miRTarBase - #MIRT462877


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pre-miRNA Information
pre-miRNA hsa-mir-506   
Genomic Coordinates chrX: 147230720 - 147230843
Synonyms MIRN506, hsa-mir-506, MIR506
Description Homo sapiens miR-506 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-506-5p
Sequence 35| UAUUCAGGAAGGUGUUACUUAA |56
Evidence Not_experimental
Experiments
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs782463365 2 dbSNP
rs781802841 18 dbSNP
rs782722056 21 dbSNP
rs782039395 22 dbSNP
Putative Targets

Gene Information
Gene Symbol ZXDB   
Synonyms ZNF905, dJ83L6.1
Description zinc finger, X-linked, duplicated B
Transcript NM_007157   
Expression
Putative miRNA Targets on ZXDB
3'UTR of ZXDB
(miRNA target sites are highlighted)		 
>ZXDB|NM_007157|3'UTR
   1 ACCAACTCTATTCATTCCTCATCATGTGGCTTACTTTTATTACAGTCAATTTTGAGGATATTCTGGACTAAATATTTAAG
  81 TGCAGTCATTTCTTTTTGGTTTGCAAAAAGAGCACAGCCCTGGACTACAAGTTTGGAGATTTAAATTCTGATCTTGAGTT
 161 TGGAACTGACAAGTTGTGTGACCCTGAGCAAGTCAGTTAACCTATCTGAGCCTTAATTTCCTTATTTATAAATTGAGGTG
 241 GTTTGAATAGATTGCTTTTAAGGTCTTTCTGCTCTGTGATTCCTTGATAATACATTTCTTTCCTTGAAAAATATGAGGAC
 321 GTTTTTCAGTGATGTGGCATGCGTTTTTTTTTAACTGCCCCCCCAGCCCTGACATGTTCTTTTTTTGGCAAACATACATA
 401 ATGTTACATCATACTATGATGAACATCCATGTACTTTTCACTCAATTTCAGCAATTATGAATCCATGAACAATCTTTTTT
 481 AACTTAGCCTCACTCACTCCCCATGTTCTAGTATTATTTTGTAACAAATAGCAGACATCTGATCATTTTATCCATAAATA
 561 TTCTTTATATATCTCTGAAAGCTATGGGATGATATGGAAAAAAATGATAATTCCATTATCGCAAGTGATATTTACAGTAA
 641 TTCTTTAATATCAGTAAATATCCAGTGAGGGTTCAAACTTCCAATTGCCTCATAAATGCTACTTGTTTTATTATTTTTAA
 721 TTAGTAGAATCCCGTAAATCTCCTAAGTGTCTTCTTAATCCGTATGTTTCCCTTTCATCTTTCTTTTTTTCCTTGCGATT
 801 TTGTTTATGAAATGAGGTTGTTTCACATGTAGCATTTGCCACAATTTAAGTTTTGCTAATTGCATCCCTATGGTAATGTT
 881 TGCTTTCCTCTATCCTCTGTTTCTTTAATTTGCTAGTTATGTCTAGAGACTTGATGAGATTGAAACATGGCTTTTGGCAT
 961 GAATGTTTCATAGGTTATGTTGTGTTCATTTAGTAGGTGGCGCATAATCTGTGGTTTTCTCTCTTTTTGTGGTATTAGCA
1041 GCTGCTGCAGATAAATGCATTAATTCATGATGCTTCTGATATGATGAGTCATCTTTGTAGAGTTACTAAGCATTAGCAAA
1121 GGAGGAAATGCTATGTAATAGAAATATTATTCAATGCCAAAATATTTTCTTAAATAGTCATAGAACTAACAAGAAAAAAT
1201 AGATAGCAAAAAAATGTGTTGGCTGTTCTCACTGTTTATCTTCCTAACTTCTTTTGATGATGGAAGGCAGTTTTGTGGAA
1281 ATTGCCAGCCAGGACTTTGACATGAAACAGACCCAGGGCTAAATTTTGGCTCTGTGGTGTTGGATAAGTGGCCTTGAATA
1361 AATTAGTTATTAAGCTTCAGTTTTCTAGCTTTTAACTGATTATAACAATGCACACACATACCTGACACACTGTTAAATTT
1441 TCTTCTCTTCCTGTTTCTTATGTTAAGGAAAGATACTCTGTGTTTTGGCATATGTTGGTGAATTTGTACCATTTTTATCC
1521 TCTCAGTCCTTCCTTTTATAAGACAATAATTGGAGTAGTTTAATCTTATTCATGTGCAGATAAAAGAGGTTTATGAAGTT
1601 TAGGGTGAAGTAGGCAAGGGAATCTGTTTACTCCCTCTTCCCTCTACTGAATAATTTTCCCTCTACTGAATAATTTTCCC
1681 TCTAAGAATTGCTGTGGGTAATACCAGGAGTGGGGACATTGCCCACATGCATAAGAGCGTATCTCTCCATTCGATCAGTT
1761 TGTCACCATCTTTGCTCTGTTTTGAAAGTCAGGCTTCTCTGTGACTGTGAAGCCTGCTGTTCCCTGAAAATCTGATAATG
1841 GAGCAGTGGAGGTTTTTTTCTTTCTGTGCTCTGTAGATCTCATTGTTTGCACTTGTAATTTCCCAGAGTTGAAAGGAAAG
