pre-miRNA Information
pre-miRNA hsa-mir-520a   
Genomic Coordinates chr19: 53690881 - 53690965
Description Homo sapiens miR-520a stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-520a-5p
Sequence 15| CUCCAGAGGGAAGUACUUUCU |35
Evidence Experimental
Experiments Array-cloned
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1172516897 2 dbSNP
rs747333607 4 dbSNP
rs1186636488 5 dbSNP
rs1461358452 13 dbSNP
rs1238887108 14 dbSNP
rs1305652558 17 dbSNP
rs371672116 20 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CALCR   
Synonyms CRT, CT-R, CTR, CTR1
Description calcitonin receptor
Transcript NM_001164737   
Other Transcripts NM_001164738 , NM_001742   
Expression
Putative miRNA Targets on CALCR
3'UTR of CALCR
(miRNA target sites are highlighted)
>CALCR|NM_001164737|3'UTR
   1 ATGTGAAGCAAACACAGCATCGTGATCACTGAGCCATCATTTCCTGGGAGAAAGACCATGCATTTAAAGTATTCTCCATC
  81 CTCCCAGGAACCGAACATATCATTTGTGAAGAATTATTCAGTGAATTTGTCCATTGTAAATCTGAAGAAAGTTATTCTTG
 161 GTACTGTTGCTTTGGGAGACAGTCTAGGAATGGAGTCTCCCACTGCAACTTGTGAACTCCATCATTCATCCAGGACTGAG
 241 ATGCAAATGTCACAGTAATGCAAGCAAAGTATCAAAGAAAAACAATGAAATTGACCTAGTTCAGATACAGGGTGCTCCTT
 321 GTCAATACTGAGCCATTTATACCTTTGAAATATTAAAATCACTGTCAATATTTTTATTTTTAACTCTGGATTTTGAATTA
 401 GATTATTTCTGTATTTGGCTATGGATCTGATTTTTAATTTTTTTAAATTTCAGTCAATTCTGATGTTACTGAGATGTTTT
 481 ACCATCCTTACAATGTAAACCACATGAACTACGTGACCTCTGCAAGACAAAGCGGCTTTCTAATAGAGAGATTAGTAAAT
 561 ATGTGAAGAAAAAGACCTGCATTTGGCAGGAAGATGTATGCTTTGAATGCAAAAGAAATTTAGAGTCAATTTGCTGAAAA
 641 CATTACATGCTCAGCTTGGTTTTGGACAAGCCTGTCCATTGGGCAGGACCTAGCTGTTGTAAAGAATTGGTCTTAATGTT
 721 GAATGTATTTTGGTTGCTGATGTTTATAAACTGAGAGGTCACAAAGAATCTATCACTAAAAATTTTTACAAAACTGCCAA
 801 AAATATAATTCTTAGTGGAAGACAATACTCCCTTTAAAGAGAGTTTGCCACTCCCCTAAACTCCAGGATTTATAAAGCAA
 881 ATTACTCCAAGGTTTATAAAGCAGATTACCTCTTGCCCTTGGGTGCTATCTAGCAGTAAAAGATAAATTTGTTGAATATT
 961 GGTAATTAAAAGACTCCACATAAGTCCATTAACTGCTTTCCACCCAGCTTCAAAGCTTAAAAAGAGCTCAGGCTTTTCCA
1041 GGAAGATCCAGGAGGGCTAATTAGAAATCAACTTGTGGTTGACCGCTTGTTTCTTGTTATTACCAAAACAGGAGGGGAAA
1121 AAATTAACTGCTCCAAATTTAACCATAAATCAATTCATGTTTAACGTTTCTCATTAAAATCCAGTATTATATTATCATAT
1201 CTCTCTTTACTTCCCAGTATAAGATTTTTGAAAATCCTGAATAAACCAGTATCGTTACTGGCACCTGAAATTAATTTGTG
1281 AATTTGCAACAGTAATCAGAGTTACCATTATTTAATTTGTATGCTAAATGAGGAGGTACATTGAAACCCTCCAAATCTCC
1361 AGTCTCATCTATGTCATATTTTGCCACTGCCTTTCAGAAGTGATTTAGTTGTGGAAAGATAATAAATTGATTTGTTATGG
1441 TTACATATTTAGCGCACCCAGAGAAAATTAATTATATTTCTACAGAGAAAATGAATTTGGGATACTAAAGTAGTTTAAGT
1521 CTCCTTTACTGAATGTAAGGGGGGGATCGAAAAGAAGGTATTTTTCCAATCACAGTGTTATGTAGTATTGTTCTATTTTT
1601 GTTTACAAACATGGAAAACAGAGTATTTCTGGCAGCTGTGGTACAAATGTGATAATATATTGCTAAAATATTTTAGATGT
1681 TATTATGCTAATATAGTAGGGGTTGAAGAAAACAAAATAGCTTATTATAGAATTGCACATAGTTCTGCCCAAATTATGTG
1761 AAATGCTTATGCTTGTGTATATGTATAAATTAATACAGAGTACGTTAAAAGCAAAAAGATGTATATTTGCATATTTTTCT
1841 AAAGAAATATATTATTCATCTTTTCATTC
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' ucuuucAUGAAGG--GAGACCUc 5'
                ||:||::  ||||||| 
Target 5' tattttTATTTTTAACTCTGGAt 3'
