miRTarBase - #MIRT059166


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pre-miRNA Information
pre-miRNA hsa-mir-3689d-1   
Genomic Coordinates chr9: 134849609 - 134849682
Description Homo sapiens miR-3689d-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3689d-2   
Genomic Coordinates chr9: 134850277 - 134850356
Description Homo sapiens miR-3689d-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3689d
Sequence 2| GGGAGGUGUGAUCUCACACUCG |23
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs551722268 8 dbSNP
rs143142996 8 dbSNP
rs1236297052 12 dbSNP
rs573148947 14 dbSNP
rs1210004979 14 dbSNP
rs1217460444 14 dbSNP
rs762590109 18 dbSNP
rs574332265 18 dbSNP
rs1164353021 21 dbSNP
rs963741171 21 dbSNP
rs1177416877 22 dbSNP
rs765777344 22 dbSNP
Putative Targets

Gene Information
Gene Symbol TXNIP   
Synonyms ARRDC6, EST01027, HHCPA78, THIF, VDUP1
Description thioredoxin interacting protein
Transcript NM_006472   
Expression
Putative miRNA Targets on TXNIP
3'UTR of TXNIP
(miRNA target sites are highlighted)		 
>TXNIP|NM_006472|3'UTR
   1 GCATGTGGAAGAAAAGAAGCAGCTTTACCTACTTGTTTCTTTTTGTCTCTCTTCCTGGACACTCACTTTTTCAGAGACTC
  81 AACAGTCTCTGCAATGGAGTGTGGGTCCACCTTAGCCTCTGACTTCCTAATGTAGGAGGTGGTCAGCAGGCAATCTCCTG
 161 GGCCTTAAAGGATGCGGACTCATCCTCAGCCAGCGCCCATGTTGTGATACAGGGGTGTTTGTTGGATGGGTTTAAAAATA
 241 ACTAGAAAAACTCAGGCCCATCCATTTTCTCAGATCTCCTTGAAAATTGAGGCCTTTTCGATAGTTTCGGGTCAGGTAAA
 321 AATGGCCTCCTGGCGTAAGCTTTTCAAGGTTTTTTGGAGGCTTTTTGTAAATTGTGATAGGAACTTTGGACCTTGAACTT
 401 ACGTATCATGTGGAGAAGAGCCAATTTAACAAACTAGGAAGATGAAAAGGGAAATTGTGGCCAAAACTTTGGGAAAAGGA
 481 GGTTCTTAAAATCAGTGTTTCCCCTTTGTGCACTTGTAGAAAAAAAAGAAAAACCTTCTAGAGCTGATTTGATGGACAAT
 561 GGAGAGAGCTTTCCCTGTGATTATAAAAAAGGAAGCTAGCTGCTCTACGGTCATCTTTGCTTAGAGTATACTTTAACCTG
 641 GCTTTTAAAGCAGTAGTAACTGCCCCACCAAAGGTCTTAAAAGCCATTTTTGGAGCCTATTGCACTGTGTTCTCCTACTG
 721 CAAATATTTTCATATGGGAGGATGGTTTTCTCTTCATGTAAGTCCTTGGAATTGATTCTAAGGTGATGTTCTTAGCACTT
 801 TAATTCCTGTCAAATTTTTTGTTCTCCCCTTCTGCCATCTTAAATGTAAGCTGAAACTGGTCTACTGTGTCTCTAGGGTT
 881 AAGCCAAAAGACAAAAAAAATTTTACTACTTTTGAGATTGCCCCAATGTACAGAATTATATAATTCTAACGCTTAAATCA
 961 TGTGAAAGGGTTGCTGCTGTCAGCCTTGCCCACTGTGACTTCAAACCCAAGGAGGAACTCTTGATCAAGATGCCCAACCC
1041 TGTGATCAGAACCTCCAAATACTGCCATGAGAAACTAGAGGGCAGGTCTTCATAAAAGCCCTTTGAACCCCCTTCCTGCC
1121 CTGTGTTAGGAGATAGGGATATTGGCCCCTCACTGCAGCTGCCAGCACTTGGTCAGTCACTCTCAGCCATAGCACTTTGT
1201 TCACTGTCCTGTGTCAGAGCACTGAGCTCCACCCTTTTCTGAGAGTTATTACAGCCAGAAAGTGTGGGCTGAAGATGGTT
1281 GGTTTCATGTTTTTGTATTATGTATCTTTTTGTATGGTAAAGACTATATTTTGTACTTAACCAGATATATTTTTACCCCA
1361 GATGGGGATATTCTTTGTAAAAAATGAAAATAAAGTTTTTTTAATGGAAAAAAAAATGTCTGTGAAAAAAAAAAAAAAAA