1921 ATTGAACTGGAATATTGTGTAAACTATCTGTCTTACATTAGTGTAGCATTTTGCAATTTGGGGAACATCTTCACAATTTG
2001 TGTCTCGTTGTTCAGAACAACCCTGTGAAGTAGTTTTGGCAATGTCTGTGTTACATTTCATGTAATTTAGCCAACTCCCA
2081 TTCCAACTAGGCTTTGGCTAAATCTGACAATTTTATATATAGCTTAAAACAAAGAATATACATTCTTTTCACCCCTCCCA
2161 GTCTACCCATCCAGCCTTCATGATTCATTCCTGTGTCAAGGTTAGTCGCTGTTTTCCATTTGAATTGGTTTCTTTTATGG
2241 TCAGTTTACTTTCTTCCCTCTCCCCTCCCTTTCCTGCACATCCCCATCCTTGCTATGCCTTTCTGTCCTCTTTTATAATG
2321 GATATATCTTTTTCCTGCCATTATCCCTCAGACATTCTCCTCATGGCACATTTTCTTCAAATGCTAACATTTACTGAGTG
2401 TACATTGAAGTTCTGTGCATACAGGAAGAAGTTATTTTCTGAGCTTAGATAATACTATGTGTATATGTGATTAAAATGAA
2481 GATTATTTTCTAAAGCCTTCAAATTAGAAGTGGATTTCTGTTTCATTACTTCCGTTTTAAAAGTTTTTGCCAGAGAGTTT
2561 TGCTAAATACTCTCTTATTTGCTCTAGTGTACTAGTCCAGTAGTGTTTGCATGTGGATGTCTGTGGATGACAGTTATTGT
2641 AGCACTTTGGCAGTGCACTAAAATTTTGCCACTATGAAATGTTTCTTTATTGTGTGTGCGTGTGTGTTTTGAAATACGCA
2721 CACAGCCACACCCACATATATATTAAAAGTGGTTGTATTCATTTAGTGAAAAACAAAAAGTAGATGTACTTCTGTAAATC
2801 AGATAAATGCTTGGAATTTGATTGTCTACCCAATCAACAGTTTTCCCTCTTTGCTCTGGAAATATTTGTACTCATATAGC
2881 ATATTTCAAAAATGTTGTCATTCATTAAGGCCTCTTAAATAGACCACTATTTTTTGTGTCTGGCAGATGAGTATGTCAAG
2961 GATTGAGATGAACACATAAGTCTTGGAAATTAAATAAATTTATAAACATAAAGATAAAAAAAAAAA
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' aaUUCAUUGUGGAAGGACUUAu 5'
            ||||::|     |:||||| 
Target 5' atAAGTGGC-----CTTGAATa 3'
 1344 - 1360 135.00 -11.50
2 
miRNA  3' aauuCAUUGUGG-----AA-GGACUUau 5'
              ||:| :||     || ||||||  
Target 5' gactGTGAAGCCTGCTGTTCCCTGAAaa 3'
 1803 - 1830 130.00 -10.10
3 
miRNA  3' aaUUCAUUG--UGGA--AGGACUUAu 5'
            |: ||||  |:||   ||| ||| 
Target 5' tcAGTTAACCTATCTGAGCCTTAATt 3'
 193 - 218 124.00 -12.23
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs751957582 3 dbSNP
rs757762385 11 dbSNP
rs1311322899 14 dbSNP
rs1160028014 17 dbSNP
rs1230697285 20 dbSNP
rs1052064394 21 dbSNP
rs910526093 22 dbSNP
rs1257387787 23 dbSNP
rs943413729 23 dbSNP
rs1401997299 26 dbSNP
rs781701402 27 dbSNP
rs746406996 33 dbSNP
rs747697294 43 dbSNP
rs1248937194 48 dbSNP
rs768160145 49 dbSNP
rs904634825 59 dbSNP
rs1193115396 67 dbSNP
rs748927699 118 dbSNP
rs1206046237 130 dbSNP
rs1464742868 131 dbSNP
rs769129481 132 dbSNP
rs1266445393 140 dbSNP
rs773259586 142 dbSNP
rs1052212475 151 dbSNP
rs1451888495 163 dbSNP
rs142398255 169 dbSNP
rs1283730291 174 dbSNP
rs1372927561 177 dbSNP
rs1460148544 187 dbSNP
rs1242719860 188 dbSNP
rs1294967456 197 dbSNP
rs1298713724 212 dbSNP
rs1391030342 215 dbSNP
rs1338563025 229 dbSNP
rs770890800 249 dbSNP
rs1382528242 257 dbSNP
rs1323312150 260 dbSNP
rs186249575 267 dbSNP
rs151282517 277 dbSNP
rs1435793687 291 dbSNP
rs1394565366 299 dbSNP
rs897834182 303 dbSNP
rs993678714 304 dbSNP
rs1013901000 315 dbSNP
rs374242556 317 dbSNP
rs1024919154 321 dbSNP
rs1471540316 330 dbSNP
rs770691087 333 dbSNP