369 - 391 153.00 -10.60
2
miRNA  3' ucuuUCAUGA-AGGGAGACCUc 5'
              :||||| |: ||:|||: 
Target 5' tcttGGTACTGTTGCTTTGGGa 3'
156 - 177 129.00 -14.10
3
miRNA  3' ucuuuCAUGAAGGGAGACCUc 5'
               |||:||  || |||| 
Target 5' tttctGTATTTGGCTATGGAt 3'
406 - 426 128.00 -7.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28486890 17 COSMIC
COSN20065192 22 COSMIC
COSN30489102 38 COSMIC
COSN30535929 47 COSMIC
COSN14309061 48 COSMIC
COSN30187085 54 COSMIC
COSN31960034 60 COSMIC
COSN30485318 83 COSMIC
COSN30184108 85 COSMIC
COSN30489287 88 COSMIC
COSN30544760 90 COSMIC
COSN28845589 92 COSMIC
COSN30455959 101 COSMIC
COSN31499211 101 COSMIC
COSN31605199 111 COSMIC
COSN30179859 121 COSMIC
COSN30179845 123 COSMIC
COSN26592085 152 COSMIC
COSN30114876 157 COSMIC
COSN16263213 180 COSMIC
COSN31542115 194 COSMIC
COSN8047257 268 COSMIC
COSN21628439 326 COSMIC
COSN31580211 332 COSMIC
COSN23581299 438 COSMIC
COSN28196165 576 COSMIC
COSN23462710 670 COSMIC
COSN31542704 766 COSMIC
COSN20104452 835 COSMIC
COSN17752025 862 COSMIC
COSN17566092 909 COSMIC
COSN8517855 927 COSMIC
COSN31578689 1082 COSMIC
COSN6899011 1171 COSMIC
COSN65357 1223 COSMIC
COSN26478508 1289 COSMIC
COSN31546746 1454 COSMIC
COSN22606698 1501 COSMIC
COSN31591318 1533 COSMIC
COSN28381981 1549 COSMIC
COSN26386813 1742 COSMIC
COSN28831951 1777 COSMIC
COSN15920490 1803 COSMIC
COSN31590011 1833 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1392175221 5 dbSNP
rs764966596 8 dbSNP
rs1430584915 13 dbSNP
rs761415794 14 dbSNP
rs772403080 15 dbSNP
rs755579776 17 dbSNP
rs1042138 18 dbSNP
rs1366777644 19 dbSNP
rs1273059926 20 dbSNP
rs939868880 21 dbSNP
rs768204242 22 dbSNP
rs1400481140 26 dbSNP
rs1330192416 28 dbSNP
rs1320944142 29 dbSNP
rs760165058 30 dbSNP
rs979722487 33 dbSNP
rs776130439 38 dbSNP
rs1433016595 39 dbSNP
rs772391380 46 dbSNP
rs35173673 49 dbSNP
rs746254897 50 dbSNP
rs879135864 59 dbSNP
rs539652103 60 dbSNP
rs981351624 62 dbSNP
rs542963660 71 dbSNP
rs574243154 74 dbSNP
rs1478270003 80 dbSNP
rs990806174 84 dbSNP
rs1198399041 85 dbSNP
rs565712734 92 dbSNP
rs922146922 94 dbSNP
rs1161494527 97 dbSNP
rs1318858906 98 dbSNP
rs1032423699 120 dbSNP
rs1308295689 129 dbSNP
rs1316926985 129 dbSNP
rs192934290 132 dbSNP
rs1228280842 134 dbSNP
rs1283006357 137 dbSNP
rs187946082 148 dbSNP
rs1229797356 157 dbSNP
rs965717435 161 dbSNP
rs1349251676 163 dbSNP
rs535082592 166 dbSNP
rs911644858 194 dbSNP
rs1452082943 199 dbSNP
rs1221512928 201 dbSNP
rs577849252 207 dbSNP
rs983209354 212 dbSNP
rs1479588655 220 dbSNP
rs200994039 221 dbSNP
rs1364597017 227 dbSNP
rs1375672674 229 dbSNP
rs1469743774 230 dbSNP
rs1156871222 251 dbSNP
rs769920327 259 dbSNP
rs1425803280 270 dbSNP
rs1027435567 272 dbSNP
rs567669831 276 dbSNP
rs1411281667 281 dbSNP
rs1329204398 283 dbSNP
rs79481528 286 dbSNP
rs1365066727 293 dbSNP
rs1022810943 301 dbSNP
rs1360104973 305 dbSNP
rs1008411217 310 dbSNP
rs1245089056 311 dbSNP
rs1289331575 313 dbSNP
rs1483952441 317 dbSNP
