miRTarBase - #MIRT260646


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pre-miRNA Information
pre-miRNA hsa-mir-4778   
Genomic Coordinates chr2: 66358249 - 66358328
Description Homo sapiens miR-4778 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4778-3p
Sequence 51| UCUUCUUCCUUUGCAGAGUUGA |72
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs936001904 2 dbSNP
rs925922703 3 dbSNP
rs184768286 8 dbSNP
rs1249073833 10 dbSNP
rs977504360 13 dbSNP
rs192300002 18 dbSNP
Putative Targets

Gene Information
Gene Symbol CDKN1A   
Synonyms CAP20, CDKN1, CIP1, MDA-6, P21, SDI1, WAF1, p21CIP1
Description cyclin dependent kinase inhibitor 1A
Transcript NM_000389   
Other Transcripts NM_078467   
Expression
Putative miRNA Targets on CDKN1A
3'UTR of CDKN1A
(miRNA target sites are highlighted)		 
>CDKN1A|NM_000389|3'UTR
   1 TCCGCCCACAGGAAGCCTGCAGTCCTGGAAGCGCGAGGGCCTCAAAGGCCCGCTCTACATCTTCTGCCTTAGTCTCAGTT
  81 TGTGTGTCTTAATTATTATTTGTGTTTTAATTTAAACACCTCCTCATGTACATACCCTGGCCGCCCCCTGCCCCCCAGCC
 161 TCTGGCATTAGAATTATTTAAACAAAAACTAGGCGGTTGAATGAGAGGTTCCTAAGAGTGCTGGGCATTTTTATTTTATG
 241 AAATACTATTTAAAGCCTCCTCATCCCGTGTTCTCCTTTTCCTCTCTCCCGGAGGTTGGGTGGGCCGGCTTCATGCCAGC
 321 TACTTCCTCCTCCCCACTTGTCCGCTGGGTGGTACCCTCTGGAGGGGTGTGGCTCCTTCCCATCGCTGTCACAGGCGGTT
 401 ATGAAATTCACCCCCTTTCCTGGACACTCAGACCTGAATTCTTTTTCATTTGAGAAGTAAACAGATGGCACTTTGAAGGG
 481 GCCTCACCGAGTGGGGGCATCATCAAAAACTTTGGAGTCCCCTCACCTCCTCTAAGGTTGGGCAGGGTGACCCTGAAGTG
 561 AGCACAGCCTAGGGCTGAGCTGGGGACCTGGTACCCTCCTGGCTCTTGATACCCCCCTCTGTCTTGTGAAGGCAGGGGGA
 641 AGGTGGGGTCCTGGAGCAGACCACCCCGCCTGCCCTCATGGCCCCTCTGACCTGCACTGGGGAGCCCGTCTCAGTGTTGA
 721 GCCTTTTCCCTCTTTGGCTCCCCTGTACCTTTTGAGGAGCCCCAGCTACCCTTCTTCTCCAGCTGGGCTCTGCAATTCCC
 801 CTCTGCTGCTGTCCCTCCCCCTTGTCCTTTCCCTTCAGTACCCTCTCAGCTCCAGGTGGCTCTGAGGTGCCTGTCCCACC
 881 CCCACCCCCAGCTCAATGGACTGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCTAGTTCTACCTCAGGCAGCTCAA
 961 GCAGCGACCGCCCCCTCCTCTAGCTGTGGGGGTGAGGGTCCCATGTGGTGGCACAGGCCCCCTTGAGTGGGGTTATCTCT
1041 GTGTTAGGGGTATATGATGGGGGAGTAGATCTTTCTAGGAGGGAGACACTGGCCCCTCAAATCGTCCAGCGACCTTCCTC
1121 ATCCACCCCATCCCTCCCCAGTTCATTGCACTTTGATTAGCAGCGGAACAAGGAGTCAGACATTTTAAGATGGTGGCAGT
1201 AGAGGCTATGGACAGGGCATGCCACGTGGGCTCATATGGGGCTGGGAGTAGTTGTCTTTCCTGGCACTAACGTTGAGCCC
1281 CTGGAGGCACTGAAGTGCTTAGTGTACTTGGAGTATTGGGGTCTGACCCCAAACACCTTCCAGCTCCTGTAACATACTGG
1361 CCTGGACTGTTTTCTCTCGGCTCCCCATGTGTCCTGGTTCCCGTTTCTCCACCTAGACTGTAAACCTCTCGAGGGCAGGG
1441 ACCACACCCTGTACTGTTCTGTGTCTTTCACAGCTCCTCCCACAATGCTGAATATACAGCAGGTGCTCAATAAATGATTC
1521 TTAGTGACTTTACTTGTAAAAAAAAAAAAAAAAAA
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' aguugagacGUUUCCUUCUUCu 5'
                   || | ||||||| 
Target 5' gaagggacaCACAAGAAGAAGg 3'
 910 - 931 149.00 -9.10
2 