rs1194578022 343 dbSNP
rs1246643493 344 dbSNP
rs1469030212 344 dbSNP
rs764446375 344 dbSNP
rs969430136 348 dbSNP
rs1208096267 354 dbSNP
rs1001885710 357 dbSNP
rs1229108027 358 dbSNP
rs753943865 358 dbSNP
rs1364191235 359 dbSNP
rs1295208502 361 dbSNP
rs1442854426 362 dbSNP
rs1331282523 364 dbSNP
rs1002399855 365 dbSNP
rs1267409722 366 dbSNP
rs1034502041 369 dbSNP
rs958454614 374 dbSNP
rs1388873391 377 dbSNP
rs1213079285 380 dbSNP
rs1251234937 385 dbSNP
rs762007319 388 dbSNP
rs1246297290 410 dbSNP
rs916878364 412 dbSNP
rs1439604738 424 dbSNP
rs967042659 446 dbSNP
rs765223906 451 dbSNP
rs1205774410 452 dbSNP
rs750976542 455 dbSNP
rs1236154414 470 dbSNP
rs925896831 499 dbSNP
rs1427161578 502 dbSNP
rs988116975 514 dbSNP
rs910819646 521 dbSNP
rs112956800 522 dbSNP
rs1050299545 526 dbSNP
rs1043041385 537 dbSNP
rs925989150 542 dbSNP
rs780489125 556 dbSNP
rs772067469 562 dbSNP
rs1176103617 564 dbSNP
rs1435706014 570 dbSNP
rs1424958812 581 dbSNP
rs1162152790 598 dbSNP
rs751950452 598 dbSNP
rs755268559 608 dbSNP
rs780836438 621 dbSNP
rs897824345 622 dbSNP
rs1249496582 626 dbSNP
rs993501397 628 dbSNP
rs1049284535 633 dbSNP
rs149989758 635 dbSNP
rs191053104 640 dbSNP
rs892280839 655 dbSNP
rs1217276393 660 dbSNP
rs1013431701 665 dbSNP
rs1033830838 670 dbSNP
rs1288624292 677 dbSNP
rs961161959 683 dbSNP
rs1013979218 699 dbSNP
rs1227192549 703 dbSNP
rs1397523616 704 dbSNP
rs1046719636 726 dbSNP
rs146537964 734 dbSNP
rs749298969 735 dbSNP
rs1449493944 736 dbSNP
rs761920988 746 dbSNP
rs1358936180 750 dbSNP
rs1332544970 752 dbSNP
rs182399935 762 dbSNP
rs186570657 763 dbSNP
rs1271347743 774 dbSNP
rs1471631740 784 dbSNP
rs1420191886 797 dbSNP
rs1331364501 798 dbSNP
rs1483502193 804 dbSNP
rs1217103860 805 dbSNP
rs750698452 820 dbSNP
rs1207707905 826 dbSNP
rs1485180883 829 dbSNP
rs925847205 853 dbSNP
rs1183903833 864 dbSNP
rs763229633 869 dbSNP
rs1448544304 871 dbSNP
rs1258724429 899 dbSNP
rs1474672527 908 dbSNP
rs1227446007 917 dbSNP
rs1326458448 941 dbSNP
rs1294660343 959 dbSNP
rs1228412229 960 dbSNP
rs1379003040 963 dbSNP
rs1185397431 964 dbSNP
rs867437230 966 dbSNP
rs1433293040 971 dbSNP
rs1389887274 975 dbSNP
rs1413499009 978 dbSNP
rs1015931638 990 dbSNP
rs1400730400 1002 dbSNP
rs759413587 1003 dbSNP
rs910353857 1012 dbSNP
rs944573630 1013 dbSNP
rs1343297011 1014 dbSNP
rs1467537036 1018 dbSNP
rs1026093527 1024 dbSNP
rs1180096149 1032 dbSNP
rs1451066684 1033 dbSNP
rs955015202 1036 dbSNP
rs987676357 1037 dbSNP
rs1040435625 1052 dbSNP
rs919366534 1059 dbSNP
rs1463226479 1063 dbSNP
rs1414367768 1066 dbSNP
rs964923380 1077 dbSNP
rs766441971 1084 dbSNP
rs1049023660 1089 dbSNP
rs1306401467 1103 dbSNP
rs925936692 1134 dbSNP
rs527955428 1144 dbSNP
rs1281451850 1145 dbSNP
rs776975499 1155 dbSNP
rs989271919 1161 dbSNP
rs917356390 1169 dbSNP
rs761907589 1171 dbSNP
rs949201809 1176 dbSNP