rs1205596095 323 dbSNP
rs118137861 324 dbSNP
rs1437432358 330 dbSNP
rs1423190376 334 dbSNP
rs1370218073 335 dbSNP
rs1445779070 342 dbSNP
rs565883602 362 dbSNP
rs1415311842 364 dbSNP
rs572644811 366 dbSNP
rs896470947 373 dbSNP
rs1168826153 380 dbSNP
rs1189797444 383 dbSNP
rs572374201 392 dbSNP
rs996462671 395 dbSNP
rs1335643271 410 dbSNP
rs898196070 413 dbSNP
rs1382802867 415 dbSNP
rs1056972389 424 dbSNP
rs1312911519 437 dbSNP
rs1262710688 440 dbSNP
rs1203649332 444 dbSNP
rs1486865016 445 dbSNP
rs999615565 445 dbSNP
rs1261408071 455 dbSNP
rs1194238359 456 dbSNP
rs1221400285 456 dbSNP
rs1320446931 468 dbSNP
rs1461880753 469 dbSNP
rs755471340 469 dbSNP
rs1241880732 471 dbSNP
rs1451844165 473 dbSNP
rs1234269430 474 dbSNP
rs1004381977 475 dbSNP
rs886920758 480 dbSNP
rs1045954383 481 dbSNP
rs116793474 484 dbSNP
rs371827319 485 dbSNP
rs922197772 489 dbSNP
rs1039259791 492 dbSNP
rs1367308419 494 dbSNP
rs1055759757 496 dbSNP
rs1294600231 500 dbSNP
rs937954222 505 dbSNP
rs1288948984 510 dbSNP
rs183776020 513 dbSNP
rs1203151692 528 dbSNP
rs1261288787 532 dbSNP
rs979513236 533 dbSNP
rs983639334 534 dbSNP
rs745399014 548 dbSNP
rs1475392982 549 dbSNP
rs756643751 552 dbSNP
rs531248041 576 dbSNP
rs967216176 578 dbSNP
rs914013165 581 dbSNP
rs920305528 582 dbSNP
rs190573032 586 dbSNP
rs969833540 596 dbSNP
rs1173662251 598 dbSNP
rs955574221 601 dbSNP
rs1191237237 612 dbSNP
rs1454250057 615 dbSNP
rs1028531246 617 dbSNP
rs1262433481 622 dbSNP
rs955539761 623 dbSNP
rs1382673719 625 dbSNP
rs997059379 645 dbSNP
rs1388346975 655 dbSNP
rs955220182 659 dbSNP
rs962375849 664 dbSNP
rs1283645520 665 dbSNP
rs1029492840 667 dbSNP
rs1467242886 669 dbSNP
rs1346416258 671 dbSNP
rs554095657 680 dbSNP
rs1223076361 685 dbSNP
rs1281466690 694 dbSNP
rs1275564172 704 dbSNP
rs1017028074 707 dbSNP
rs1014152074 708 dbSNP
rs1260707083 713 dbSNP
rs1003904060 723 dbSNP
rs376116605 727 dbSNP
rs571444690 728 dbSNP
rs1035021526 731 dbSNP
rs1045540957 732 dbSNP
rs1196752193 736 dbSNP
rs3802054 747 dbSNP
rs1327829985 748 dbSNP
rs902604921 755 dbSNP
rs746916253 768 dbSNP
rs1303555682 775 dbSNP
rs1011092536 781 dbSNP
rs199868950 789 dbSNP
rs1055685361 790 dbSNP
rs141735026 800 dbSNP
rs1301589932 805 dbSNP
rs777578009 806 dbSNP
rs766426506 814 dbSNP
rs935931009 815 dbSNP
rs80348774 822 dbSNP
rs1327788822 832 dbSNP
rs1248731785 833 dbSNP
rs1292965581 841 dbSNP
rs201545010 841 dbSNP
rs3839835 841 dbSNP
rs1399205813 844 dbSNP
rs1220699885 851 dbSNP
rs1234300345 852 dbSNP
rs866583211 854 dbSNP
rs1165946693 855 dbSNP
rs1176152410 856 dbSNP
rs1463394704 858 dbSNP
rs1446379937 859 dbSNP
rs1373846486 866 dbSNP
rs925285174 877 dbSNP
rs1175682418 882 dbSNP
rs116023686 888 dbSNP
rs945425716 892 dbSNP
rs529588294 894 dbSNP
rs1170217045 899 dbSNP
rs563993815 905 dbSNP
rs1443145581 907 dbSNP
rs1194743734 910 dbSNP
rs1457713946 916 dbSNP
rs1371189327 917 dbSNP
rs1454642551 918 dbSNP
rs1316424260 924 dbSNP
rs1249116016 925 dbSNP
rs1359319733 933 dbSNP
rs912095391 938 dbSNP
