miRTarBase - #MIRT644682


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pre-miRNA Information
pre-miRNA hsa-mir-628   
Genomic Coordinates chr15: 55372940 - 55373034
Synonyms MIRN628, hsa-mir-628, MIR628
Description Homo sapiens miR-628 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-628-3p
Sequence 61| UCUAGUAAGAGUGGCAGUCGA |81
Evidence Experimental
Experiments Microarray
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 7 15 - 55372968 29233923 MiREDiBase
A-to-I 8 15 - 55372967 29233923 MiREDiBase
C-to-U 19 15 - 55372956 20591823 MiREDiBase
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26969715 1 COSMIC
COSN30123186 10 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1410255602 2 dbSNP
rs1401315366 3 dbSNP
rs1322836365 4 dbSNP
rs1158103480 8 dbSNP
rs1216611749 11 dbSNP
rs749619551 13 dbSNP
rs778157225 18 dbSNP
rs756600789 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TMCO1   
Synonyms HP10122, PCIA3, PNAS-136, TMCC4
Description transmembrane and coiled-coil domains 1
Transcript NM_019026   
Expression
Putative miRNA Targets on TMCO1
3'UTR of TMCO1
(miRNA target sites are highlighted)		 
>TMCO1|NM_019026|3'UTR
   1 ACTCAAGAACTCTTTATTTTCTATCATTCTTTCTAGACACACACACATCAGACTGGCAACTGTTTTGTAGCAAGAGCCAT
  81 AGGTAGCCTTACTACTTGGGCCTCTTTCTAGTTTTGAATTATTTCTAAGCCTTTTGGGTATGATTAGAGTGAAAATGGCA
 161 GCCAGCAAACTTGATAGTGCTTTTGGTCCTAGATGATTTTTATCAAATAAGTGGATTGATTAGTTAAGTTCAGGTAATGT
 241 TTATGTAATGAAAAACAAATAGCATCCTTCTTGTTTCATTTACATAAGTATTTTCTGTGGGACCGACTCTCAAGGCACTG
 321 TGTATGCCCTGCAAGTTGGCTGTCTATGAGCATTTAGAGATTTAGAAGAAAAATTTAGTTTGTTTAACCCTTGTAACTGT
 401 TTGTTTTGTTGTTGTTTTTTTTTCAAGCCAAATACATGACATAAGATCAATAAAGAGGCCAAATTTTTAGCTGTTTTATG
 481 TACAAGGAGAGATCTGTTTCATTTTGTTTTGCCGTATTTCTAGATATAAGTTTTAGCATGGGCCAGGAAGGACTAAAATA
 561 AAAGTTTTTAAGGTACTGTACTTTTTGCCATACTTGACTCATATACTCAAAATACAGAGTTGTCTTGGTGTAGGAATTGG
 641 AAAGCAAGAGTGGAAAGGAACGTAATAACTCGTTGGAGTTTAAAAATGAGGGTCTTGGCAAGTAACACTGATGTCTGAAA
 721 AAAAATTAAATATAAATAAATAAATAAAAATGAGGGTCCTCAGCTGTTCTCTTCATATCCTATTACAGTCTCTCAGATTC
 801 TTGTGGGGGCACTCTTAGATCTCCCTTGGAGACAAGGTTATAGTTATATGTTGTTAATCTCGCAGAGCTTCCTTTTAGTC
 881 ACAATAGCCTTCATTTTCTGCCATGCCCCTTCATAAGGGAGAAGGATGTTTGTACCATGATCCTCCCCGCATAATCTATG
 961 GAATTAGGAGTCCTGTGTGGAGTCTTATCAATAAATATGCACATTCATCAAATGTCTACTTAAATGTGAGTATTCTACCA
1041 GTGAGAAAAAACACATAATTTTCAAGGTAATCATTGTTAAACCAACAGCAAACTTCTTTCTTATCAGCACCATAAAGTCC
1121 AGAAGACAGTAGAAAAGTATCTTCAAAGTGCTGAGGAAAATAAGTATCAACTTAGAATTTTATGTACAATATTGGAGGCA
1201 AAATAAAGACATGTTTAGACATACAAAACTAAGAGAGTTGAATTATTAAAGGTTATATTCCAAGGACAAAAAAGAGGATC