miRNA  3' aguUGAGA-----CGUUUCCUUCUUCu 5'
             |||:|     |||: |||| ||| 
Target 5' tgcACTTTGATTAGCAGCGGAACAAGg 3'
 1147 - 1173 131.00 -11.70
3 
miRNA  3' agUUGAGACGUUUCCUUCUUCu 5'
            |: ||| :  ||||:|:|| 
Target 5' gtAGATCTTTCTAGGAGGGAGa 3'
 1065 - 1086 128.00 -15.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN8871647 4 COSMIC
COSN30107428 13 COSMIC
COSN17136499 21 COSMIC
COSN24388178 36 COSMIC
COSN30512604 38 COSMIC
COSN26970192 40 COSMIC
COSN30166588 65 COSMIC
COSN24301745 80 COSMIC
COSN30488608 90 COSMIC
COSN30469357 137 COSMIC
COSN30533369 148 COSMIC
COSN32056942 195 COSMIC
COSN17181950 363 COSMIC
COSN21122568 516 COSMIC
COSN8514252 516 COSMIC
COSN20590362 520 COSMIC
COSN26644634 575 COSMIC
COSN32057748 625 COSMIC
COSN31576773 708 COSMIC
COSN15779126 787 COSMIC
COSN28791109 848 COSMIC
COSN8514253 848 COSMIC
COSN26566755 989 COSMIC
COSN31541982 1111 COSMIC
COSN31595516 1138 COSMIC
COSN9781735 1206 COSMIC
COSN21510222 1432 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs139304346 4 dbSNP
rs747014318 5 dbSNP
rs1184573689 9 dbSNP
rs1396765368 11 dbSNP
rs1445659229 11 dbSNP
rs777207887 12 dbSNP
rs1376040331 15 dbSNP
rs1226999329 17 dbSNP
rs1059234 21 dbSNP
rs770267002 22 dbSNP
rs775069456 23 dbSNP
rs945802868 24 dbSNP
rs1475096701 28 dbSNP
rs762632530 29 dbSNP
rs201408395 32 dbSNP
rs375173291 33 dbSNP
rs41272170 34 dbSNP
rs1482370511 35 dbSNP
rs150869821 36 dbSNP
rs3176357 39 dbSNP
rs754567385 40 dbSNP
rs1166992411 41 dbSNP
rs755968076 44 dbSNP
rs1423988118 48 dbSNP
rs111926164 52 dbSNP
rs575815855 53 dbSNP
rs998171288 56 dbSNP
rs1028124783 57 dbSNP
rs952159534 59 dbSNP
rs983400213 67 dbSNP
rs907923458 69 dbSNP
rs760541872 75 dbSNP
rs1428687704 80 dbSNP
rs976707693 105 dbSNP
rs1451995360 114 dbSNP
rs951389423 117 dbSNP
rs763632708 118 dbSNP
rs1394250512 125 dbSNP
rs1322653551 126 dbSNP
rs779826646 133 dbSNP
rs922225207 136 dbSNP
rs187742871 137 dbSNP
rs914304254 138 dbSNP
rs1443635232 139 dbSNP
rs564494785 143 dbSNP
rs112675295 144 dbSNP
rs1041396487 145 dbSNP
rs1317251949 152 dbSNP
rs1210788045 155 dbSNP
rs1489707452 157 dbSNP
rs866686724 158 dbSNP
rs1245438449 163 dbSNP
rs1343160898 179 dbSNP
rs546659289 182 dbSNP
rs756718995 195 dbSNP
rs191431994 196 dbSNP
rs529170426 208 dbSNP
rs755706954 209 dbSNP
rs1056094900 222 dbSNP
rs960959039 226 dbSNP
rs1301078579 240 dbSNP
rs1423551932 245 dbSNP
rs1370821103 248 dbSNP
rs543585485 249 dbSNP
rs114982296 258 dbSNP
rs778242620 260 dbSNP
rs781689614 268 dbSNP
rs1372999209 283 dbSNP
rs41272172 284 dbSNP
rs1043234187 287 dbSNP
rs1483485414 291 dbSNP
rs925724850 291 dbSNP
rs1277091698 292 dbSNP
rs796185918 297 dbSNP
rs184374036 305 dbSNP
rs1039501629 307 dbSNP
rs1275518074 308 dbSNP
rs1387758636 311 dbSNP
rs539152524 313 dbSNP
