pre-miRNA Information
pre-miRNA hsa-mir-4445   
Genomic Coordinates chr3: 109602828 - 109602897
Description Homo sapiens miR-4445 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4445-5p
Sequence 8| AGAUUGUUUCUUUUGCCGUGCA |29
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1171699104 7 dbSNP
rs1436192424 17 dbSNP
rs76069948 18 dbSNP
rs1364939646 20 dbSNP
rs1268373315 21 dbSNP
rs1471410503 22 dbSNP
Putative Targets

Gene Information
Gene Symbol UBE2V1   
Synonyms CIR1, CROC-1, CROC1, UBE2V, UEV-1, UEV1, UEV1A
Description ubiquitin conjugating enzyme E2 V1
Transcript NM_001032288   
Other Transcripts NM_021988 , NM_022442 , NM_199144   
Expression
Putative miRNA Targets on UBE2V1
3'UTR of UBE2V1
(miRNA target sites are highlighted)
>UBE2V1|NM_001032288|3'UTR
   1 TCAAAAAGAAAAACCACAGGCCCTTCCCCTTCCCCCCAATTCGATTTAATCAGTCTTCATTTTCCACAGTAGTAAATTTT
  81 CTAGATACGTCTTGTAGACCTCAAAGTACCGGAAAGGAAGCTCCCATTCAAAGGAAATTTATCTTAAGATACTGTAAATG
 161 ATACTAATTTTTTGTCCATTTGAAATATATAAGTTGTGCTATAACAAATCATCCTGTCAAGTGTAACCACTGTCCACGTA
 241 GTTGAACTTCTGGGATCAAGAAAGTCTATTTAAATTGATTCCCATCATAACTGGTGGGGCACATCTAACTCAACTGTGAA
 321 AAGACACATCACACAATCACCTTGCTGCTGATTACACGGCCTGGGGTCTCTGCCTTCTCCCCTTACCCTCCCGCCTCCCA
 401 CCCTCCCTGCAACAACAGCCCTCTAGCCTGGGGGGCTTGTTAGAGTAGATGTGAAGGTTTCAGGTCGCAGCCTGTGGGAC
 481 TACTGCTAGGTGTGTGGGGTGTTTCGCCTGCACCCCTGGTTTCTTTAAGTCTTAAGTGATGCCCCTTCCAAACCATCATC
 561 CTGTCCCCACGCTCCTCCACTCCCGCCCTTGGCCGAAGCATAGATTGTAACCCCTCCACTCCCCTCTGAGATTGGCCTTC
 641 GGTGAGGAATTCAGGGCTTTCCCCATATCTTCTCTCCCCCACCTTTATCGAGGGGTGCTGCTTTTTCTCCCTCCTCCTCA
 721 AGTTCCTTTTTGCACCGTCACCACCCAACACCTTCCATGACACTTCCTTGCTTTGGCCAGAAGCCATCAGGTAAGGTTGG
 801 AAAGAGCCTCTGACCTCCCTTGTTTAGTTTTGGAACCATACTCACTCACTCTCCACCAGCCTGGGAAATGAATATTGGGT
 881 CCTCAGCCCTGCCACCCTCTGCTGTCATCAGCTGATGCATTGTTTTTAGCTCAGGTTTTGATAAGGTGAAAAGAATAGTC
 961 ACCAGGGTTACTCAGACCTGCCAGCTCTCGGAGTCCTTGGTGGTTGAACTTGGAGAAAGACCGCATGAAGATACTTGTAA
1041 GCACACATGATCCCTCTGAATTGTTTTACTTTCCTGTAACTGCTTTTGCTTTTAAAAATTGAAGAAGTTTTAAACAGGGC
1121 TTTCATTTGGTCATCCTTGCAATCCATTGGGGTCTAGTTTGGAATCTGACAACTGGAACAAAAAGAACCTTGAATCCGGT
1201 GCATGCCTTGGTTTTGGTGCTGCTGCTGCTTCCCAAGATCCTCAGCAGGGATTAAGAAGGAACCCGGTGTGCACAGCAGA
1281 TCCCCGAAATTGGTGGGCTTGACCTCCTGGCAAATTGCTGCGTCTTTCCACTTGCTGTTCAGGACCACTAAATGCTGAAA
1361 TGTGGATGCATACCGAAATAAAAGCAATTCATTGTGTACTAAAGGTTTTTTTTTTTTTTTTAATTTAGTATTTGTGTAAA
1441 ACCACCTTTTGAAGCAGCAACTATCAAGTCTGAAAAGCAATTGATGTTTCCATTAATCTTTTTCTGGGGGGAAAACCTTA
1521 GTTCTAAGGATTTAACATCCTGTAAGTGAAGTTTAACATAACAGTATTCCATAAGCAGCCTTTTTATTGTCAGACCATTG
1601 CCTGATTTTAATATAATAAAAAAAAAGTGTGCGTTAATATTTAA
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' acGUGCCGUUUUCUUUGUUAGa 5'