1281 TGCCCAAGGTGAAGGTATGGCATACAAGAAACAATGGTCAACAGAGAAATAAAATATATGGATGAATATATGGATAAATT
1361 TGAGTGTTTTATGGATTATCTAATTTAAGGATTATCCCAAGACAGCCCTACAAGGTAATTACTGTTCTTACCTTCATTTA
1441 ACAGATGAGGAAACTGGGGCAGGGGAGGTTAGTAACTTGCTCTGCATCACAGAGCTATTGAGTGGCAGTCAGGATTTGAA
1521 TTCAACCAGTGTAAAGCCTAATAGTCCAGGCTGTCAAGCTCTATATTACAGCCTCCTCATGGGTATGTGGTGATTCTCTT
1601 CTCATCCCATCTCCTCAACTAGAGTGTGTGAGCTCTCTAAAGTTGGACTTTGTCTTTTTTTTTGTTCTCCTTATTACAAA
1681 GTAGTCAACGTGGGTGGAAACACAGCAGGAGCTCAATAAAAGCAGATGAAAGGGAACAGAAGTCCCTATTCTGAGACTAG
1761 TTTTATCAGAAGGATGTCTGATAATGGATGGTAATGACTTTTAATGGTCTTTTCTCCATATCATTGACCACTCTAAGCAA
1841 AATAATAATTCGAATGATAATGAAGAAAATGATGCCCATGATAACAATAATGACAAATATGAAATGGCTAAAATAAAACA
1921 TGAAACCATCCTCAAAATTCTGCCATCACCTTTTTAAAGTGAGAATATATAGCACACTCTATCACTCATACCCTGAGGCT
2001 TTGAAGTTGGTGCTTTCTAATCAGACTTCTTATGGACCAGGTTTTCATATACAAATTATGTTTCCATGGTAAGGAATAAA
2081 TAAGAGGGAGAAGTTAAAAAGGAGAGATTACATCTATTCACCCTATTCATTAAAATTTTTTTAAATTTTTTTCCAAATAT
2161 GTTCTGCTTATGTATATTCACTCTATTCTTAAAAGCACAATAACAAAGATATATTACAGAGGAAATAAAACTATCACAAG
2241 AATTAAATTCAAGGAGTTATTAAGGGCTACTGCAGCCTCACAATTAGTTTTTTAAAATTTCTTGTCCTGAAGAAATTTCA
2321 AGACTAGTTATTTGGATGACACTCTAGGTCCACAGCATCACCAGATCATTGGAGATGACATTTCAAGACAGGCCTCTGAA
2401 CATCTCTCATAACACATAATTTGGTTATTTTCCCTATGTAAGATGGATTGTCTCCTGTCTAGGGAAGAAAAACAGCCATT
2481 ACTAATATCTGCATTAGTCTACTCAGGTTGCAATCATAATATGCTAAAGTAGTAAACTTTTAAAAATGACAGTAAACCTG
2561 AGTTTATTAACAGGTTACATTCTAAAAGCTAAGCTAGTTTGGAAATTGGAAAGCAAATGTGTGTAGATATTCATATGTCC
2641 TTGACCAGACTGGGCCTTTCTCTTCCCAGGTAAGTCATTCTCTCCAATGGGGCCAGTTACTTAAAATTACATCAGACAAT
2721 TGATAGAGCTTCTAGATCCCCCTTCTAAAACAAAAGCATTTTGCCACAAACTAGGATGGAGTAGGTTTTTTTCAGACTAT
2801 TTATACTTATTTTATGTATTTCAATACTGCCCTTTAAGTAAAAGTACTATATACTTTCTCTTTTTTTAGATTAATTCTGC
2881 TTAAGTCAGTCTTTTAATTTATTCTAGTTTGAGTTTTTAAAAAATTTTAGAATGAAAAATCTCAAAAATATACTATTATG
2961 TATATACACTATTTTATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGA
3041 GAGAATAAAGAACACCTAGGTAACCCATCCTCCACCTTCGACAATTATCAGCTCCTAGCTAATTTGTGTCATCTGTAACC
3121 CCACCTGCTTCTGCCCTTTCTGTATTATTTTGAAGCAAATCTTATCATTTATCTGTAAATATTTCAGGACTTTAAAAAAT
3201 ATGTGTAATCTGAATACCATTTTTACACCTAAGAAAATGGACAATTCCTTAATATAATGTGTTGTCTATAGATGTCAAAA
3281 ATTTTTGCAGTTTTTTGGAATCAGGAACCAAGTAAGGTACTGAATATTGCAGTTAGCTGATACACATCCTAAATTTCTTC
3361 AATTGTTGTGGTCCTCAAACTAGAGTGTATCAGAATCACTAGAGCCTTGTTAGAACACAAACTGCTGGGCCCCACCCCAG
3441 AGCTGGTGATCTGTAAGTCTGCTGTGGAGTCTGGGAATTTGCATCTCTAACAAATTCCCAGGTGATGCTGAAGCTGCAGG
3521 TTTGGGGTTCACTCACCTATTGGTTCATCAGCATCTCTCTGCCCTCTTACAATATATTTGTTGAAGAAGTTGTGTTGTTT
3601 ACCTTGTAGAGTTTTTCTTAGTTTGGATTTTGGTGATAGCATGCTGGTTTTTTCATACTATTGGTTGTCTCTGTAATGCG