rs1233808733 315 dbSNP
rs1347344575 321 dbSNP
rs866398753 327 dbSNP
rs189270770 330 dbSNP
rs566360271 333 dbSNP
rs1370764937 336 dbSNP
rs1046926038 344 dbSNP
rs1374607192 345 dbSNP
rs1407714364 352 dbSNP
rs377595930 355 dbSNP
rs887116254 358 dbSNP
rs181350370 377 dbSNP
rs1017456404 381 dbSNP
rs1302198995 385 dbSNP
rs3176358 386 dbSNP
rs1002260135 397 dbSNP
rs373590939 397 dbSNP
rs1454501485 398 dbSNP
rs1338842504 412 dbSNP
rs1363084136 416 dbSNP
rs866383890 416 dbSNP
rs976121091 430 dbSNP
rs1179838684 434 dbSNP
rs1296509107 440 dbSNP
rs575126168 442 dbSNP
rs1035203096 443 dbSNP
rs535732427 444 dbSNP
rs1309634071 451 dbSNP
rs960823517 458 dbSNP
rs922162572 467 dbSNP
rs1261233743 476 dbSNP
rs953675606 478 dbSNP
rs532581570 482 dbSNP
rs1281079083 488 dbSNP
rs777824384 489 dbSNP
rs879879447 493 dbSNP
rs1245700146 494 dbSNP
rs749588003 497 dbSNP
rs879309299 498 dbSNP
rs1176417316 499 dbSNP
rs1458233139 501 dbSNP
rs1410545818 513 dbSNP
rs557591236 514 dbSNP
rs1469781325 526 dbSNP
rs1238310449 527 dbSNP
rs914777007 529 dbSNP
rs978433655 530 dbSNP
rs1439329339 532 dbSNP
rs925725564 533 dbSNP
rs942480428 537 dbSNP
rs1039405016 541 dbSNP
rs575878563 545 dbSNP
rs1186756151 547 dbSNP
rs572991639 548 dbSNP
rs1241195720 553 dbSNP
rs946204604 587 dbSNP
rs1431092774 592 dbSNP
rs541799707 606 dbSNP
rs1286032990 612 dbSNP
rs1221894791 613 dbSNP
rs922442057 615 dbSNP
rs933792625 616 dbSNP
rs546335483 618 dbSNP
rs1047001332 625 dbSNP
rs1055493853 632 dbSNP
rs894366694 638 dbSNP
rs367706888 640 dbSNP
rs995702977 642 dbSNP
rs1316639627 646 dbSNP
rs1400543397 648 dbSNP
rs1414782201 651 dbSNP
rs184742749 655 dbSNP
rs941387040 656 dbSNP
rs1048397424 664 dbSNP
rs370572240 665 dbSNP
rs189202045 668 dbSNP
rs757862523 669 dbSNP
rs1289515919 683 dbSNP
rs540666701 692 dbSNP
rs1213364316 693 dbSNP
rs1446277683 700 dbSNP
rs1292232768 702 dbSNP
rs1247641087 708 dbSNP
rs774512258 709 dbSNP
rs1364417768 711 dbSNP
rs1004007357 717 dbSNP
rs1268992201 723 dbSNP
rs1014932119 733 dbSNP
rs1350764432 737 dbSNP
rs1305357860 741 dbSNP
rs1002289641 742 dbSNP
rs1365225649 743 dbSNP
rs1346497851 750 dbSNP
rs1225909893 754 dbSNP
rs1035067351 755 dbSNP
rs1169270853 760 dbSNP
rs997905489 770 dbSNP
rs1266718439 772 dbSNP
rs6457937 775 dbSNP
rs1269272527 778 dbSNP
rs529198430 781 dbSNP
rs990366166 796 dbSNP
rs544057426 812 dbSNP
rs1009737725 815 dbSNP
rs1021650885 821 dbSNP
rs968318210 822 dbSNP
rs1292832469 834 dbSNP
rs562367477 841 dbSNP
rs1214437185 843 dbSNP
rs139090547 846 dbSNP
rs967514962 851 dbSNP
rs980065929 853 dbSNP
rs1345101601 858 dbSNP
rs181534480 870 dbSNP
rs551145694 874 dbSNP
rs566590564 877 dbSNP
rs186592256 880 dbSNP
rs10046116 885 dbSNP
rs548971366 897 dbSNP
rs1401216744 907 dbSNP
rs567103693 914 dbSNP