rs986887717 941 dbSNP
rs1307736383 944 dbSNP
rs1197907768 946 dbSNP
rs955501852 947 dbSNP
rs1340555192 952 dbSNP
rs374089771 953 dbSNP
rs921442333 956 dbSNP
rs1251491205 958 dbSNP
rs1462313515 959 dbSNP
rs1047393562 967 dbSNP
rs755614530 969 dbSNP
rs963269298 971 dbSNP
rs1017212804 972 dbSNP
rs1345058715 974 dbSNP
rs1305011269 980 dbSNP
rs1441467976 995 dbSNP
rs1188071913 996 dbSNP
rs1419896344 997 dbSNP
rs920356364 1001 dbSNP
rs1170091251 1006 dbSNP
rs1398361117 1009 dbSNP
rs973111293 1012 dbSNP
rs533621884 1015 dbSNP
rs1337432151 1019 dbSNP
rs1382733818 1020 dbSNP
rs1451031190 1021 dbSNP
rs1272300003 1024 dbSNP
rs1363180712 1031 dbSNP
rs1214340764 1042 dbSNP
rs948578446 1043 dbSNP
rs144859264 1048 dbSNP
rs1325210449 1059 dbSNP
rs1326840097 1067 dbSNP
rs1392896914 1071 dbSNP
rs1396986764 1074 dbSNP
rs569809869 1084 dbSNP
rs78344515 1085 dbSNP
rs1396893823 1089 dbSNP
rs1242625823 1092 dbSNP
rs959994302 1100 dbSNP
rs1031969986 1101 dbSNP
rs1177269018 1103 dbSNP
rs1421809663 1103 dbSNP
rs1481516628 1103 dbSNP
rs1405364528 1105 dbSNP
rs1024021450 1109 dbSNP
rs1439223148 1122 dbSNP
rs1320922985 1123 dbSNP
rs978105690 1127 dbSNP
rs760436912 1128 dbSNP
rs1268752443 1131 dbSNP
rs1022418154 1135 dbSNP
rs1010978153 1136 dbSNP
rs1282097766 1138 dbSNP
rs900701405 1141 dbSNP
rs1224951628 1144 dbSNP
rs1014020127 1146 dbSNP
rs1284930527 1152 dbSNP
rs1209639964 1155 dbSNP
rs1250402615 1156 dbSNP
rs1213419322 1157 dbSNP
rs1017778829 1165 dbSNP
rs1282102816 1166 dbSNP
rs1200319548 1170 dbSNP
rs767436406 1172 dbSNP
rs1477111027 1173 dbSNP
rs1409397896 1182 dbSNP
rs557738610 1186 dbSNP
rs894285559 1189 dbSNP
rs151013460 1190 dbSNP
rs1296751335 1196 dbSNP
rs1000057391 1199 dbSNP
rs1405931243 1200 dbSNP
rs1302209561 1210 dbSNP
rs904424809 1211 dbSNP
rs1443792493 1213 dbSNP
rs572070817 1214 dbSNP
rs1349894599 1217 dbSNP
rs898814852 1220 dbSNP
rs1241126952 1225 dbSNP
rs1336066557 1228 dbSNP
rs945368879 1235 dbSNP
rs1359969533 1241 dbSNP
rs1268501794 1246 dbSNP
rs555292647 1247 dbSNP
rs1184110347 1249 dbSNP
rs1051096454 1251 dbSNP
rs751335333 1253 dbSNP
rs535614384 1254 dbSNP
rs934093953 1256 dbSNP
rs1163302308 1261 dbSNP
rs143632843 1276 dbSNP
rs1382916592 1293 dbSNP
rs556410986 1300 dbSNP
rs1334587789 1305 dbSNP
rs975536815 1311 dbSNP
rs941569988 1312 dbSNP
rs868809676 1314 dbSNP
rs910122153 1326 dbSNP
rs1383403155 1330 dbSNP
rs114304795 1336 dbSNP
rs763147921 1339 dbSNP
rs148941896 1348 dbSNP
rs1197707559 1349 dbSNP
rs992555773 1354 dbSNP
rs958426856 1355 dbSNP
rs1476425850 1370 dbSNP
rs1273972232 1372 dbSNP
rs1034130237 1373 dbSNP
rs1437377929 1373 dbSNP
rs1183389069 1375 dbSNP
rs767350988 1375 dbSNP
rs1000429814 1384 dbSNP
rs1367021415 1387 dbSNP
rs989445990 1396 dbSNP
rs1259152314 1402 dbSNP
rs551330282 1405 dbSNP
rs534815608 1408 dbSNP
rs964825899 1416 dbSNP
rs1211207213 1419 dbSNP
rs1463645140 1420 dbSNP
rs566145927 1427 dbSNP
rs1338085832 1440 dbSNP
rs1018081969 1453 dbSNP
rs529481491 1454 dbSNP
rs773366692 1468 dbSNP
