720 dbSNP
Experimental Support 1 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' gauucuGGUUCGGAGGAAGgga 5'
                |||  || |||||   
Target 5' ccccccCCA--CCGCCUUC--- 3'
2 - 18
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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000248114.6 | 3UTR | GCCCCCCCCACCGCCUUC
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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