rs191015153 1177 dbSNP
rs938236302 1178 dbSNP
rs1253471935 1186 dbSNP
rs1055792550 1189 dbSNP
rs1457452378 1201 dbSNP
rs1348251465 1205 dbSNP
rs1470313516 1208 dbSNP
rs1431615909 1214 dbSNP
rs1046234867 1244 dbSNP
rs905061364 1263 dbSNP
rs758291368 1271 dbSNP
rs937909954 1292 dbSNP
rs1405241370 1298 dbSNP
rs751969347 1299 dbSNP
rs1487868728 1303 dbSNP
rs1263226880 1320 dbSNP
rs1013799986 1323 dbSNP
rs1343410471 1330 dbSNP
rs1037647908 1332 dbSNP
rs183123679 1336 dbSNP
rs781773321 1366 dbSNP
rs1302208916 1375 dbSNP
rs1432579513 1379 dbSNP
rs1386491169 1383 dbSNP
rs902963039 1421 dbSNP
rs998617067 1428 dbSNP
rs1032655057 1430 dbSNP
rs1410523996 1431 dbSNP
rs1356437462 1437 dbSNP
rs61182524 1442 dbSNP
rs55673535 1446 dbSNP
rs56224731 1448 dbSNP
rs957271395 1449 dbSNP
rs1026460245 1454 dbSNP
rs1443275383 1461 dbSNP
rs890215851 1469 dbSNP
rs986058880 1473 dbSNP
rs1009446529 1479 dbSNP
rs1017978963 1491 dbSNP
rs965833042 1492 dbSNP
rs975919706 1508 dbSNP
rs1371326376 1518 dbSNP
rs964870487 1520 dbSNP
rs978970830 1527 dbSNP
rs1264829851 1529 dbSNP
rs919106490 1548 dbSNP
rs1183661600 1570 dbSNP
rs1483109454 1571 dbSNP
rs1251698972 1574 dbSNP
rs1347823224 1584 dbSNP
rs762979607 1614 dbSNP
rs1232469073 1634 dbSNP
rs1033237062 1635 dbSNP
rs1233004372 1636 dbSNP
rs956014540 1636 dbSNP
rs1310597393 1638 dbSNP
rs1438036833 1638 dbSNP
rs988828276 1639 dbSNP
rs1229033786 1649 dbSNP
rs1203464798 1655 dbSNP
rs1350008290 1659 dbSNP
rs929371787 1664 dbSNP
rs1307328318 1665 dbSNP
rs985284690 1679 dbSNP
rs909179329 1697 dbSNP
rs766875246 1702 dbSNP
rs1193742234 1705 dbSNP
rs980635075 1707 dbSNP
rs1189195000 1712 dbSNP
rs1997715 1715 dbSNP
rs1160987611 1719 dbSNP
rs926426019 1740 dbSNP
rs937859049 1744 dbSNP
rs755393591 1759 dbSNP
rs1444579450 1766 dbSNP
rs1257490987 1776 dbSNP
rs1200200939 1794 dbSNP
rs755735631 1795 dbSNP
rs1420047042 1814 dbSNP
rs1482496475 1815 dbSNP
rs1270229928 1827 dbSNP
rs1037593980 1848 dbSNP
rs1286466219 1853 dbSNP
rs899100872 1853 dbSNP
rs1247088152 1856 dbSNP
rs1342150401 1860 dbSNP
rs1313373566 1864 dbSNP
rs896751529 1872 dbSNP
rs1395215655 1892 dbSNP
rs1410713276 1921 dbSNP
rs1322132006 1944 dbSNP
rs781406947 1947 dbSNP
rs1156236778 1952 dbSNP
rs1352997213 1967 dbSNP
rs1473513069 1977 dbSNP
rs752436637 1990 dbSNP
rs890156331 1997 dbSNP
rs1326664500 2007 dbSNP
rs1422407648 2007 dbSNP
rs1008628085 2008 dbSNP
rs1464557565 2023 dbSNP
rs145513027 2025 dbSNP
rs1039224005 2032 dbSNP
rs1300266460 2044 dbSNP
rs900649577 2048 dbSNP
rs1340552531 2049 dbSNP
rs1213604871 2061 dbSNP
rs1000336991 2076 dbSNP
rs777436804 2082 dbSNP
rs138125694 2087 dbSNP
rs1323177644 2088 dbSNP
rs1363962295 2091 dbSNP
rs1033183043 2097 dbSNP
rs1406580907 2108 dbSNP
rs1033210576 2113 dbSNP
rs1163187871 2134 dbSNP
rs778379249 2135 dbSNP
rs1007661852 2141 dbSNP
rs1024309328 2142 dbSNP