rs1010164826 1469 dbSNP
rs892439708 1473 dbSNP
rs1271043409 1475 dbSNP
rs1351302446 1475 dbSNP
rs1026545733 1477 dbSNP
rs1196862849 1480 dbSNP
rs559681572 1482 dbSNP
rs1462163569 1484 dbSNP
rs934020351 1493 dbSNP
rs1254674636 1495 dbSNP
rs1194312209 1499 dbSNP
rs1430722348 1499 dbSNP
rs774162832 1510 dbSNP
rs1012958933 1514 dbSNP
rs1343453483 1521 dbSNP
rs1320378124 1523 dbSNP
rs563875008 1530 dbSNP
rs550498923 1533 dbSNP
rs1163466062 1534 dbSNP
rs1387022223 1539 dbSNP
rs1382609620 1540 dbSNP
rs1463316815 1541 dbSNP
rs1039829266 1545 dbSNP
rs752931001 1546 dbSNP
rs894245468 1546 dbSNP
rs1188150877 1547 dbSNP
rs1324438961 1547 dbSNP
rs941485460 1548 dbSNP
rs765502553 1549 dbSNP
rs1487115244 1555 dbSNP
rs1206117619 1557 dbSNP
rs910058812 1566 dbSNP
rs1041696092 1570 dbSNP
rs767942866 1573 dbSNP
rs1201219127 1577 dbSNP
rs1429539158 1580 dbSNP
rs1194676395 1581 dbSNP
rs947293302 1588 dbSNP
rs1272437036 1591 dbSNP
rs145757804 1594 dbSNP
rs1336609819 1596 dbSNP
rs1157794719 1611 dbSNP
rs1273599635 1620 dbSNP
rs1358313278 1621 dbSNP
rs755278074 1624 dbSNP
rs983409381 1644 dbSNP
rs1360132767 1651 dbSNP
rs1386316787 1654 dbSNP
rs1299226674 1668 dbSNP
rs1319270340 1669 dbSNP
rs930230651 1673 dbSNP
rs917529109 1677 dbSNP
rs1343788395 1678 dbSNP
rs1352039566 1682 dbSNP
rs536774504 1682 dbSNP
rs1272208904 1686 dbSNP
rs748771882 1687 dbSNP
rs1487930345 1688 dbSNP
rs1188973772 1691 dbSNP
rs992482176 1692 dbSNP
rs989500185 1695 dbSNP
rs1370395410 1696 dbSNP
rs1324423130 1702 dbSNP
rs1443766983 1719 dbSNP
rs144758332 1721 dbSNP
rs796531582 1724 dbSNP
rs1034100787 1726 dbSNP
rs1366454762 1727 dbSNP
rs978540209 1729 dbSNP
rs1457546212 1735 dbSNP
rs968924322 1740 dbSNP
rs1375709167 1743 dbSNP
rs1042139 1745 dbSNP
rs987939841 1748 dbSNP
rs1020130902 1750 dbSNP
rs1010507598 1755 dbSNP
rs373937172 1757 dbSNP
rs1248669869 1765 dbSNP
rs954613410 1766 dbSNP
rs1320756832 1767 dbSNP
rs753981318 1770 dbSNP
rs1169324205 1774 dbSNP
rs540998375 1775 dbSNP
rs1251854599 1776 dbSNP
rs993594238 1782 dbSNP
rs183459170 1795 dbSNP
rs1480704655 1799 dbSNP
rs998137068 1801 dbSNP
rs115692520 1803 dbSNP
rs75343103 1804 dbSNP
rs894119943 1810 dbSNP
rs1412718382 1813 dbSNP
rs1421830683 1820 dbSNP
rs1005647030 1821 dbSNP
rs1163025263 1829 dbSNP
rs1356477034 1840 dbSNP
rs1203544281 1848 dbSNP
rs62466836 1849 dbSNP
rs1275344473 1850 dbSNP
rs1047210282 1851 dbSNP
rs1454992754 1853 dbSNP
rs1003033731 1856 dbSNP
rs571139496 1859 dbSNP
rs555901673 1860 dbSNP
rs866200402 1865 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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' ucuuucaugaaggGAGACCUc 5'
                       ||||||| 
Target 5' -----------aaCUCUGGAu 3'
1 - 10
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 SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ucuuucaugaaggGAGACCUc 5'
                       ||||||| 
Target 5' ------------aCUCUGGAu 3'
1 - 9
