pre-miRNA Information
pre-miRNA hsa-mir-4330   
Genomic Coordinates chrX: 151168222 - 151168326
Description Homo sapiens miR-4330 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4330
Sequence 77| CCUCAGAUCAGAGCCUUGC |95
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1247337555 6 dbSNP
rs777851226 7 dbSNP
rs1295014011 13 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
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' cgUUC---CGA---GACUAGACUCc 5'
            |||   |:|   || ||||||| 
Target 5' gcAAGTCAGTTAACCT-ATCTGAGc 3'
188 - 211 144.00 -10.80
2
miRNA  3' cguUCCGAGAC-----UAGACUcc 5'
             |||||:||     ||||||  
Target 5' actAGGCTTTGGCTAAATCTGAca 3'
2086 - 2109 140.00 -15.00
3
miRNA  3' cguuccGAGACUAG-ACUCc 5'
                :||||||| |||| 
Target 5' tttaaaTTCTGATCTTGAGt 3'
140 - 159 129.00 -13.70
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 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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' cguuccgaGACUAGACUCc 5'
                  || ||||||| 
Target 5' ---uuaacCU-AUCUGAGc 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 HEK293
Disease 158586.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' cguuccgaGACUAGACUCc 5'
                  || ||||||| 
Target 5' ---uuaacCU-AUCUGAGc 3'
1 - 15
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 3 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.

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 4 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HCT116
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 ERX177608. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_2_10 PAR-CLIP data was present in ERX177620. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_10 PAR-CLIP data was present in ERX177632. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_4_10 ...

- Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research.