rs772094412 918 dbSNP
rs991560468 919 dbSNP
rs1479367670 922 dbSNP
rs933848673 943 dbSNP
rs74801436 948 dbSNP
rs908342499 966 dbSNP
rs557652835 970 dbSNP
rs1203248566 971 dbSNP
rs1324860987 972 dbSNP
rs1265599057 987 dbSNP
rs1346545037 991 dbSNP
rs1323184962 998 dbSNP
rs1308173710 1008 dbSNP
rs1393307997 1013 dbSNP
rs1059247 1023 dbSNP
rs1486210553 1028 dbSNP
rs191000568 1031 dbSNP
rs1286834345 1032 dbSNP
rs1448911279 1043 dbSNP
rs1038653449 1049 dbSNP
rs1178582184 1050 dbSNP
rs375384268 1051 dbSNP
rs939842159 1055 dbSNP
rs1373329428 1061 dbSNP
rs1040878666 1067 dbSNP
rs540064877 1071 dbSNP
rs1258434302 1089 dbSNP
rs1308574600 1104 dbSNP
rs937985105 1105 dbSNP
rs776135188 1111 dbSNP
rs558063177 1112 dbSNP
rs889082589 1115 dbSNP
rs1261637880 1119 dbSNP
rs1011602474 1121 dbSNP
rs1315327520 1122 dbSNP
rs1306631788 1135 dbSNP
rs761473919 1142 dbSNP
rs1385000901 1148 dbSNP
rs1232064352 1152 dbSNP
rs1450298684 1161 dbSNP
rs573326094 1165 dbSNP
rs3176359 1166 dbSNP
rs903998141 1177 dbSNP
rs960052426 1184 dbSNP
rs1157825566 1190 dbSNP
rs555737213 1191 dbSNP
rs1386505260 1206 dbSNP
rs1181247844 1207 dbSNP
rs1461236031 1210 dbSNP
rs749899530 1213 dbSNP
rs1263105800 1224 dbSNP
rs1207246532 1226 dbSNP
rs573926464 1227 dbSNP
rs1223431084 1228 dbSNP
rs544119216 1234 dbSNP
rs1163000989 1236 dbSNP
rs930958513 1238 dbSNP
rs983778153 1243 dbSNP
rs1296287341 1251 dbSNP
rs1802569 1257 dbSNP
rs1383705783 1265 dbSNP
rs1382434582 1266 dbSNP
rs1297375941 1267 dbSNP
rs1424855287 1270 dbSNP
rs1426782231 1272 dbSNP
rs908447221 1273 dbSNP
rs1161106457 1277 dbSNP
rs1443541621 1279 dbSNP
rs1306606588 1281 dbSNP
rs1802570 1296 dbSNP
rs182235412 1299 dbSNP
rs185976780 1300 dbSNP
rs544851636 1304 dbSNP
rs1261412400 1309 dbSNP
rs1200644254 1311 dbSNP
rs1490893779 1314 dbSNP
rs1300371776 1319 dbSNP
rs1376345118 1321 dbSNP
rs1340234208 1328 dbSNP
rs1244523840 1350 dbSNP
rs963715824 1361 dbSNP
rs1324648171 1365 dbSNP
rs1277296198 1375 dbSNP
rs745953295 1380 dbSNP
rs1361208671 1382 dbSNP
rs932480638 1386 dbSNP
rs11550973 1388 dbSNP
rs527383432 1389 dbSNP
rs1396519804 1390 dbSNP
rs1169167214 1392 dbSNP
rs548775480 1394 dbSNP
rs1011571683 1397 dbSNP
rs1423597658 1398 dbSNP
rs73730143 1403 dbSNP
rs903433616 1404 dbSNP
rs982916069 1416 dbSNP
rs1267037831 1426 dbSNP
rs531369735 1431 dbSNP
rs778257166 1432 dbSNP
rs1194188901 1434 dbSNP
rs1183138065 1440 dbSNP
rs1337340457 1441 dbSNP
rs1257405417 1445 dbSNP
rs1223890425 1449 dbSNP
rs1036363838 1452 dbSNP
rs1385906506 1460 dbSNP
rs766360274 1460 dbSNP
rs1446722024 1461 dbSNP
rs1166317774 1462 dbSNP
rs564442732 1473 dbSNP
rs1419284609 1477 dbSNP
rs941154808 1479 dbSNP
rs1136646 1483 dbSNP
rs1471247583 1499 dbSNP
rs1427573585 1509 dbSNP
rs549777937 1512 dbSNP