rs745705059 2146 dbSNP
rs971829398 2147 dbSNP
rs1449278634 2161 dbSNP
rs1246393391 2164 dbSNP
rs1190475519 2172 dbSNP
rs1452239386 2183 dbSNP
rs771733485 2187 dbSNP
rs1208138620 2189 dbSNP
rs975991838 2191 dbSNP
rs187456227 2208 dbSNP
rs1184590092 2209 dbSNP
rs1341242590 2242 dbSNP
rs1268018981 2252 dbSNP
rs959170321 2259 dbSNP
rs1026066785 2282 dbSNP
rs529735372 2285 dbSNP
rs1322246375 2289 dbSNP
rs920477508 2298 dbSNP
rs192829395 2306 dbSNP
rs1169829425 2317 dbSNP
rs1048130165 2324 dbSNP
rs149096436 2325 dbSNP
rs944384224 2327 dbSNP
rs1478440352 2328 dbSNP
rs1377297481 2329 dbSNP
rs1196786574 2332 dbSNP
rs1307891725 2334 dbSNP
rs1484093804 2346 dbSNP
rs772029068 2356 dbSNP
rs1038735983 2358 dbSNP
rs769926051 2368 dbSNP
rs909325992 2374 dbSNP
rs1482595850 2386 dbSNP
rs775122601 2395 dbSNP
rs1000283649 2396 dbSNP
rs938006658 2404 dbSNP
rs1430410041 2405 dbSNP
rs1345229066 2407 dbSNP
rs1273914085 2414 dbSNP
rs1054542801 2429 dbSNP
rs148225910 2433 dbSNP
rs917936690 2443 dbSNP
rs1409823610 2444 dbSNP
rs949591457 2448 dbSNP
rs1025008388 2449 dbSNP
rs1336493929 2450 dbSNP
rs1042664428 2454 dbSNP
rs1271951443 2461 dbSNP
rs1332092205 2462 dbSNP
rs924099499 2464 dbSNP
rs1210074433 2466 dbSNP
rs1001962032 2468 dbSNP
rs936863268 2475 dbSNP
rs1054193378 2478 dbSNP
rs769938547 2497 dbSNP
rs1472193491 2498 dbSNP
rs1231132002 2533 dbSNP
rs761931654 2534 dbSNP
rs773415474 2534 dbSNP
rs141185322 2535 dbSNP
rs766647393 2540 dbSNP
rs950635673 2550 dbSNP
rs774397909 2554 dbSNP
rs1239049841 2558 dbSNP
rs997355898 2564 dbSNP
rs1371748168 2570 dbSNP
rs1286497863 2573 dbSNP
rs750336551 2582 dbSNP
rs950549816 2584 dbSNP
rs1006488414 2588 dbSNP
rs1358994980 2589 dbSNP
rs1188974222 2590 dbSNP
rs1016334785 2608 dbSNP
rs959692687 2610 dbSNP
rs547807021 2638 dbSNP
rs1474239783 2643 dbSNP
rs1331427476 2654 dbSNP
rs183353424 2660 dbSNP
rs1160403149 2662 dbSNP
rs1158462991 2664 dbSNP
rs774905100 2676 dbSNP
rs1399062245 2682 dbSNP
rs1405664697 2692 dbSNP
rs760005871 2698 dbSNP
rs990938276 2700 dbSNP
rs944347339 2701 dbSNP
rs917884299 2718 dbSNP
rs767976122 2719 dbSNP
rs1206274067 2723 dbSNP
rs753027218 2729 dbSNP
rs1377691679 2741 dbSNP
rs756463718 2752 dbSNP
rs1414993526 2755 dbSNP
rs1465929706 2756 dbSNP
rs921635744 2771 dbSNP
rs1207506955 2775 dbSNP
rs1292236424 2789 dbSNP
rs970724685 2799 dbSNP
rs187794867 2802 dbSNP
rs1292614942 2810 dbSNP
rs978337846 2817 dbSNP
rs376647495 2829 dbSNP
rs753487879 2834 dbSNP
rs936842193 2838 dbSNP
rs1054336667 2846 dbSNP
rs1279641724 2847 dbSNP
rs756890223 2860 dbSNP
rs1349858990 2874 dbSNP
rs1428700680 2876 dbSNP
rs35285949 2880 dbSNP
rs1045961099 2882 dbSNP
rs1166828644 2893 dbSNP
rs1405817465 2899 dbSNP
rs1203393142 2902 dbSNP
rs911414622 2910 dbSNP
rs1280438523 2911 dbSNP
rs1248225276 2917 dbSNP
rs1185620225 2920 dbSNP
rs907450977 2926 dbSNP
rs1248014050 2936 dbSNP