Article - Krell J; Stebbing J; Carissimi C; Dabrowska et al.
- Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000374888.1 | 3UTR | UUAACCUAUCUGAGCCUUAAUUUCCUUAUUUAUAAAUUG
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 GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000374888.1 | 3UTR | UUAACCUAUCUGAGCCUUAAUUUCCUUAUUUAUAAAUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000374888.1 | 3UTR | UUAACCUAUCUGAGCCUUAAUUUCCUUAUUUAUAAAUUG
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
79 hsa-miR-4330 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT092330 EDEM1 ER degradation enhancing alpha-mannosidase like protein 1 2 6
MIRT092536 KBTBD8 kelch repeat and BTB domain containing 8 2 6
MIRT102900 INSIG1 insulin induced gene 1 2 6
MIRT271430 ETNK1 ethanolamine kinase 1 2 2
MIRT327637 ZXDB zinc finger, X-linked, duplicated B 2 6
MIRT441799 BCAS1 breast carcinoma amplified sequence 1 2 2
MIRT442396 ILDR1 immunoglobulin like domain containing receptor 1 2 2
MIRT452817 INTS2 integrator complex subunit 2 2 2
MIRT455523 C6orf106 chromosome 6 open reading frame 106 2 2
MIRT455885 KIF2C kinesin family member 2C 2 2
MIRT462197 NDUFS1 NADH:ubiquinone oxidoreductase core subunit S1 2 2
MIRT462697 SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 2 2
MIRT464698 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465961 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466045 TMEM189 transmembrane protein 189 2 2
MIRT473479 MCFD2 multiple coagulation factor deficiency 2 2 2
MIRT473562 MATR3 matrin 3 2 2
MIRT473945 LYN LYN proto-oncogene, Src family tyrosine kinase 2 2
MIRT475053 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT475532 HOXA3 homeobox A3 2 8
MIRT475980 GTPBP2 GTP binding protein 2 2 2
MIRT477066 FAM208B family with sequence similarity 208 member B 2 4
MIRT479327 CERS2 ceramide synthase 2 2 2
MIRT479895 CCDC117 coiled-coil domain containing 117 2 2
MIRT481542 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT482406 ADRB1 adrenoceptor beta 1 2 10
MIRT482911 ZNF845 zinc finger protein 845 2 2
MIRT489975 DDB1 damage specific DNA binding protein 1 2 2
MIRT490346 PEX10 peroxisomal biogenesis factor 10 2 2
MIRT493585 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 6
MIRT496153 RPS15A ribosomal protein S15a 2 2
MIRT500620 TXNIP thioredoxin interacting protein 2 2
MIRT503158 ANKRD11 ankyrin repeat domain 11 2 2
MIRT504479 HSF5 heat shock transcription factor 5 2 6
MIRT504633 MFSD8 major facilitator superfamily domain containing 8 2 6
MIRT507122 GIGYF1 GRB10 interacting GYF protein 1 2 6
MIRT514631 MTRNR2L7 MT-RNR2-like 7 2 2
MIRT521270 RTN4 reticulon 4 2 6
MIRT533902 TBL1X transducin beta like 1X-linked 2 2
MIRT537583 ESYT2 extended synaptotagmin 2 2 2
MIRT540430 FAM83F family with sequence similarity 83 member F 2 2
MIRT544324 TMEM81 transmembrane protein 81 2 4
MIRT548303 EPHA7 EPH receptor A7 2 2
MIRT552766 YIPF6 Yip1 domain family member 6 2 2
MIRT555669 PGAM4 phosphoglycerate mutase family member 4 2 2
MIRT561279 ZCCHC3 zinc finger CCHC-type containing 3 2 2
MIRT564575 ZXDA zinc finger, X-linked, duplicated A 2 2
MIRT565812 SDCCAG3 serologically defined colon cancer antigen 3 2 2
MIRT568741 MTRNR2L1 MT-RNR2-like 1 2 2
MIRT569363 PRMT6 protein arginine methyltransferase 6 2 2
MIRT570608 MTRNR2L11 MT-RNR2-like 11 2 2
MIRT572424 PTGES3L prostaglandin E synthase 3 like 2 2
MIRT576542 Txlna taxilin alpha 2 2
MIRT610568 HIST3H2BB histone cluster 3 H2B family member b 2 2
MIRT617497 IFT46 intraflagellar transport 46 2 2
MIRT617773 C17orf105 chromosome 17 open reading frame 105 2 2
MIRT619275 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT624618 ATXN7L3B ataxin 7 like 3B 2 2
MIRT628001 MELK maternal embryonic leucine zipper kinase 2 2
MIRT646325 MVB12B multivesicular body subunit 12B 2 2
MIRT648697 TNFRSF13C TNF receptor superfamily member 13C 2 2
MIRT665675 TOR1B torsin family 1 member B 2 2
MIRT669730 ZBTB8B zinc finger and BTB domain containing 8B 2 2
MIRT676242 PARP2 poly(ADP-ribose) polymerase 2 2 2
MIRT683205 MBNL1 muscleblind like splicing regulator 1 2 2
MIRT684425 TUFT1 tuftelin 1 2 2
MIRT688864 CAMKK2 calcium/calmodulin dependent protein kinase kinase 2 2 2
MIRT693406 NUDT16 nudix hydrolase 16 2 2
MIRT694597 AAR2 AAR2 splicing factor homolog 2 2
MIRT698399 TMED10 transmembrane p24 trafficking protein 10 2 2
MIRT698435 TM4SF1 transmembrane 4 L six family member 1 2 2
MIRT708290 ZNF24 zinc finger protein 24 2 2
MIRT709766 GPR183 G protein-coupled receptor 183 2 2
MIRT710713 KRTAP6-1 keratin associated protein 6-1 2 2
MIRT711643 LIPG lipase G, endothelial type 2 2
MIRT713246 SLC22A3 solute carrier family 22 member 3 2 2
MIRT714008 IL6R interleukin 6 receptor 2 2
MIRT721851 C1QTNF3 C1q and TNF related 3 2 2
MIRT724003 TMEM174 transmembrane protein 174 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4330 Doxorubicin 31703 NSC123127 approved sensitive cell line (BAS)
hsa-miR-4330 Platinum 23939 sensitive tissue
hsa-miR-4330 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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