3681 AGCAGCTTTTGATCTATTAATTAATGAGATATTAAAAGTGATGGTATTCTAAAAAAAAAA
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' agcuGACGGUGAGAAUGAUCu 5'
              || :||:|||| |||| 
Target 5' ttttCTATCATTCTTTCTAGa 3'
 17 - 37 137.00 -16.10
2 
miRNA  3' agcUGACGGUGAGAAUGAUcu 5'
             || ||||   ||||||  
Target 5' aaaACAGCCA---TTACTAat 3'
 2469 - 2486 135.00 -6.90
3 
miRNA  3' agcUGACGGUGAGAAUGAUcu 5'
             |: | :|  |||||||  
Target 5' gccATAGGTAGCCTTACTAct 3'
 76 - 96 130.00 -7.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30544640 4 COSMIC
COSN6006730 5 COSMIC
COSN30515880 7 COSMIC
COSN31569497 7 COSMIC
COSN30186266 36 COSMIC
COSN30522842 46 COSMIC
COSN31492066 59 COSMIC
COSN30151912 74 COSMIC
COSN30496159 104 COSMIC
COSN31557707 146 COSMIC
COSN20095532 414 COSMIC
COSN14456471 514 COSMIC
COSN30375091 541 COSMIC
COSN25975020 717 COSMIC
COSN16186480 758 COSMIC
COSN29400361 919 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs928077940 2 dbSNP
rs758217263 4 dbSNP
rs752091077 7 dbSNP
rs1322833861 16 dbSNP
rs1438820020 21 dbSNP
rs765006399 23 dbSNP
rs1291895059 25 dbSNP
rs1450871075 27 dbSNP
rs757302422 39 dbSNP
rs1435743269 40 dbSNP
rs1299717547 45 dbSNP
rs753789740 47 dbSNP
rs1182003791 49 dbSNP
rs764294913 53 dbSNP
rs760783276 62 dbSNP
rs1165063517 70 dbSNP
rs950859904 76 dbSNP
rs1264354740 80 dbSNP
rs200627818 80 dbSNP
rs1189839242 81 dbSNP
rs1250438778 82 dbSNP
rs1448085809 87 dbSNP
rs767694399 88 dbSNP
rs563828358 95 dbSNP
rs1026918963 96 dbSNP
rs1414931253 98 dbSNP
rs973644613 102 dbSNP
rs1446002513 107 dbSNP
rs769785900 108 dbSNP
rs1407303403 114 dbSNP
rs771251066 116 dbSNP
rs748108266 120 dbSNP
rs1349434446 121 dbSNP
rs763480887 132 dbSNP
rs1244355082 136 dbSNP
rs1344794753 140 dbSNP
rs1298707424 141 dbSNP
rs1017266869 144 dbSNP
rs1434212287 149 dbSNP
rs1049739628 150 dbSNP
rs1380980832 151 dbSNP
rs773659118 156 dbSNP
rs1221172134 159 dbSNP
rs890194840 163 dbSNP
rs768167494 173 dbSNP
rs780739996 175 dbSNP
rs1030056269 176 dbSNP
rs746437636 181 dbSNP
rs1390050155 189 dbSNP
rs1210021122 191 dbSNP
rs1302511415 204 dbSNP
rs1422601150 206 dbSNP
rs998623406 207 dbSNP
rs779602323 211 dbSNP
rs1474914928 216 dbSNP
rs543955118 222 dbSNP
rs776087665 242 dbSNP
rs578139014 244 dbSNP
rs778606117 245 dbSNP
rs558227875 257 dbSNP
rs1473971212 259 dbSNP
rs1445487808 263 dbSNP
rs543396419 269 dbSNP
rs947318397 271 dbSNP
rs73020510 284 dbSNP
rs1334335983 288 dbSNP
rs1484316001 289 dbSNP
rs1055032503 290 dbSNP
rs988960185 298 dbSNP
rs1456641509 301 dbSNP
rs772651000 304 dbSNP
rs749255085 305 dbSNP