rs1485906418 2945 dbSNP
rs1221665545 2960 dbSNP
rs1209919036 2963 dbSNP
rs1321596132 2972 dbSNP
rs778531595 2975 dbSNP
rs1254236609 2976 dbSNP
rs943075490 2977 dbSNP
rs1484816565 2995 dbSNP
rs1034344634 3010 dbSNP
rs898538920 3014 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aauUCAUUGUGGAAGGAcuuau 5'
             | |  | |:| |||     
Target 5' uuuACUCCCUCUUCCCUcuacu 3'
 		1 - 22
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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000374888.1 | 3UTR | UUUACUCCCUCUUCCCUCUACUG
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
76 hsa-miR-506-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT081146 LDLR low density lipoprotein receptor 2 2
MIRT083631 PRNP prion protein 2 2
MIRT157309 IKZF2 IKAROS family zinc finger 2 2 2
MIRT172369 LONRF1 LON peptidase N-terminal domain and ring finger 1 2 2
MIRT175463 ZBTB33 zinc finger and BTB domain containing 33 2 2
MIRT178171 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT209107 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT254771 XRCC6 X-ray repair cross complementing 6 2 6
MIRT264771 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 4
MIRT309156 FGF2 fibroblast growth factor 2 2 6
MIRT334098 SFT2D2 SFT2 domain containing 2 2 2
MIRT386044 RORA RAR related orphan receptor A 2 2
MIRT453248 FTSJ3 FtsJ RNA methyltransferase homolog 3 2 2
MIRT455924 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT456349 OLIG3 oligodendrocyte transcription factor 3 2 8
MIRT462877 ZXDB zinc finger, X-linked, duplicated B 2 2
MIRT465017 LINC00598 long intergenic non-protein coding RNA 598 2 2
MIRT466897 STMN1 stathmin 1 2 2
MIRT467919 SLC20A1 solute carrier family 20 member 1 2 2
MIRT467927 SLC16A7 solute carrier family 16 member 7 2 2
MIRT468172 SGPL1 sphingosine-1-phosphate lyase 1 2 4
MIRT483372 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT484061 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT492425 RGL2 ral guanine nucleotide dissociation stimulator like 2 2 2
MIRT495350 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT496983 DNAJC27 DnaJ heat shock protein family (Hsp40) member C27 2 2
MIRT503380 SOD2 superoxide dismutase 2 2 4
MIRT505598 SLC38A1 solute carrier family 38 member 1 2 6
MIRT507384 EN2 engrailed homeobox 2 2 6
MIRT508638 RPL23A ribosomal protein L23a 2 6
MIRT509813 SULT1B1 sulfotransferase family 1B member 1 2 4
MIRT509883 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 2 4
MIRT512038 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 4
MIRT512513 BTBD19 BTB domain containing 19 2 2
MIRT513071 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT514049 AGO2 argonaute 2, RISC catalytic component 2 6
MIRT516464 RAB32 RAB32, member RAS oncogene family 2 4
MIRT523441 GPR137C G protein-coupled receptor 137C 2 4