rs1470615589 1515 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 1026.0
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 GSM714647. RNA binding protein: AGO2. Condition:mildMNase ...

- 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' aguugagacguuucCUUCUUCu 5'
                        ||||||| 
Target 5' -------------aGAAGAAGg 3'
 		1 - 9
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]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_000389 | 3UTR | UCAAUGGACUGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_000389 | 3UTR | UGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_000389 | 3UTR | UGGACUGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_000389 | 3UTR | GACUGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_078467 | 3UTR | GACUGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_000389 | 3UTR | GGACUGGAAGGGGAAGGGACACACAAGAAGAAGGGCACCCUAGUUCUACCUCAGGCAGCUCAAGCAGCGACCGCCCCCUCCUCUAGCUGUGGGGGUGAGGGUCCCAUGUGGUGGCACAGGCCCCCUUGAGUGGGGUUAUCUCUGUGUUAGGGGUAUAUGAUGGGGGAGUAGAUCUUUCUAGGAGGGAGACACUGGCCCCUCAAAUCGUCCAGCGACCUUCCUCAUCCACCCCAUCCCUCCCCAGUUCAUUGCACUUUGAUUAGCAGCGGAACAAGGAGUCAGACAUUUUAAGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM714647
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repB
Location of target site ENST00000244741.5 | 3UTR | AGAAGAAGGGCACCCUAGUUCUACCUCAGGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
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
169 hsa-miR-4778-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT199338 YES1 YES proto-oncogene 1, Src family tyrosine kinase 2 4
MIRT203028 MAP3K2 mitogen-activated protein kinase kinase kinase 2 2 2
MIRT260646 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT336468 SRP9 signal recognition particle 9 2 2
MIRT389212 SERTAD2 SERTA domain containing 2 2 2
MIRT441814 TENM1 teneurin transmembrane protein 1 2 2
MIRT444029 GREM1 gremlin 1, DAN family BMP antagonist 2 4
MIRT454171 HIST1H2BK histone cluster 1 H2B family member k 2 2
MIRT469663 RABEPK Rab9 effector protein with kelch motifs 2 2
MIRT495579 PLEKHA8 pleckstrin homology domain containing A8 2 2
MIRT498340 PRELID2 PRELI domain containing 2 2 2
MIRT498696 LYRM2 LYR motif containing 2 2 6
MIRT504156 OPN5 opsin 5 2 4
MIRT506321 OTUD4 OTU deubiquitinase 4 2 4
MIRT507608 DCAF7 DDB1 and CUL4 associated factor 7 2 2
MIRT525431 PROX2 prospero homeobox 2 2 2
MIRT526973 PAX7 paired box 7 2 2
MIRT527814 TMEM74B transmembrane protein 74B 2 2
MIRT527960 MTAP methylthioadenosine phosphorylase 2 2
MIRT528083 NOL9 nucleolar protein 9 2 2
MIRT528480 STAMBPL1 STAM binding protein like 1 2 2
MIRT528947 PNMA5 paraneoplastic Ma antigen family member 5 2 2
MIRT530687 C8orf46 chromosome 8 open reading frame 46 2 2