rs577576640 306 dbSNP
rs1445535996 307 dbSNP
rs182144516 312 dbSNP
rs1350702099 315 dbSNP
rs1229809443 316 dbSNP
rs1276856631 318 dbSNP
rs756121402 319 dbSNP
rs752773603 320 dbSNP
rs79658899 321 dbSNP
rs1472658902 322 dbSNP
rs1403087088 324 dbSNP
rs1279951637 327 dbSNP
rs1444537850 328 dbSNP
rs755191842 331 dbSNP
rs1208436491 335 dbSNP
rs919423128 338 dbSNP
rs1329335896 340 dbSNP
rs1409128621 342 dbSNP
rs756804431 345 dbSNP
rs1174000256 350 dbSNP
rs115026771 351 dbSNP
rs1409862063 363 dbSNP
rs1428003170 374 dbSNP
rs1196647963 375 dbSNP
rs1473882108 378 dbSNP
rs995474539 381 dbSNP
rs1181658997 383 dbSNP
rs567512207 389 dbSNP
rs896970928 390 dbSNP
rs1036895880 392 dbSNP
rs557385473 393 dbSNP
rs1201263188 397 dbSNP
rs1370869126 398 dbSNP
rs1323077158 399 dbSNP
rs1261412043 404 dbSNP
rs1230265671 405 dbSNP
rs754512890 407 dbSNP
rs891229302 414 dbSNP
rs1436540682 415 dbSNP
rs986393261 415 dbSNP
rs79111961 417 dbSNP
rs932663408 417 dbSNP
rs1441341646 423 dbSNP
rs1044368372 424 dbSNP
rs35952900 424 dbSNP
rs534432920 424 dbSNP
rs191912742 434 dbSNP
rs76436126 436 dbSNP
rs992363781 437 dbSNP
rs959755958 441 dbSNP
rs773712375 448 dbSNP
rs1331355033 451 dbSNP
rs1173698952 462 dbSNP
rs1308997790 473 dbSNP
rs868550057 474 dbSNP
rs181922339 478 dbSNP
rs1063701 483 dbSNP
rs138477165 484 dbSNP
rs1063702 486 dbSNP
rs753514301 491 dbSNP
rs1412015150 501 dbSNP
rs555126901 506 dbSNP
rs1469004623 512 dbSNP
rs762360286 513 dbSNP
rs559909961 514 dbSNP
rs1461068621 515 dbSNP
rs1241500510 527 dbSNP
rs1405544533 530 dbSNP
rs1324992732 533 dbSNP
rs1328781171 538 dbSNP
rs1210767975 546 dbSNP
rs549352625 549 dbSNP
rs1283567502 553 dbSNP
rs73020508 555 dbSNP
rs894381288 557 dbSNP
rs1285775689 560 dbSNP
rs1231031708 561 dbSNP
rs1246414927 562 dbSNP
rs1272812949 569 dbSNP
rs1381710071 575 dbSNP
rs1055610208 576 dbSNP
rs1436747592 582 dbSNP
rs1210616967 583 dbSNP
rs1345289125 589 dbSNP
rs1317007325 590 dbSNP
rs1002766601 599 dbSNP
rs1416545790 600 dbSNP
rs771568850 601 dbSNP
rs752374783 602 dbSNP
rs1444417094 606 dbSNP
rs1451157875 607 dbSNP
rs1383726534 608 dbSNP
rs1186473281 615 dbSNP
rs73020507 617 dbSNP
rs1319515196 620 dbSNP
rs73020504 625 dbSNP
rs1241655292 628 dbSNP
rs1213695759 631 dbSNP
rs1390226215 634 dbSNP
rs1388017544 636 dbSNP
rs929401881 651 dbSNP
rs187994736 652 dbSNP
rs770851535 655 dbSNP
rs1246573836 657 dbSNP
rs919358636 661 dbSNP
rs1312578735 662 dbSNP
rs1015818310 665 dbSNP
rs1293914567 669 dbSNP
rs1008074996 671 dbSNP
rs183635612 672 dbSNP
rs942163167 674 dbSNP
rs1428010605 676 dbSNP
rs1286173449 677 dbSNP