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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000359558.2 | 3UTR | AACUCUGGAUUUUGAA
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 0.471 1.0e-2 0.509 5.5e-3 24 Click to see details
GSE17498 Multiple myeloma 0.289 3.5e-2 0.134 2.0e-1 40 Click to see details
GSE26953 Aortic valvular endothelial cells -0.336 5.4e-2 -0.347 4.8e-2 24 Click to see details
GSE28260 Renal cortex and medulla -0.414 8.0e-2 -0.374 1.0e-1 13 Click to see details
GSE21687 Ependynoma primary tumors -0.151 1.2e-1 -0.192 6.4e-2 64 Click to see details
GSE32688 Pancreatic cancer 0.203 1.3e-1 0.146 2.1e-1 32 Click to see details
GSE14794 Lymphoblastoid cells 0.08 2.3e-1 -0.009 4.7e-1 90 Click to see details
GSE38226 Liver fibrosis 0.169 2.3e-1 -0.094 3.4e-1 21 Click to see details
GSE42095 Differentiated embryonic stem cells 0.154 2.4e-1 0.227 1.5e-1 23 Click to see details
GSE17306 Multiple myeloma 0.074 3.1e-1 0.442 7.4e-4 49 Click to see details
GSE27834 Pluripotent stem cells 0.124 3.2e-1 0.124 3.2e-1 16 Click to see details
GSE19350 CNS germ cell tumors 0.116 3.6e-1 0.084 4.0e-1 12 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.039 4.4e-1 -0.083 3.6e-1 20 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.018 4.7e-1 0.079 3.5e-1 25 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.018 4.7e-1 0.079 3.5e-1 25 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.018 4.7e-1 0.079 3.5e-1 25 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.018 4.7e-1 0.079 3.5e-1 25 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
PRAD 0.906 0.05 1.000 0.5 4 Click to see details
BRCA -0.55 0.05 -0.697 0.01 10 Click to see details
BLCA 0.621 0.19 0.600 0.2 4 Click to see details
LUSC 0.289 0.36 0.200 0.4 4 Click to see details
HNSC 0.099 0.41 0.190 0.33 8 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
LIHC 0.142 0.41 -0.100 0.44 5 Click to see details
115 hsa-miR-520a-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT092732 SETD5 SET domain containing 5 2 4
MIRT168595 HMGA1 high mobility group AT-hook 1 2 4
MIRT232084 CCSAP centriole, cilia and spindle associated protein 2 2
MIRT252430 MIDN midnolin 2 4
MIRT294600 ZNF460 zinc finger protein 460 2 2
MIRT343114 IGF1R insulin like growth factor 1 receptor 2 2
MIRT441904 SEPN1 selenoprotein N 2 2
MIRT443233 ALG8 ALG8, alpha-1,3-glucosyltransferase 2 2
MIRT446250 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT448001 GPR63 G protein-coupled receptor 63 2 2
MIRT451560 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT455285 BCL2L1 BCL2 like 1 2 2
MIRT456170 ZDHHC6 zinc finger DHHC-type containing 6 2 2
MIRT456679 LDB1 LIM domain binding 1 2 2
MIRT458206 FOXL2 forkhead box L2 2 2
MIRT461267 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT461683 ZNF426 zinc finger protein 426 2 2
MIRT462656 HMOX1 heme oxygenase 1 2 4
MIRT464368 URM1 ubiquitin related modifier 1 2 2
MIRT468138 SH3BP4 SH3 domain binding protein 4 2 2
MIRT468234 SGK1 serum/glucocorticoid regulated kinase 1 2 2