MIRT531733 SLC2A9 solute carrier family 2 member 9 2 2
MIRT532445 PLGRKT plasminogen receptor with a C-terminal lysine 2 2
MIRT533331 UNK unkempt family zinc finger 2 2
MIRT534205 SLC38A9 solute carrier family 38 member 9 2 2
MIRT534322 SHISA6 shisa family member 6 2 2
MIRT535197 PLCL1 phospholipase C like 1 (inactive) 2 2
MIRT538076 DIAPH2 diaphanous related formin 2 2 2
MIRT539250 ANKRD50 ankyrin repeat domain 50 2 2
MIRT548733 CREBRF CREB3 regulatory factor 2 2
MIRT556406 LRRC8B leucine rich repeat containing 8 VRAC subunit B 2 2
MIRT559576 AP1AR adaptor related protein complex 1 associated regulatory protein 2 2
MIRT567661 ERGIC2 ERGIC and golgi 2 2 2
MIRT572750 FAM204A family with sequence similarity 204 member A 2 2
MIRT609355 ZNF664 zinc finger protein 664 2 2
MIRT611194 TMEM105 transmembrane protein 105 2 2
MIRT611545 BIRC5 baculoviral IAP repeat containing 5 2 4
MIRT611690 NODAL nodal growth differentiation factor 2 2
MIRT611810 FCRL4 Fc receptor like 4 2 2
MIRT612746 MYOCD myocardin 2 2
MIRT614177 FAM53B family with sequence similarity 53 member B 2 2
MIRT614431 TAZ tafazzin 2 2
MIRT614586 SDC1 syndecan 1 2 2
MIRT615547 TNFSF15 TNF superfamily member 15 2 2
MIRT615872 BRD3 bromodomain containing 3 2 2
MIRT615970 ASCL1 achaete-scute family bHLH transcription factor 1 2 2
MIRT616024 PRRG4 proline rich and Gla domain 4 2 4
MIRT616242 NFIC nuclear factor I C 2 2
MIRT616282 HMGB1 high mobility group box 1 2 2
MIRT616674 PRR15 proline rich 15 2 2
MIRT618302 COL4A4 collagen type IV alpha 4 chain 2 2
MIRT618657 ATP6AP1L ATPase H+ transporting accessory protein 1 like 2 2
MIRT618754 SLC38A5 solute carrier family 38 member 5 2 2
MIRT619505 TXLNB taxilin beta 2 2
MIRT619545 GABRG2 gamma-aminobutyric acid type A receptor gamma2 subunit 2 2
MIRT619605 MKKS McKusick-Kaufman syndrome 2 2
MIRT619804 CDC42EP4 CDC42 effector protein 4 2 2
MIRT619923 NLRP9 NLR family pyrin domain containing 9 2 2
MIRT620442 SEMA3E semaphorin 3E 2 4
MIRT620730 CCL16 C-C motif chemokine ligand 16 2 2
MIRT625345 TAPBP TAP binding protein 2 2
MIRT627510 ST8SIA3 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 2 2
MIRT632584 PLCXD3 phosphatidylinositol specific phospholipase C X domain containing 3 2 2
MIRT636901 RABGAP1L RAB GTPase activating protein 1 like 2 2
MIRT637873 UTP6 UTP6, small subunit processome component 2 2
MIRT639011 ABI2 abl interactor 2 2 2
MIRT639054 FPR1 formyl peptide receptor 1 2 2
MIRT639085 ADCYAP1 adenylate cyclase activating polypeptide 1 2 2
MIRT639589 RGS5 regulator of G protein signaling 5 2 2
MIRT639718 NPRL3 NPR3 like, GATOR1 complex subunit 2 2
MIRT639904 SRGAP2 SLIT-ROBO Rho GTPase activating protein 2 2 2
MIRT640392 ZNF785 zinc finger protein 785 2 2