rs910740883 681 dbSNP
rs777702511 683 dbSNP
rs1268803777 684 dbSNP
rs1424510373 688 dbSNP
rs954949762 691 dbSNP
rs1364114887 698 dbSNP
rs1170858963 701 dbSNP
rs1429405981 702 dbSNP
rs1419048336 704 dbSNP
rs1183942164 706 dbSNP
rs1184954739 711 dbSNP
rs1448089164 712 dbSNP
rs756172964 713 dbSNP
rs758079005 714 dbSNP
rs996925477 715 dbSNP
rs754137018 725 dbSNP
rs1490163556 726 dbSNP
rs922924748 726 dbSNP
rs535317975 731 dbSNP
rs1206999125 732 dbSNP
rs1307761038 733 dbSNP
rs1271876974 736 dbSNP
rs967136928 745 dbSNP
rs569927853 749 dbSNP
rs1263763704 750 dbSNP
rs1413477981 756 dbSNP
rs945603762 758 dbSNP
rs74121417 759 dbSNP
rs1057007984 761 dbSNP
rs181198069 766 dbSNP
rs754972149 768 dbSNP
rs958763147 781 dbSNP
rs1310293861 783 dbSNP
rs939500147 786 dbSNP
rs1232862915 789 dbSNP
rs1289073993 791 dbSNP
rs1462835667 803 dbSNP
rs1331248202 805 dbSNP
rs1354269830 810 dbSNP
rs926815963 812 dbSNP
rs1416328552 814 dbSNP
rs755039219 815 dbSNP
rs1034150870 821 dbSNP
rs751745016 822 dbSNP
rs1483475787 825 dbSNP
rs1266654522 831 dbSNP
rs1178826823 834 dbSNP
rs549844361 840 dbSNP
rs773264677 844 dbSNP
rs1250482175 846 dbSNP
rs1202021279 847 dbSNP
rs919566831 849 dbSNP
rs1313575464 854 dbSNP
rs1263293098 861 dbSNP
rs1002735443 862 dbSNP
rs1320738568 865 dbSNP
rs1290789069 866 dbSNP
rs1392412456 867 dbSNP
rs973783511 872 dbSNP
rs766523316 876 dbSNP
rs1157608848 877 dbSNP
rs961560658 878 dbSNP
rs73018602 881 dbSNP
rs1407076512 883 dbSNP
rs1174715167 884 dbSNP
rs1414414129 885 dbSNP
rs1175859839 888 dbSNP
rs986557609 903 dbSNP
rs1468315566 913 dbSNP
rs114582888 916 dbSNP
rs1161203525 917 dbSNP
rs1363722911 920 dbSNP
rs573602271 921 dbSNP
rs1306259006 922 dbSNP
rs1419538427 923 dbSNP
rs771834094 925 dbSNP
rs1175260986 926 dbSNP
rs1291278226 928 dbSNP
rs1462407695 935 dbSNP
rs1243350181 936 dbSNP
rs150123019 937 dbSNP
rs1205514122 940 dbSNP
rs1459597808 941 dbSNP
rs1350944909 942 dbSNP
rs530893448 948 dbSNP
rs750835389 949 dbSNP
rs1240463219 950 dbSNP
rs1316843318 951 dbSNP
rs142042113 954 dbSNP
rs1434264980 958 dbSNP
rs1230369343 959 dbSNP
rs1383923760 961 dbSNP
rs1169390058 966 dbSNP
rs1336352883 972 dbSNP
rs1038166449 973 dbSNP
rs1450634851 974 dbSNP
rs1434479908 975 dbSNP
rs942129560 977 dbSNP
rs1289508750 979 dbSNP
rs1454306124 988 dbSNP
rs571582788 998 dbSNP
rs1022695622 1001 dbSNP
rs1156728251 1011 dbSNP
rs557959121 1012 dbSNP
rs762257158 1020 dbSNP
rs777145260 1026 dbSNP
rs892679745 1027 dbSNP
rs1459690857 1030 dbSNP
rs1050618261 1031 dbSNP
rs571552376 1037 dbSNP
rs1485857678 1039 dbSNP
rs1247167874 1048 dbSNP