MIRT470357 PPP2R5E protein phosphatase 2 regulatory subunit B'epsilon 2 2
MIRT472039 NPAT nuclear protein, coactivator of histone transcription 2 2
MIRT475941 GXYLT1 glucoside xylosyltransferase 1 2 2
MIRT477880 DYNLL2 dynein light chain LC8-type 2 2 2
MIRT480419 C17orf85 nuclear cap binding subunit 3 2 2
MIRT482642 RPL18A ribosomal protein L18a 2 2
MIRT485666 CDC25B cell division cycle 25B 2 2
MIRT485740 CALCR calcitonin receptor 2 2
MIRT488906 TSTD2 thiosulfate sulfurtransferase like domain containing 2 2 6
MIRT490412 NRXN3 neurexin 3 2 2
MIRT494726 ARHGAP1 Rho GTPase activating protein 1 2 6
MIRT495957 TBC1D19 TBC1 domain family member 19 2 2
MIRT498087 SEMA7A semaphorin 7A (John Milton Hagen blood group) 2 2
MIRT507449 EIF6 eukaryotic translation initiation factor 6 2 2
MIRT522992 INPP4A inositol polyphosphate-4-phosphatase type I A 2 4
MIRT526008 RBM4B RNA binding motif protein 4B 2 2
MIRT527693 IL17REL interleukin 17 receptor E like 2 2
MIRT528202 NELFE negative elongation factor complex member E 2 2
MIRT529123 HOMEZ homeobox and leucine zipper encoding 2 2
MIRT529484 TPD52L3 tumor protein D52 like 3 2 2
MIRT530760 ZNF582 zinc finger protein 582 2 2
MIRT531930 IL12RB2 interleukin 12 receptor subunit beta 2 2 2
MIRT532347 PLEK pleckstrin 2 2
MIRT532819 ZNF827 zinc finger protein 827 2 2
MIRT533262 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT533518 TRIM13 tripartite motif containing 13 2 2
MIRT534279 SLC12A7 solute carrier family 12 member 7 2 2
MIRT534483 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT538555 CELF1 CUGBP Elav-like family member 1 2 4
MIRT538801 C2CD5 C2 calcium dependent domain containing 5 2 2
MIRT553759 TAOK1 TAO kinase 1 2 2
MIRT556035 MXD1 MAX dimerization protein 1 2 2
MIRT557541 GOSR1 golgi SNAP receptor complex member 1 2 2
MIRT562451 CSDE1 cold shock domain containing E1 2 2
MIRT563686 RPS26 ribosomal protein S26 2 2
MIRT568249 BTF3L4 basic transcription factor 3 like 4 2 2
MIRT568422 ATF7IP activating transcription factor 7 interacting protein 2 2
MIRT574053 PROSC pyridoxal phosphate binding protein 2 2
MIRT606825 APBB2 amyloid beta precursor protein binding family B member 2 2 2
MIRT609585 GPM6B glycoprotein M6B 2 2
MIRT609680 TMEM213 transmembrane protein 213 2 2
MIRT611223 ZNF274 zinc finger protein 274 2 2
MIRT612585 SYNGAP1 synaptic Ras GTPase activating protein 1 2 4
MIRT613585 MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 2 2
MIRT614396 C11orf45 chromosome 11 open reading frame 45 2 2
MIRT615562 JPH2 junctophilin 2 2 2
MIRT615852 RASGRP1 RAS guanyl releasing protein 1 2 2
MIRT615934 MAP1LC3B microtubule associated protein 1 light chain 3 beta 2 2
MIRT617635 RXRA retinoid X receptor alpha 2 2
MIRT618058 PCDH19 protocadherin 19 2 2
MIRT618747 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT623739 GRIN2B glutamate ionotropic receptor NMDA type subunit 2B 2 2
MIRT629609 NOL10 nucleolar protein 10 2 2
