miRTarBase - #MIRT508846


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pre-miRNA Information
pre-miRNA hsa-mir-4280   
Genomic Coordinates chr5: 87114879 - 87114954
Description Homo sapiens miR-4280 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4280
Sequence 11| GAGUGUAGUUCUGAGCAGAGC |31
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1267452683 6 dbSNP
rs921418201 13 dbSNP
rs975577876 15 dbSNP
rs562687273 20 dbSNP
rs968639930 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
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' cgAGACGAGUCU--U-GAUGUGAg 5'
            |:| :|||||  | :||:||| 
Target 5' gtTTTTTTCAGACTATTTATACTt 3'
 2785 - 2808 129.00 -13.30
2 
miRNA  3' cgaGACGAGUCU-UGAUGUGAg 5'
             :| :| ||: |||::||| 
Target 5' aagTTTTTAAGGTACTGTACTt 3'
 562 - 583 122.00 -10.20
3 
miRNA  3' cgaGACGAGUCUUGAUGUGAg 5'
             |||:  ||  |||:|:| 
Target 5' aggCTGTCAAGCTCTATATTa 3'
 1548 - 1568 122.00 -11.30
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 HEK293
Disease 54499.0
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.

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 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 54499.0
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. 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]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000392129.6 | 3UTR | AUUUUAUAUAUAUAUAUAUAUAUAUAUAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000392129.6 | 3UTR | CUAUUUUAUAUAUAUAUAUAUAUAUAUAUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000392129.6 | 3UTR | AUUUUAUAUAUAUAUAUAUAUAUAUA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
67 hsa-miR-4280 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT065612 DAZAP2 DAZ associated protein 2 2 10
MIRT084985 BACH1 BTB domain and CNC homolog 1 2 2
MIRT088053 UBXN2A UBX domain protein 2A 2 4
MIRT097327 SCAMP1 secretory carrier membrane protein 1 2 2
MIRT099148 MYLIP myosin regulatory light chain interacting protein 2 12
MIRT127042 FAM208B family with sequence similarity 208 member B 2 4
MIRT140479 BNIP2 BCL2 interacting protein 2 2 6
MIRT154889 GNAS GNAS complex locus 2 4
MIRT187983 MBD6 methyl-CpG binding domain protein 6 2 2
MIRT190440 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT240673 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT295049 EVI5L ecotropic viral integration site 5 like 2 2
MIRT324749 ACER2 alkaline ceramidase 2 2 2
MIRT366075 FAM127A retrotransposon Gag like 8C 2 4
MIRT442625 LOX lysyl oxidase 2 2
MIRT445224 TYRP1 tyrosinase related protein 1 2 2
MIRT448967 CCNT2 cyclin T2 2 4
MIRT450137 PFN4 profilin family member 4 2 2
MIRT464350 USP46 ubiquitin specific peptidase 46 2 2
MIRT470460 PPP1R15B protein phosphatase 1 regulatory subunit 15B 2 2
MIRT473691 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT480188 CALM2 calmodulin 2 2 6
MIRT486355 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 2 2
MIRT486708 TROVE2 TROVE domain family member 2 2 4
MIRT488337 SCD stearoyl-CoA desaturase 2 2
MIRT489322 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT491791 ZNF24 zinc finger protein 24 2 2
MIRT491970 USP37 ubiquitin specific peptidase 37 2 2
MIRT492029 TWF1 twinfilin actin binding protein 1 2 4
MIRT492063 TMEM245 transmembrane protein 245 2 2
MIRT492247 SLC39A9 solute carrier family 39 member 9 2 2
MIRT492254 SLC35F5 solute carrier family 35 member F5 2 2
MIRT492592 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT493436 KAT7 lysine acetyltransferase 7 2 2
MIRT493470 IPMK inositol polyphosphate multikinase 2 2
MIRT493639 HECTD1 HECT domain E3 ubiquitin protein ligase 1 2 2
MIRT493919 FAM127B retrotransposon Gag like 8A 2 4
MIRT494639 ARNTL aryl hydrocarbon receptor nuclear translocator like 2 2
MIRT500032 ABCF2 ATP binding cassette subfamily F member 2 2 8
MIRT504589 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide 2 4
MIRT505535 SP4 Sp4 transcription factor 2 6
MIRT507539 DNAJB6 DnaJ heat shock protein family (Hsp40) member B6 2 6
MIRT508846 TMCO1 transmembrane and coiled-coil domains 1 2 4
MIRT510488 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 2
MIRT511402 IFNAR2 interferon alpha and beta receptor subunit 2 2 6
MIRT523252 HIST1H2AH histone cluster 1 H2A family member h 2 2
MIRT525939 C11orf74 chromosome 11 open reading frame 74 2 2
MIRT531453 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT533317 UNKL unkempt family like zinc finger 2 2
MIRT541034 STRBP spermatid perinuclear RNA binding protein 2 8
MIRT546734 RNF217 ring finger protein 217 2 2
MIRT555125 PTPRJ protein tyrosine phosphatase, receptor type J 2 2
MIRT556105 MOAP1 modulator of apoptosis 1 2 2
MIRT560205 AK4 adenylate kinase 4 2 2
MIRT561087 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT566967 LBR lamin B receptor 2 2
MIRT567344 H3F3B H3 histone family member 3B 2 2
MIRT567863 DCAF12 DDB1 and CUL4 associated factor 12 2 2
MIRT574449 SCML2 Scm polycomb group protein like 2 2 2
MIRT575700 Map1b microtubule-associated protein 1B 2 2
MIRT651432 YIPF6 Yip1 domain family member 6 2 2
MIRT659728 CCDC93 coiled-coil domain containing 93 2 2
MIRT686937 SFT2D3 SFT2 domain containing 3 2 2
MIRT699385 SLC30A6 solute carrier family 30 member 6 2 2
MIRT710287 CSNK1G3 casein kinase 1 gamma 3 2 2
MIRT715123 PANK3 pantothenate kinase 3 2 2
MIRT721847 VLDLR very low density lipoprotein receptor 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-4280 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4280 Platinum 23939 resistant tissue
hsa-miR-4280 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4280 Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-4280 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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