1441 AA
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' gcUCACACUCUAGUGUGGAGgg 5'
            |||||| |:|| |||||:  
Target 5' ggAGTGTG-GGTC-CACCTTag 3'
 96 - 115 134.00 -23.70
2 
miRNA  3' gcucacACUCUAGU-GUGGAGGg 5'
                || |||||  |||||| 
Target 5' caacccTGTGATCAGAACCTCCa 3'
 1035 - 1057 132.00 -17.00
3 
miRNA  3' gcucacacucuAGUGUGGAGGg 5'
                     ||| |:|||| 
Target 5' catccattttcTCAGATCTCCt 3'
 259 - 280 107.00 -11.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31613608 26 COSMIC
COSN23013884 29 COSMIC
COSN30498918 54 COSMIC
COSN26345387 86 COSMIC
COSN31518012 87 COSMIC
COSN31544793 97 COSMIC
COSN13465511 153 COSMIC
COSN30168748 176 COSMIC
COSN22854620 212 COSMIC
COSN32082653 300 COSMIC
COSN20215506 357 COSMIC
COSN25793126 567 COSMIC
COSN31481257 609 COSMIC
COSN28929309 699 COSMIC
COSN31487417 731 COSMIC
COSN8319264 786 COSMIC
COSN7175900 895 COSMIC
COSN16130546 903 COSMIC
COSN31541469 950 COSMIC
COSN1404851 989 COSMIC
COSN31566757 1020 COSMIC
COSN30175504 1198 COSMIC
COSN28813251 1210 COSMIC
COSN31563457 1215 COSMIC
COSN17255712 1341 COSMIC
COSN8635856 1344 COSMIC
COSN16130598 1349 COSMIC
COSN8319265 1407 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs782324253 5 dbSNP
rs781922861 6 dbSNP
rs782164728 10 dbSNP
rs1042196726 11 dbSNP
rs1378865015 12 dbSNP
rs1238192616 14 dbSNP
rs1322340577 17 dbSNP
rs1223844421 20 dbSNP
rs782412186 20 dbSNP
rs782011331 23 dbSNP
rs1263824209 27 dbSNP
rs775233794 27 dbSNP
rs782126186 28 dbSNP
rs371598136 29 dbSNP
rs781829085 35 dbSNP
rs1179845309 39 dbSNP
rs762566229 45 dbSNP
rs187591491 47 dbSNP
rs782695925 49 dbSNP
rs1438233194 53 dbSNP
rs1176339594 56 dbSNP
rs1406774368 58 dbSNP
rs1405664156 61 dbSNP
rs371239177 62 dbSNP
rs763445640 66 dbSNP
rs191199120 68 dbSNP
rs1331993431 80 dbSNP
rs926556698 85 dbSNP
rs980068913 86 dbSNP
rs942069156 94 dbSNP
rs1380153984 102 dbSNP
rs1230279460 103 dbSNP
rs1310607527 110 dbSNP
rs1321232464 111 dbSNP
rs1199751130 115 dbSNP
rs1260570451 117 dbSNP
rs782040268 123 dbSNP
rs782156144 126 dbSNP
rs1198407308 128 dbSNP
rs1238455155 128 dbSNP
rs1472910620 134 dbSNP
rs1183259112 139 dbSNP
rs1410937390 144 dbSNP
rs1474596615 150 dbSNP
rs1171229323 157 dbSNP
rs1402347354 160 dbSNP
rs1464057644 161 dbSNP
rs1327900605 164 dbSNP
rs1359573889 167 dbSNP
rs983462122 171 dbSNP
rs1450421426 172 dbSNP
rs782151618 175 dbSNP
rs782730266 176 dbSNP
rs1219316893 182 dbSNP
rs751580661 189 dbSNP
rs1316562673 194 dbSNP
rs757127542 195 dbSNP
rs1279726855 196 dbSNP
rs782458723 199 dbSNP
rs1444522337 202 dbSNP