rs1259510695 1052 dbSNP
rs1225313643 1053 dbSNP
rs1339731105 1056 dbSNP
rs1360617205 1056 dbSNP
rs1273648969 1061 dbSNP
rs1314727426 1064 dbSNP
rs1244126698 1065 dbSNP
rs1328420000 1066 dbSNP
rs1296433380 1073 dbSNP
rs1056713135 1075 dbSNP
rs1276450478 1076 dbSNP
rs1381697389 1078 dbSNP
rs1305442496 1084 dbSNP
rs939615999 1093 dbSNP
rs1287053519 1094 dbSNP
rs756603565 1098 dbSNP
rs1265530887 1099 dbSNP
rs766948013 1102 dbSNP
rs1162693308 1103 dbSNP
rs1489169243 1103 dbSNP
rs1216166740 1104 dbSNP
rs1442441166 1107 dbSNP
rs1251642885 1108 dbSNP
rs761772681 1112 dbSNP
rs1374417657 1114 dbSNP
rs905346107 1115 dbSNP
rs1193397290 1131 dbSNP
rs1427435308 1135 dbSNP
rs1189630566 1137 dbSNP
rs923541868 1138 dbSNP
rs1045279710 1140 dbSNP
rs1426963446 1142 dbSNP
rs1490651573 1144 dbSNP
rs1291590452 1145 dbSNP
rs542495841 1148 dbSNP
rs919698436 1149 dbSNP
rs1323867282 1160 dbSNP
rs1393672343 1161 dbSNP
rs1252131036 1163 dbSNP
rs776946693 1164 dbSNP
rs770761621 1166 dbSNP
rs1285259762 1170 dbSNP
rs974113120 1171 dbSNP
rs190014309 1180 dbSNP
rs1346039652 1183 dbSNP
rs1312986715 1187 dbSNP
rs1302368268 1191 dbSNP
rs1323037651 1202 dbSNP
rs1422542413 1206 dbSNP
rs1398316984 1209 dbSNP
rs945676011 1210 dbSNP
rs1271929087 1212 dbSNP
rs773184926 1214 dbSNP
rs1461117118 1221 dbSNP
rs939705364 1224 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000392129.6 | 3UTR | ACUAGAGAGGCUGAGGCAGGAGAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000392129.6 | 3UTR | ACUAGAGAGGCUGAGGCAGGAGAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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 0.62 6.2e-4 0.624 5.6e-4 24 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis 0.629 1.5e-3 0.668 6.4e-4 20 Click to see details
GSE19536 Breast cancer 0.264 4.0e-3 0.243 7.4e-3 100 Click to see details
GSE32688 Pancreatic cancer -0.458 4.2e-3 -0.475 3.0e-3 32 Click to see details
GSE19783 ER- ER- breast cancer 0.282 5.9e-3 0.253 1.2e-2 79 Click to see details
GSE19783 ER+ ER+ breast cancer 0.522 9.1e-3 0.537 7.3e-3 20 Click to see details
GSE14794 Lymphoblastoid cells 0.248 9.2e-3 0.217 2.0e-2 90 Click to see details
GSE42095 Differentiated embryonic stem cells 0.484 9.6e-3 0.362 4.5e-2 23 Click to see details
GSE28260 Renal cortex and medulla -0.608 1.4e-2 -0.500 4.1e-2 13 Click to see details
GSE21687 Ependynoma primary tumors -0.193 6.3e-2 -0.155 1.1e-1 64 Click to see details
GSE19350 CNS germ cell tumors -0.413 9.1e-2 -0.483 5.6e-2 12 Click to see details
GSE26953 Aortic valvular endothelial cells -0.246 1.2e-1 -0.366 3.9e-2 24 Click to see details