MIRT640786 GRIK3 glutamate ionotropic receptor kainate type subunit 3 2 2
MIRT641290 SLAMF1 signaling lymphocytic activation molecule family member 1 2 2
MIRT641442 PELO pelota mRNA surveillance and ribosome rescue factor 2 2
MIRT642426 STAT3 signal transducer and activator of transcription 3 2 2
MIRT642682 KRT74 keratin 74 2 2
MIRT643362 TRIM10 tripartite motif containing 10 2 2
MIRT643982 DUSP28 dual specificity phosphatase 28 2 2
MIRT644466 ZNF747 zinc finger protein 747 2 2
MIRT644561 SPOP speckle type BTB/POZ protein 2 2
MIRT645748 FAM213A family with sequence similarity 213 member A 2 2
MIRT646737 FADS1 fatty acid desaturase 1 2 2
MIRT647446 SIX6 SIX homeobox 6 2 2
MIRT648317 SCNN1G sodium channel epithelial 1 gamma subunit 2 2
MIRT649327 POLG DNA polymerase gamma, catalytic subunit 2 2
MIRT649453 WDR70 WD repeat domain 70 2 2
MIRT650066 CCDC134 coiled-coil domain containing 134 2 2
MIRT650156 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT650317 TMX4 thioredoxin related transmembrane protein 4 2 2
MIRT650429 BBS9 Bardet-Biedl syndrome 9 2 2
MIRT651325 ZCCHC2 zinc finger CCHC-type containing 2 2 2
MIRT651843 USP13 ubiquitin specific peptidase 13 2 2
MIRT652532 TM9SF3 transmembrane 9 superfamily member 3 2 2
MIRT652816 TARDBP TAR DNA binding protein 2 2
MIRT652971 SUN2 Sad1 and UNC84 domain containing 2 2 2
MIRT653466 SLC5A12 solute carrier family 5 member 12 2 4
MIRT653568 SLC35B3 solute carrier family 35 member B3 2 2
MIRT655678 NUMBL NUMB like, endocytic adaptor protein 2 2
MIRT656785 KPNA4 karyopherin subunit alpha 4 2 2
MIRT656798 KNTC1 kinetochore associated 1 2 2
MIRT656988 KDM5A lysine demethylase 5A 2 2
MIRT657292 HOXB5 homeobox B5 2 2
MIRT657497 HBEGF heparin binding EGF like growth factor 2 4
MIRT658012 GABRB1 gamma-aminobutyric acid type A receptor beta1 subunit 2 2
MIRT658146 STXBP2 syntaxin binding protein 2 2 2
MIRT658259 FAXC failed axon connections homolog 2 2
MIRT659051 DGKH diacylglycerol kinase eta 2 2
MIRT659171 DCTN3 dynactin subunit 3 2 2
MIRT659936 CACHD1 cache domain containing 1 2 2
MIRT660079 BZW1 basic leucine zipper and W2 domains 1 2 2
MIRT660167 BNIP3L BCL2 interacting protein 3 like 2 2
MIRT660292 BICC1 BicC family RNA binding protein 1 2 2
MIRT660317 BDP1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 2 2
MIRT660340 BCAT1 branched chain amino acid transaminase 1 2 2
MIRT660447 ATP1A2 ATPase Na+/K+ transporting subunit alpha 2 2 2
MIRT661634 UGT2B28 UDP glucuronosyltransferase family 2 member B28 2 2
MIRT662438 RALGAPA1 Ral GTPase activating protein catalytic alpha subunit 1 2 2
MIRT664202 TBCA tubulin folding cofactor A 2 2
MIRT666436 SH2B3 SH2B adaptor protein 3 2 2
MIRT666666 RBM47 RNA binding motif protein 47 2 4