rs964973982 214 dbSNP
rs1018315568 215 dbSNP
rs1211711784 216 dbSNP
rs1235396722 239 dbSNP
rs1485173889 242 dbSNP
rs1193744753 246 dbSNP
rs1425196792 247 dbSNP
rs1000527363 251 dbSNP
rs782095422 264 dbSNP
rs782735059 269 dbSNP
rs1425527728 277 dbSNP
rs1415978448 281 dbSNP
rs1020648610 286 dbSNP
rs1375066981 292 dbSNP
rs182339054 293 dbSNP
rs896250928 294 dbSNP
rs1430590223 300 dbSNP
rs186992970 307 dbSNP
rs587669942 308 dbSNP
rs1280146264 309 dbSNP
rs1346661958 315 dbSNP
rs1216943737 318 dbSNP
rs1264644353 325 dbSNP
rs372245117 327 dbSNP
rs1247206460 328 dbSNP
rs1479008383 331 dbSNP
rs905099575 334 dbSNP
rs1394305473 335 dbSNP
rs1420489469 337 dbSNP
rs587633419 347 dbSNP
rs1358627658 351 dbSNP
rs1400205301 353 dbSNP
rs1324348440 357 dbSNP
rs587688547 366 dbSNP
rs880001759 372 dbSNP
rs1434993978 373 dbSNP
rs1303097894 380 dbSNP
rs1240339979 388 dbSNP
rs1378137080 388 dbSNP
rs1287737864 397 dbSNP
rs1348176239 402 dbSNP
rs7211 402 dbSNP
rs909194389 403 dbSNP
rs1252106635 405 dbSNP
rs139816793 405 dbSNP
rs983429530 408 dbSNP
rs1180677079 410 dbSNP
rs11537988 416 dbSNP
rs1378681121 420 dbSNP
rs1469875254 421 dbSNP
rs1163879673 425 dbSNP
rs1393031655 431 dbSNP
rs929395114 432 dbSNP
rs1325860264 434 dbSNP
rs1401411327 444 dbSNP
rs782760634 447 dbSNP
rs1449452453 451 dbSNP
rs1307615133 453 dbSNP
rs1333591721 454 dbSNP
rs923375748 455 dbSNP
rs587595014 458 dbSNP
rs144336702 461 dbSNP
rs587721930 462 dbSNP
rs979655270 466 dbSNP
rs1272484245 470 dbSNP
rs968300777 475 dbSNP
rs1458201715 478 dbSNP
rs782603988 483 dbSNP
rs1200297110 486 dbSNP
rs1248193527 499 dbSNP
rs1437439441 507 dbSNP
rs1188533701 516 dbSNP
rs1370225266 517 dbSNP
rs1020617601 518 dbSNP
rs1164375997 528 dbSNP
rs1471852789 528 dbSNP
rs1424966048 530 dbSNP
rs60016427 532 dbSNP
rs1329704935 535 dbSNP
rs1396260982 536 dbSNP
rs1390424829 537 dbSNP
rs1334409691 538 dbSNP
rs1341676501 540 dbSNP
rs1230906272 543 dbSNP
rs1009258927 547 dbSNP
rs960484146 549 dbSNP
rs1292204396 555 dbSNP
rs1318464304 556 dbSNP
rs1220448927 559 dbSNP
rs1249351897 560 dbSNP
rs1480204605 573 dbSNP
rs1201181041 578 dbSNP
rs17221751 580 dbSNP
rs1001967957 584 dbSNP
rs904984593 585 dbSNP
rs1491098482 591 dbSNP
rs1491237619 592 dbSNP
rs1479063432 600 dbSNP
rs1169206620 603 dbSNP
rs1372803185 604 dbSNP
rs1466890670 605 dbSNP
rs1038185991 606 dbSNP
rs1174735186 608 dbSNP
rs1005396171 609 dbSNP
rs887055645 610 dbSNP
rs1412581170 612 dbSNP
rs1311718841 614 dbSNP
rs1173796060 624 dbSNP
rs1293355589 625 dbSNP
rs1401723505 625 dbSNP
rs1306645745 627 dbSNP
rs1233700693 636 dbSNP
rs587625832 637 dbSNP