GSE38974 Chronic obstructive pulmonary disease 0.176 2.0e-1 0.227 1.4e-1 25 Click to see details
GSE38226 Liver fibrosis -0.168 2.3e-1 -0.059 4.0e-1 21 Click to see details
GSE27834 Pluripotent stem cells -0.174 2.6e-1 0.062 4.1e-1 16 Click to see details
GSE17498 Multiple myeloma 0.082 3.1e-1 0.046 3.9e-1 40 Click to see details
GSE21849 B cell lymphoma 0.088 3.2e-1 0.108 2.9e-1 29 Click to see details
GSE17306 Multiple myeloma -0.005 4.9e-1 0.087 2.8e-1 49 Click to see details
GSE17306 Multiple myeloma -0.005 4.9e-1 0.087 2.8e-1 49 Click to see details
GSE17306 Multiple myeloma -0.005 4.9e-1 0.087 2.8e-1 49 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
LIHC -0.3 0.02 -0.299 0.02 49 Click to see details
KIRC 0.306 0.03 0.331 0.02 40 Click to see details
LUAD 0.526 0.06 0.721 0.01 10 Click to see details
STAD 0.301 0.06 0.360 0.03 28 Click to see details
KIRP 0.283 0.07 0.292 0.06 29 Click to see details
CHOL 0.557 0.1 0.571 0.09 7 Click to see details
BLCA 0.227 0.19 0.211 0.21 17 Click to see details
KICH 0.194 0.19 0.194 0.19 22 Click to see details
ESCA 0.269 0.21 0.155 0.32 11 Click to see details
PAAD -0.547 0.23 -0.400 0.3 4 Click to see details
PCPG -0.596 0.3 -0.500 0.33 3 Click to see details
UCEC 0.122 0.31 -0.032 0.45 18 Click to see details
LUSC -0.078 0.33 -0.056 0.37 35 Click to see details
BRCA 0.067 0.35 0.063 0.36 34 Click to see details
THCA 0.049 0.36 0.065 0.31 58 Click to see details
CESC 0.227 0.43 0.500 0.33 3 Click to see details
HNSC 0.012 0.47 0.041 0.41 35 Click to see details
PRAD 0.001 0.5 0.036 0.42 36 Click to see details
PRAD 0.001 0.5 0.036 0.42 36 Click to see details
27 hsa-miR-628-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT039584 CDC14A cell division cycle 14A 1 1
MIRT039585 AGO1 argonaute 1, RISC catalytic component 2 3
MIRT039586 TGFBRAP1 transforming growth factor beta receptor associated protein 1 1 1
MIRT039587 LRP6 LDL receptor related protein 6 1 1
MIRT071876 BTF3L4 basic transcription factor 3 like 4 2 2
MIRT097443 JMY junction mediating and regulatory protein, p53 cofactor 2 4
MIRT100100 ABT1 activator of basal transcription 1 2 8
MIRT147692 CBX4 chromobox 4 2 2
MIRT408248 PURA purine rich element binding protein A 2 2
MIRT442047 LRAT lecithin retinol acyltransferase 2 2
MIRT444412 RAB3IP RAB3A interacting protein 2 2
MIRT452599 REPIN1 replication initiator 1 2 2
MIRT469515 RBFOX2 RNA binding protein, fox-1 homolog 2 2 8
MIRT498192 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT500151 CREBBP CREB binding protein 2 2