            :| ||::||| :||:|:|| 
Target 5' gaTAAGGTGAAAAGAATAGTCa 3'
940 - 961 136.00 -9.40
2
miRNA  3' acgUGCCG-UUUUCU------U-UGUUAGa 5'
             || |: ||||||      | |||||| 
Target 5' tcaACTGTGAAAAGACACATCACACAATCa 3'
310 - 339 125.00 -5.90
3
miRNA  3' acguGCCGUUUUCUUUGUUaga 5'
              :| |||  |:|||||   
Target 5' aatcTGACAACTGGAACAAaaa 3'
1163 - 1184 118.00 -6.52
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN24307096 3 COSMIC
COSN26998937 22 COSMIC
COSN30476187 28 COSMIC
COSN30505513 31 COSMIC
COSN30458627 32 COSMIC
COSN30458620 33 COSMIC
COSN30169210 52 COSMIC
COSN31567363 75 COSMIC
COSN13867558 88 COSMIC
COSN26998936 89 COSMIC
COSN30144721 107 COSMIC
COSN30502742 112 COSMIC
COSN30184289 115 COSMIC
COSN31559335 244 COSMIC
COSN28824255 287 COSMIC
COSN26563719 360 COSMIC
COSN28677500 382 COSMIC
COSN26325394 427 COSMIC
COSN22596479 456 COSMIC
COSN31579035 497 COSMIC
COSN31519043 505 COSMIC
COSN31512891 513 COSMIC
COSN28648771 522 COSMIC
COSN8000421 570 COSMIC
COSN26665932 737 COSMIC
COSN26665931 752 COSMIC
COSN21694650 755 COSMIC
COSN26646230 761 COSMIC
COSN31608558 764 COSMIC
COSN26665930 788 COSMIC
COSN9141735 827 COSMIC
COSN26644422 881 COSMIC
COSN26637891 882 COSMIC
COSN31585404 906 COSMIC
COSN26580109 945 COSMIC
COSN31484609 1058 COSMIC
COSN8899531 1144 COSMIC
COSN30176705 1286 COSMIC
COSN28402157 1322 COSMIC
COSN26548224 1348 COSMIC
COSN31596053 1392 COSMIC
COSN31529740 1404 COSMIC
COSN19660945 1406 COSMIC
COSN31518694 1441 COSMIC
COSN31529170 1498 COSMIC
COSN23222315 1617 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1327160254 7 dbSNP
rs750111448 8 dbSNP
rs765043055 13 dbSNP
rs761226884 15 dbSNP
rs1472196388 16 dbSNP
rs1363988460 18 dbSNP
rs1183602229 20 dbSNP
rs200602780 21 dbSNP
rs528812995 23 dbSNP
rs1214104193 26 dbSNP
rs1469722543 27 dbSNP
rs760688909 28 dbSNP
rs201295239 29 dbSNP
rs187204768 32 dbSNP
rs1262699317 33 dbSNP
rs773415961 35 dbSNP
rs1194254182 36 dbSNP
rs779631764 36 dbSNP
rs1376444799 38 dbSNP
rs371693730 39 dbSNP
rs899700274 40 dbSNP
rs748150641 42 dbSNP
rs368141343 43 dbSNP
rs1005431935 56 dbSNP
rs780048962 58 dbSNP
rs1351757693 61 dbSNP
rs182869336 71 dbSNP
rs557493991 88 dbSNP
rs1369437294 89 dbSNP
rs1242899650 93 dbSNP
rs73611765 104 dbSNP
rs73611764 110 dbSNP
rs1366614450 111 dbSNP
rs1270503795 112 dbSNP
rs1432674901 115 dbSNP
rs1343596496 121 dbSNP
rs1049065708 124 dbSNP
rs1448546963 130 dbSNP
rs929329105 135 dbSNP
rs897810106 139 dbSNP
rs1056989975 144 dbSNP
rs527244006 152 dbSNP
rs939444041 153 dbSNP
rs1416251387 170 dbSNP
rs544387060 172 dbSNP
rs1377397162 175 dbSNP