rs1210470225 640 dbSNP
rs1286782430 651 dbSNP
rs782317952 663 dbSNP
rs1489316693 676 dbSNP
rs929338953 678 dbSNP
rs923374357 680 dbSNP
rs1261621694 686 dbSNP
rs1434316789 688 dbSNP
rs1201416620 696 dbSNP
rs1393705612 697 dbSNP
rs1432427649 700 dbSNP
rs1172659571 707 dbSNP
rs1360531020 709 dbSNP
rs587680878 712 dbSNP
rs1361150127 715 dbSNP
rs1387331419 717 dbSNP
rs1303074471 720 dbSNP
rs755859477 720 dbSNP
rs1368560706 732 dbSNP
rs943471171 734 dbSNP
rs1287031216 735 dbSNP
rs1356195735 736 dbSNP
rs184403951 757 dbSNP
rs1260255804 760 dbSNP
rs1489078465 762 dbSNP
rs979622524 764 dbSNP
rs879951227 765 dbSNP
rs587616307 768 dbSNP
rs968269660 772 dbSNP
rs1380513567 778 dbSNP
rs914194992 783 dbSNP
rs1420548122 786 dbSNP
rs987815665 789 dbSNP
rs587697781 795 dbSNP
rs1327851862 797 dbSNP
rs1391945520 798 dbSNP
rs587738475 799 dbSNP
rs1439880342 802 dbSNP
rs188801165 813 dbSNP
rs1034694017 814 dbSNP
rs1222326818 816 dbSNP
rs1306316807 824 dbSNP
rs1002338477 826 dbSNP
rs1322437540 827 dbSNP
rs17215345 829 dbSNP
rs1247537919 846 dbSNP
rs1271839122 855 dbSNP
rs969178468 869 dbSNP
rs1199631976 871 dbSNP
rs1240471150 871 dbSNP
rs1481382993 872 dbSNP
rs1175151496 877 dbSNP
rs1406527116 881 dbSNP
rs1166547639 886 dbSNP
rs879991460 893 dbSNP
rs1491067549 894 dbSNP
rs17215338 897 dbSNP
rs1331759889 899 dbSNP
rs1016711766 900 dbSNP
rs1297825524 901 dbSNP
rs1356080896 901 dbSNP
rs1440237012 901 dbSNP
rs1379912358 908 dbSNP
rs1230086645 914 dbSNP
rs1005366474 922 dbSNP
rs887026030 924 dbSNP
rs1334743209 928 dbSNP
rs199827526 932 dbSNP
rs998124411 939 dbSNP
rs1201940875 940 dbSNP
rs1231944411 943 dbSNP
rs587637170 946 dbSNP
rs901803859 949 dbSNP
rs193055505 950 dbSNP
rs587754573 951 dbSNP
rs11537987 952 dbSNP
rs943433626 954 dbSNP
rs1408014581 959 dbSNP
rs1169551439 961 dbSNP
rs1359958985 962 dbSNP
rs1416911570 974 dbSNP
rs1311094732 979 dbSNP
rs1354936972 981 dbSNP
rs1401073154 982 dbSNP
rs910662203 984 dbSNP
rs1272447258 992 dbSNP
rs1360566475 1002 dbSNP
rs1214348658 1006 dbSNP
rs1279834666 1011 dbSNP
rs587707558 1017 dbSNP
rs1312385871 1018 dbSNP
rs1212604008 1026 dbSNP
rs1277515542 1027 dbSNP
rs778849135 1031 dbSNP
rs587631368 1033 dbSNP
rs946900640 1034 dbSNP
rs7212 1035 dbSNP
rs1474423371 1037 dbSNP
rs1185681179 1038 dbSNP
rs1425637740 1040 dbSNP
rs185869681 1044 dbSNP
rs4755 1045 dbSNP
rs11537984 1056 dbSNP
rs782111820 1062 dbSNP
rs747400980 1067 dbSNP
rs939637061 1072 dbSNP
rs1374865849 1074 dbSNP
rs782357128 1081 dbSNP
rs587663814 1082 dbSNP
rs1320449964 1086 dbSNP
rs1325170860 1087 dbSNP
rs587731065 1088 dbSNP
rs1275758715 1100 dbSNP