MIRT507319 FAM60A SIN3-HDAC complex associated factor 2 6
MIRT508343 ZNF273 zinc finger protein 273 2 6
MIRT520480 TRIM13 tripartite motif containing 13 2 2
MIRT522461 MMP16 matrix metallopeptidase 16 2 4
MIRT547116 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 2 2
MIRT548675 CRNKL1 crooked neck pre-mRNA splicing factor 1 2 2
MIRT553756 TARBP2 TARBP2, RISC loading complex RNA binding subunit 2 4
MIRT559437 ARSJ arylsulfatase family member J 2 2
MIRT610490 GPC4 glypican 4 2 2
MIRT644682 TMCO1 transmembrane and coiled-coil domains 1 2 2
MIRT658214 FBXO21 F-box protein 21 2 2
MIRT756083 TP53 tumor protein p53 4 1
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-628 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved resistant High Tongue Squamous Cell Carcinoma cell line (Tca8113)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (MCF-7, LY2)
hsa-miR-628-3p Erlotinib 176870 NSC718781 approved sensitive High Epithelial Cancer cell line (A549, UKY-29, H460, H1975, H1650, H3255, PC-9, H358)
hsa-miR-628-3p Siop Treatment Protocol sensitive High Nephroblastoma tissue
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant High Metastatic Renal Cell Carcinoma tissue and cell line (Caki-2)
hsa-miR-628-3p Chemotherapy sensitive High Epithelial Ovarian Cancer tissue
hsa-miR-628-3p Platinum-based doublet chemotherapy resistant Low Lung Adenocarcinoma tissue
hsa-miR-628-3p Doxorubicin 31703 NSC123127 approved sensitive High Gastric Cancer cell line (SGC7901)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (TAMR8)
hsa-miR-628-3p Aromatase Inhibitor sensitive Low Breast Cancer cell line (MCF-7)
hsa-miR-628-3p Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-628-3p Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-628-3p Platinum 23939 sensitive High High-Grade Serous Ovarian Cancer tissue
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive High Bladder Cancer cell line (CDDP-R-BOY, CDDP-R-T24)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-628-3p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-628-3p Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-628-3p Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-628-3p Tamoxifen 2733525 NSC180973 approved resistant cell line (TamR8)
hsa-miR-628-3p Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-628-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-628-3p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-628-3p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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