MIRT635219 CD59 CD59 molecule (CD59 blood group) 2 2
MIRT638035 SHPK sedoheptulokinase 2 2
MIRT638545 KIAA1549 KIAA1549 2 2
MIRT645853 AFF2 AF4/FMR2 family member 2 2 2
MIRT646023 S100A7A S100 calcium binding protein A7A 2 2
MIRT646562 ALDH5A1 aldehyde dehydrogenase 5 family member A1 2 2
MIRT646735 FADS1 fatty acid desaturase 1 2 2
MIRT652853 TACC1 transforming acidic coiled-coil containing protein 1 2 2
MIRT654754 PRKCB protein kinase C beta 2 2
MIRT655238 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT655627 ONECUT1 one cut homeobox 1 2 2
MIRT655892 NEK9 NIMA related kinase 9 2 2
MIRT656184 MON1B MON1 homolog B, secretory trafficking associated 2 2
MIRT656551 LZIC leucine zipper and CTNNBIP1 domain containing 2 2
MIRT657743 GNG12 G protein subunit gamma 12 2 2
MIRT659981 C2CD2L C2CD2 like 2 2
MIRT660824 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT663511 AGMO alkylglycerol monooxygenase 2 2
MIRT666613 REEP2 receptor accessory protein 2 2 2
MIRT668266 FOXO3 forkhead box O3 2 2
MIRT669395 BACE2 beta-site APP-cleaving enzyme 2 2 2
MIRT669512 ARHGAP26 Rho GTPase activating protein 26 2 2
MIRT678895 TTLL12 tubulin tyrosine ligase like 12 2 2
MIRT685122 ADAT1 adenosine deaminase, tRNA specific 1 2 2
MIRT685674 PSMB7 proteasome subunit beta 7 2 2
MIRT690647 RPF2 ribosome production factor 2 homolog 2 2
MIRT697114 OTUD5 OTU deubiquitinase 5 2 2
MIRT697742 USP5 ubiquitin specific peptidase 5 2 2
MIRT698584 TEX261 testis expressed 261 2 2
MIRT700075 RNF38 ring finger protein 38 2 2
MIRT709340 ZNF35 zinc finger protein 35 2 2
MIRT711071 NLGN2 neuroligin 2 2 2
MIRT714634 TM4SF18 transmembrane 4 L six family member 18 2 2
MIRT715421 SPOPL speckle type BTB/POZ protein like 2 2
MIRT718663 HNF4A hepatocyte nuclear factor 4 alpha 2 2
MIRT718931 TRIM66 tripartite motif containing 66 2 2
MIRT720640 ELF5 E74 like ETS transcription factor 5 2 2
MIRT720788 PRKRIP1 PRKR interacting protein 1 2 2
MIRT721289 TRABD2A TraB domain containing 2A 2 2
MIRT722893 LRRC20 leucine rich repeat containing 20 2 2
MIRT724307 KCNH1 potassium voltage-gated channel subfamily H member 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-520a-5p Imatinib 5291 NSC743414 approved sensitive High Gastrointestinal Stromal Tumor cell line (882R-NC, 882R-OE, 882R-KD)
hsa-miR-520a-5p Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (A375)
hsa-miR-520a-5p Vemurafenib 42611257 NSC761431 approved resistant cell line (451Lu)
hsa-miR-520a-5p Paclitaxel 36314 NSC125973 approved resistant cell line (HS578T)
hsa-miR-520a-5p Doxorubicin 31703 NSC123127 approved sensitive cell line (HS578T)
hsa-miR-520a-5p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-520a-5p Sunitinib 5329102 NSC750690 approved resistant tissue (CardA)
hsa-miR-520a-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-520a-5p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide sensitive cell line (Bads-200)

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