MIRT523957 DYNLT1 dynein light chain Tctex-type 1 2 4
MIRT524143 LDHD lactate dehydrogenase D 2 4
MIRT524632 C4orf32 family with sequence similarity 241 member A 2 4
MIRT531710 TFEC transcription factor EC 2 2
MIRT532813 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT534244 SLC16A1 solute carrier family 16 member 1 2 2
MIRT534328 SHISA6 shisa family member 6 2 2
MIRT543334 UTP14C UTP14C, small subunit processome component 2 2
MIRT545944 ZBTB18 zinc finger and BTB domain containing 18 2 4
MIRT549008 CCDC6 coiled-coil domain containing 6 2 2
MIRT549226 BAZ2B bromodomain adjacent to zinc finger domain 2B 2 2
MIRT550121 RPF2 ribosome production factor 2 homolog 2 2
MIRT551421 SERTM1 serine rich and transmembrane domain containing 1 2 2
MIRT556787 KLF13 Kruppel like factor 13 2 2
MIRT561372 UBXN2B UBX domain protein 2B 2 2
MIRT561849 NPTX1 neuronal pentraxin 1 2 2
MIRT563981 SLFN11 schlafen family member 11 2 2
MIRT565747 SERTAD3 SERTA domain containing 3 2 2
MIRT569130 TMC5 transmembrane channel like 5 2 4
MIRT572714 LHX6 LIM homeobox 6 2 2
MIRT624539 BROX BRO1 domain and CAAX motif containing 2 2
MIRT637034 SPTLC3 serine palmitoyltransferase long chain base subunit 3 2 2
MIRT643213 TYW3 tRNA-yW synthesizing protein 3 homolog 2 2
MIRT646884 PLSCR1 phospholipid scramblase 1 2 2
MIRT650183 LILRA2 leukocyte immunoglobulin like receptor A2 2 2
MIRT651561 WISP1 WNT1 inducible signaling pathway protein 1 2 2
MIRT665188 HAUS5 HAUS augmin like complex subunit 5 2 2
MIRT665466 WDR13 WD repeat domain 13 2 2
MIRT668763 DDR2 discoidin domain receptor tyrosine kinase 2 2 2
MIRT680605 ZNF611 zinc finger protein 611 2 2
MIRT688564 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT698121 TOPBP1 DNA topoisomerase II binding protein 1 2 2
MIRT699130 SMNDC1 survival motor neuron domain containing 1 2 2
MIRT712282 PPIP5K2 diphosphoinositol pentakisphosphate kinase 2 2 2
MIRT712561 CENPO centromere protein O 2 2
MIRT715358 VCAM1 vascular cell adhesion molecule 1 2 2
MIRT720209 KCNN1 potassium calcium-activated channel subfamily N member 1 2 2
MIRT732331 MTDH metadherin 2 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-506 Glucose NULL 5793 Microarray endothelial cells 24394957 2014 up-regulated
miR-506 17beta-estradiol (E2) approved 5757 Microarray MCF-7 breast cancer cells 19528081 2009 down-regulated
miR-506 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-506 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-506 Cisplatin 5460033 NSC119875 approved resistant cell line (CP20)
hsa-miR-506-5p Cisplatin + Decitabine sensitive High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-506-5p Tripterygium wilfordii Hook F resistant tissue
hsa-miR-506-5p Leuprorelin/Goserelin + Bicalutamide resistant tissue (prostate cancer)

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