rs577095993 180 dbSNP
rs1172293414 189 dbSNP
rs148757188 198 dbSNP
rs191054982 208 dbSNP
rs1449714514 210 dbSNP
rs1330103976 214 dbSNP
rs41283596 215 dbSNP
rs1474636788 229 dbSNP
rs73611763 237 dbSNP
rs946969330 238 dbSNP
rs915467088 253 dbSNP
rs1272049911 261 dbSNP
rs1331994721 265 dbSNP
rs1200527091 266 dbSNP
rs988379194 268 dbSNP
rs1437104695 280 dbSNP
rs1179400646 283 dbSNP
rs554507531 288 dbSNP
rs1029326485 303 dbSNP
rs976940985 314 dbSNP
rs1467243302 315 dbSNP
rs1169053770 319 dbSNP
rs1396425563 338 dbSNP
rs1485693876 341 dbSNP
rs1408641796 355 dbSNP
rs963794287 357 dbSNP
rs1356483318 358 dbSNP
rs1018084315 361 dbSNP
rs1292292850 365 dbSNP
rs1353088599 367 dbSNP
rs1219950926 368 dbSNP
rs1251317536 378 dbSNP
rs8585 382 dbSNP
rs1193955471 383 dbSNP
rs775806445 384 dbSNP
rs1485858324 389 dbSNP
rs1025541554 392 dbSNP
rs1255651312 396 dbSNP
rs1478890544 396 dbSNP
rs1216093844 401 dbSNP
rs1372533106 406 dbSNP
rs144341721 413 dbSNP
rs1447090241 418 dbSNP
rs1277771319 420 dbSNP
rs1174801340 426 dbSNP
rs1376519226 430 dbSNP
rs897855587 443 dbSNP
rs1311381438 445 dbSNP
rs73611762 458 dbSNP
rs149631469 466 dbSNP
rs1383519690 467 dbSNP
rs879941567 478 dbSNP
rs1311098113 479 dbSNP
rs1225201538 482 dbSNP
rs1056436022 483 dbSNP
rs1305530392 490 dbSNP
rs1348394533 494 dbSNP
rs1209902067 498 dbSNP
rs1465608196 505 dbSNP
rs747116362 506 dbSNP
rs1205887038 512 dbSNP
rs905254358 513 dbSNP
rs1426811509 514 dbSNP
rs1045270254 517 dbSNP
rs1049679 522 dbSNP
rs1454169890 523 dbSNP
rs915393538 532 dbSNP
rs1053153792 533 dbSNP
rs73611761 536 dbSNP
rs1455069553 538 dbSNP
rs935587429 545 dbSNP
rs759598047 548 dbSNP
rs1383697942 549 dbSNP
rs922267379 550 dbSNP
rs73611760 552 dbSNP
rs1327261702 567 dbSNP
rs976404142 568 dbSNP
rs964150271 570 dbSNP
rs73611759 571 dbSNP
rs1259221627 582 dbSNP
rs1185068827 584 dbSNP
rs774173278 585 dbSNP
rs1260353908 592 dbSNP
rs1482676227 595 dbSNP
rs1211720825 599 dbSNP
rs1233380662 613 dbSNP
rs1253661334 619 dbSNP
rs73611758 622 dbSNP
rs1468447440 624 dbSNP
rs1192284516 632 dbSNP
rs1240455774 633 dbSNP
rs73611757 640 dbSNP
rs1305526283 641 dbSNP
rs752721921 651 dbSNP
rs73611756 655 dbSNP
rs1166502575 662 dbSNP
rs1394510605 664 dbSNP
rs1440138786 665 dbSNP
rs868658306 674 dbSNP
rs6095755 676 dbSNP
rs1375335838 677 dbSNP
rs1391777014 678 dbSNP
rs1025425012 680 dbSNP
rs1235316253 681 dbSNP
rs1337135154 683 dbSNP
rs994499953 689 dbSNP
rs1212438777 690 dbSNP
rs959945210 694 dbSNP
rs1481212921 695 dbSNP
rs80158980 707 dbSNP
rs1176991228 716 dbSNP
rs1374234484 717 dbSNP
rs1189594783 720 dbSNP
rs770370283 720 dbSNP
rs1003516625 725 dbSNP
rs1440716704 726 dbSNP