MIRT669253 C4orf36 chromosome 4 open reading frame 36 2 2
MIRT669502 ARL3 ADP ribosylation factor like GTPase 3 2 2
MIRT693912 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 2 2
MIRT700435 PURB purine rich element binding protein B 2 2
MIRT702857 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT708857 TMSB4X thymosin beta 4, X-linked 2 2
MIRT709030 KBTBD13 kelch repeat and BTB domain containing 13 2 2
MIRT709609 CXorf23 BCLAF1 and THRAP3 family member 3 2 2
MIRT709810 AR androgen receptor 2 2
MIRT709872 A1CF APOBEC1 complementation factor 2 2
MIRT710208 ENAH ENAH, actin regulator 2 2
MIRT710964 CMKLR1 chemerin chemokine-like receptor 1 2 2
MIRT711173 EMCN endomucin 2 2
MIRT711219 RETSAT retinol saturase 2 2
MIRT711345 FMNL2 formin like 2 2 2
MIRT711441 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT711631 PEBP1 phosphatidylethanolamine binding protein 1 2 2
MIRT711823 MAPK8IP3 mitogen-activated protein kinase 8 interacting protein 3 2 2
MIRT712164 SURF4 surfeit 4 2 2
MIRT712632 RNF103-CHMP3 RNF103-CHMP3 readthrough 2 2
MIRT713692 CYB5R4 cytochrome b5 reductase 4 2 2
MIRT714906 CHMP3 charged multivesicular body protein 3 2 2
MIRT715161 FIG4 FIG4 phosphoinositide 5-phosphatase 2 2
MIRT715430 SOCS5 suppressor of cytokine signaling 5 2 2
MIRT715660 ZBTB25 zinc finger and BTB domain containing 25 2 2
MIRT715968 FADS3 fatty acid desaturase 3 2 2
MIRT716203 TYW3 tRNA-yW synthesizing protein 3 homolog 2 2
MIRT716234 SRSF12 serine and arginine rich splicing factor 12 2 2
MIRT716251 PALM2 paralemmin 2 2 2
MIRT716375 CCBE1 collagen and calcium binding EGF domains 1 2 2
MIRT716490 PHACTR2 phosphatase and actin regulator 2 2 2
MIRT716744 APOL6 apolipoprotein L6 2 2
MIRT717624 AGPAT4 1-acylglycerol-3-phosphate O-acyltransferase 4 2 2
MIRT718480 TMEM151A transmembrane protein 151A 2 2
MIRT718805 PRKCB protein kinase C beta 2 2
MIRT719276 SETD7 SET domain containing lysine methyltransferase 7 2 2
MIRT719432 NPTX2 neuronal pentraxin 2 2 2
MIRT721011 ZNF619 zinc finger protein 619 2 2
MIRT721819 HEATR5A HEAT repeat containing 5A 2 2
MIRT721997 CLLU1OS chronic lymphocytic leukemia up-regulated 1 opposite strand 2 2
MIRT723143 METTL24 methyltransferase like 24 2 2
MIRT723213 PIP5K1C phosphatidylinositol-4-phosphate 5-kinase type 1 gamma 2 2
MIRT723427 MC2R melanocortin 2 receptor 2 2
MIRT723436 ADI1 acireductone dioxygenase 1 2 2
MIRT723542 PAGR1 PAXIP1 associated glutamate rich protein 1 2 2
MIRT724474 MMD monocyte to macrophage differentiation associated 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4778-3p Platinum 23939 sensitive tissue (non-small cell lung cancer)
hsa-miR-4778-3p Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)

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