rs781954705 1102 dbSNP
rs1235949373 1103 dbSNP
rs148808239 1104 dbSNP
rs1300821227 1105 dbSNP
rs1346774785 1107 dbSNP
rs1216697503 1109 dbSNP
rs13340 1112 dbSNP
rs969092902 1115 dbSNP
rs75291601 1117 dbSNP
rs1445163633 1118 dbSNP
rs1215023304 1120 dbSNP
rs1247001755 1121 dbSNP
rs587742862 1123 dbSNP
rs1455432809 1128 dbSNP
rs1191582395 1133 dbSNP
rs587632424 1134 dbSNP
rs1440595578 1137 dbSNP
rs1025436781 1138 dbSNP
rs782067883 1143 dbSNP
rs1382907398 1146 dbSNP
rs1324782358 1149 dbSNP
rs1397061837 1152 dbSNP
rs1439140528 1153 dbSNP
rs901116218 1156 dbSNP
rs1369745291 1160 dbSNP
rs1239380532 1162 dbSNP
rs1280747961 1164 dbSNP
rs13203 1168 dbSNP
rs1223087601 1173 dbSNP
rs1469822683 1180 dbSNP
rs73004671 1181 dbSNP
rs1252203121 1182 dbSNP
rs1458344032 1184 dbSNP
rs1184283201 1185 dbSNP
rs1362065982 1186 dbSNP
rs1163966506 1192 dbSNP
rs1469702544 1192 dbSNP
rs889195041 1193 dbSNP
rs1043797905 1203 dbSNP
rs1460375002 1209 dbSNP
rs1325623390 1223 dbSNP
rs782809435 1224 dbSNP
rs1391541737 1226 dbSNP
rs946785983 1234 dbSNP
rs1060179 1239 dbSNP
rs1333683268 1246 dbSNP
rs1293420506 1248 dbSNP
rs1440836776 1248 dbSNP
rs782123605 1249 dbSNP
rs1231405845 1251 dbSNP
rs1272265404 1251 dbSNP
rs1339831652 1252 dbSNP
rs781886945 1256 dbSNP
rs1248667835 1268 dbSNP
rs939585610 1269 dbSNP
rs1188706047 1271 dbSNP
rs928262975 1274 dbSNP
rs1259759524 1279 dbSNP
rs1474484411 1285 dbSNP
rs980844449 1286 dbSNP
rs1164841981 1288 dbSNP
rs1424714665 1290 dbSNP
rs1463841426 1293 dbSNP
rs1166587935 1295 dbSNP
rs1393839142 1298 dbSNP
rs587744932 1301 dbSNP
rs17215352 1304 dbSNP
rs1356845442 1312 dbSNP
rs587697405 1314 dbSNP
rs1292610322 1315 dbSNP
rs951155166 1319 dbSNP
rs782761667 1326 dbSNP
rs1327009960 1328 dbSNP
rs1229331365 1330 dbSNP
rs1249443048 1334 dbSNP
rs587759329 1341 dbSNP
rs1211893044 1348 dbSNP
rs1484739763 1356 dbSNP
rs1282482732 1357 dbSNP
rs139537792 1359 dbSNP
rs1263042191 1360 dbSNP
rs587711312 1362 dbSNP
rs1430853212 1367 dbSNP
rs965670628 1373 dbSNP
rs1191461016 1379 dbSNP
rs1372896149 1381 dbSNP
rs1474856821 1384 dbSNP
rs1173878766 1385 dbSNP
rs1376677555 1390 dbSNP
rs1432309416 1391 dbSNP
rs1311815383 1395 dbSNP
rs1385539659 1402 dbSNP
rs1383900622 1403 dbSNP
rs1293116545 1404 dbSNP
rs1325670923 1411 dbSNP
rs1018223865 1413 dbSNP
rs1210215430 1417 dbSNP
rs1305882263 1417 dbSNP
rs143469330 1417 dbSNP
rs79787359 1417 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 GSM545214. RNA binding protein: AGO3. Condition:Control PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' gcucacacucuagugUGGAGGg 5'
                         |||||| 