rs528773295 733 dbSNP
rs73611755 737 dbSNP
rs754594279 740 dbSNP
rs114097793 742 dbSNP
rs894010518 746 dbSNP
rs1162340301 755 dbSNP
rs1370882745 759 dbSNP
rs73611754 761 dbSNP
rs181019888 762 dbSNP
rs1294129970 768 dbSNP
rs1408137007 770 dbSNP
rs59124899 782 dbSNP
rs73611753 784 dbSNP
rs1231543169 786 dbSNP
rs1275125492 791 dbSNP
rs1308627808 793 dbSNP
rs1204375556 796 dbSNP
rs1250024552 804 dbSNP
rs1456351686 814 dbSNP
rs1237495207 815 dbSNP
rs1486838574 816 dbSNP
rs1214022611 818 dbSNP
rs1257803242 820 dbSNP
rs935583318 830 dbSNP
rs1271508513 837 dbSNP
rs1244392235 841 dbSNP
rs1317572762 849 dbSNP
rs374126556 852 dbSNP
rs545495098 853 dbSNP
rs1169620042 856 dbSNP
rs1352615743 859 dbSNP
rs1436338365 859 dbSNP
rs1313200964 861 dbSNP
rs1375075469 863 dbSNP
rs751129605 864 dbSNP
rs1413119490 874 dbSNP
rs1272020927 875 dbSNP
rs1041683241 878 dbSNP
rs578177787 886 dbSNP
rs1376727045 888 dbSNP
rs777590807 892 dbSNP
rs558706247 895 dbSNP
rs942395810 897 dbSNP
rs1280016716 904 dbSNP
rs1392791136 909 dbSNP
rs1361971820 912 dbSNP
rs1243387885 918 dbSNP
rs1485907657 920 dbSNP
rs1185916313 925 dbSNP
rs1388262194 926 dbSNP
rs1455480410 928 dbSNP
rs1174063318 940 dbSNP
rs1394193833 946 dbSNP
rs910887394 954 dbSNP
rs1320495288 955 dbSNP
rs1345930033 957 dbSNP
rs1430124432 962 dbSNP
rs1287125744 968 dbSNP
rs983869694 971 dbSNP
rs1291407801 973 dbSNP
rs1303193371 981 dbSNP
rs1346130710 983 dbSNP
rs1457052224 986 dbSNP
rs952432084 989 dbSNP
rs73611752 990 dbSNP
rs755701683 996 dbSNP
rs1317077628 1012 dbSNP
rs879458095 1019 dbSNP
rs1469784005 1021 dbSNP
rs1437288446 1022 dbSNP
rs540060498 1023 dbSNP
rs1160571546 1025 dbSNP
rs573044579 1033 dbSNP
rs1408994300 1041 dbSNP
rs1400303487 1044 dbSNP
rs1157068231 1047 dbSNP
rs1396766423 1056 dbSNP
rs1442334469 1063 dbSNP
rs1325821177 1068 dbSNP
rs1369319531 1073 dbSNP
rs190672140 1074 dbSNP
rs1444828879 1076 dbSNP
rs1280434152 1082 dbSNP
rs1373645674 1091 dbSNP
rs972570791 1099 dbSNP
rs1194262082 1117 dbSNP
rs765923024 1130 dbSNP
rs1265745096 1133 dbSNP
rs1455399165 1136 dbSNP
rs762699970 1141 dbSNP
rs1265068992 1146 dbSNP
rs1209049303 1147 dbSNP
rs535813598 1151 dbSNP
rs1233198266 1158 dbSNP
rs960241899 1164 dbSNP
rs1180249701 1188 dbSNP
rs568498428 1197 dbSNP
rs1486294844 1198 dbSNP
rs1164232469 1203 dbSNP
rs556570713 1205 dbSNP
rs1412091779 1207 dbSNP
rs1262719681 1210 dbSNP
rs1329996253 1217 dbSNP
rs980407866 1220 dbSNP
rs1213660633 1225 dbSNP
rs1353150640 1227 dbSNP
rs2733 1233 dbSNP
rs1233380045 1238 dbSNP
rs1292094517 1241 dbSNP
rs535738819 1244 dbSNP
rs1369457027 1245 dbSNP
rs1011001131 1265 dbSNP
rs765686922 1266 dbSNP
rs1031603733 1267 dbSNP
rs1203354214 1273 dbSNP
rs15218 1282 dbSNP
rs115164526 1285 dbSNP
rs1290320039 1286 dbSNP
rs1475619019 1289 dbSNP
rs901321066 1293 dbSNP
rs73611751 1295 dbSNP
rs1476701953 1299 dbSNP
rs1168962884 1306 dbSNP
rs368384878 1309 dbSNP
rs186621934 1313 dbSNP
rs1376935527 1315 dbSNP
rs762056905 1317 dbSNP
rs1436456382 1320 dbSNP
rs1332988963 1321 dbSNP
rs777176288 1322 dbSNP
rs942949266 1323 dbSNP
rs1270685435 1324 dbSNP
rs1363373433 1335 dbSNP
rs374324590 1337 dbSNP
rs1428912944 1341 dbSNP
rs1225910254 1354 dbSNP
rs1282143095 1355 dbSNP
rs1486133858 1362 dbSNP
rs1210412389 1366 dbSNP
rs1254217844 1375 dbSNP
rs889457438 1375 dbSNP
rs1191826713 1381 dbSNP
rs1487990461 1385 dbSNP
rs1373022045 1398 dbSNP
rs1448129799 1401 dbSNP
rs1281066370 1405 dbSNP
rs1213149742 1406 dbSNP
rs35338409 1406 dbSNP
rs1343402798 1408 dbSNP
rs1255931478 1409 dbSNP
rs1399513469 1410 dbSNP
rs1048011735 1411 dbSNP
rs931083930 1412 dbSNP
rs201099481 1421 dbSNP
rs1271986371 1422 dbSNP
rs1353042650 1422 dbSNP
rs1432746752 1422 dbSNP
rs566510389 1422 dbSNP
rs74435910 1422 dbSNP
rs878876092 1422 dbSNP
rs1328625645 1423 dbSNP
rs1205794427 1424 dbSNP
rs972879830 1424 dbSNP
rs1297242339 1427 dbSNP
rs752330982 1427 dbSNP
rs1397809291 1428 dbSNP
rs1339472928 1430 dbSNP
rs1174333184 1434 dbSNP
rs1312916426 1434 dbSNP
rs1375579599 1442 dbSNP
rs2664563 1444 dbSNP
rs1454988695 1452 dbSNP
rs938551200 1460 dbSNP
rs1387243547 1463 dbSNP
rs1455608963 1484 dbSNP
rs1327830454 1490 dbSNP
rs1371532175 1495 dbSNP
rs1386020825 1504 dbSNP
rs1298832061 1509 dbSNP
rs1240003244 1512 dbSNP
rs1337784130 1512 dbSNP
rs1049871 1514 dbSNP
rs1327157604 1518 dbSNP
rs1216160245 1521 dbSNP
rs2664532 1524 dbSNP
rs1274370806 1536 dbSNP
rs1208925504 1542 dbSNP
rs1189876483 1543 dbSNP
rs1253044829 1555 dbSNP
rs1420551660 1557 dbSNP
rs1171986317 1558 dbSNP
rs1182039828 1561 dbSNP
rs1462301497 1567 dbSNP
rs980050190 1569 dbSNP
rs1395129720 1571 dbSNP
rs1457306679 1576 dbSNP
rs1291620766 1579 dbSNP
rs1398328634 1584 dbSNP
rs761101085 1590 dbSNP
rs969926367 1594 dbSNP
rs1374631996 1600 dbSNP
rs1168298684 1612 dbSNP
rs567922169 1613 dbSNP
rs1258489626 1614 dbSNP
rs989456149 1616 dbSNP
rs1190084659 1617 dbSNP
rs1235224359 1618 dbSNP
rs1293945527 1626 dbSNP
rs10567504 1627 dbSNP
rs1219973741 1627 dbSNP
rs1253488306 1627 dbSNP
rs1322759081 1629 dbSNP
rs1481160284 1630 dbSNP
rs1205497350 1632 dbSNP
rs201015788 1632 dbSNP
rs1044975480 1633 dbSNP
rs1189482605 1637 dbSNP
rs775575773 1639 dbSNP
rs754458946 1645 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 PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection ...

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

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 7335.0
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

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

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 HEK293
Disease 7335.0
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 GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 4 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.

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 5 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 ERX177606. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_8 ...

- 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]
Experimental Support 6 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 SRX1760597. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_C ...

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

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 GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUGA
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 GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1065668
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_7
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000371657.5 | 3UTR | ACACAUCACACAAUCACCUUGCUGCUG
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
43 hsa-miR-4445-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT063885 RASSF8 Ras association domain family member 8 2 6
MIRT087576 PTMA prothymosin, alpha 2 8
MIRT092537 KBTBD8 kelch repeat and BTB domain containing 8 2 6
MIRT204613 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 8
MIRT204644 MOB4 MOB family member 4, phocein 2 8
MIRT249009 PUM1 pumilio RNA binding family member 1 2 4
MIRT305656 MBNL1 muscleblind like splicing regulator 1 2 2
MIRT443971 SSH2 slingshot protein phosphatase 2 2 2
MIRT457186 ERC1 ELKS/RAB6-interacting/CAST family member 1 2 2
MIRT463721 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 8
MIRT466974 STARD7 StAR related lipid transfer domain containing 7 2 4
MIRT473413 MDM4 MDM4, p53 regulator 2 2
MIRT484984 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 8
MIRT485021 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 8
MIRT485040 TMEM189 transmembrane protein 189 2 8
MIRT503747 CEP19 centrosomal protein 19 2 6
MIRT505080 ZBTB18 zinc finger and BTB domain containing 18 2 4
MIRT505649 SHMT1 serine hydroxymethyltransferase 1 2 4
MIRT507020 HMGA2 high mobility group AT-hook 2 2 6
MIRT507080 GXYLT1 glucoside xylosyltransferase 1 2 6
MIRT507679 COIL coilin 2 6
MIRT511378 IKZF3 IKAROS family zinc finger 3 2 4
MIRT528246 BMS1 BMS1, ribosome biogenesis factor 2 2
MIRT537033 GREB1 growth regulation by estrogen in breast cancer 1 2 2
MIRT537063 GPR176 G protein-coupled receptor 176 2 2
MIRT540927 OIP5 Opa interacting protein 5 2 2
MIRT544346 SNAP47 synaptosome associated protein 47 2 2
MIRT544749 C8orf33 chromosome 8 open reading frame 33 2 2
MIRT552417 ZNF460 zinc finger protein 460 2 4
MIRT554646 ROBO1 roundabout guidance receptor 1 2 2
MIRT555803 PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 2 2
MIRT557337 HECTD2 HECT domain E3 ubiquitin protein ligase 2 2 2
MIRT563240 QRFPR pyroglutamylated RFamide peptide receptor 2 2
MIRT572692 NCMAP non-compact myelin associated protein 2 2
MIRT607777 HS6ST3 heparan sulfate 6-O-sulfotransferase 3 2 4
MIRT612106 CHRM3 cholinergic receptor muscarinic 3 2 2
MIRT616193 SATB2 SATB homeobox 2 2 2
MIRT627774 RAB30 RAB30, member RAS oncogene family 2 2
MIRT691689 FLOT2 flotillin 2 2 2
MIRT712623 GTF2H5 general transcription factor IIH subunit 5 2 2
MIRT719695 STX6 syntaxin 6 2 2
MIRT723575 SWAP70 SWAP switching B-cell complex subunit 70 2 2
MIRT724077 NCKAP1L NCK associated protein 1 like 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4445 Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-mir-4445 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-4445 Tamoxifen 2733525 NSC180973 approved resistant cell line (MCF7)

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