Target 5' -------uguucagaACCUCCa 3'
 		1 - 15
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 10628.0
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 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]
CLIP-seq Support 1 for dataset GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_006472 | 3UTR | AAACCCAAGGAGGAACUCUUGAUCAAGAUGCCGAACCCUGUGUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903826
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_NS
Location of target site NM_006472 | 3UTR | AAACCCAAGGAGGAACUCUUGAUCAAGAUGCCGAACCCUGUGUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_006472 | 3UTR | CCCUGUGUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_006472 | 3UTR | CCUGUGUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_006472 | 3UTR | CAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_006472 | 3UTR | UGUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_006472 | 3UTR | AGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_006472 | 3UTR | GUUCAGAACCUCCAAAUACUGCCAUGAGAAACUAGAGGGCAGGUCUUCAUAAAAGCCCUUUGAACCCCCUUCCUGCCCUGUGUUAGGAGAUAGGGAUAUUGGCCCCUCACUGCAGCUGCCAGCACU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000369317.4 | 3UTR | UGUUCAGAACCUCCAAAUACUGCCAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000369317.4 | 3UTR | UGUUCAGAACCUCCAAAUACUGCCAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000369317.4 | 3UTR | UGUUCAGAACCUCCAAAUACUGCCAUG
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
231 hsa-miR-3689d Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059166 TXNIP thioredoxin interacting protein 2 4
MIRT080699 KIAA1468 KIAA1468 2 2
MIRT218770 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT278059 KHNYN KH and NYN domain containing 2 2
MIRT345933 EIF4A1 eukaryotic translation initiation factor 4A1 2 2
MIRT366238 VMA21 VMA21, vacuolar ATPase assembly factor 2 2
MIRT449689 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT451149 C19orf53 chromosome 19 open reading frame 53 2 2
MIRT451266 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT451375 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451570 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451585 HIRIP3 HIRA interacting protein 3 2 2
MIRT451614 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT451763 ZNF611 zinc finger protein 611 2 6
MIRT452383 LY6E lymphocyte antigen 6 family member E 2 4
MIRT452573 ZFP69B ZFP69 zinc finger protein B 2 2
MIRT452735 PTGES3L prostaglandin E synthase 3 like 2 6
MIRT452867 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT452975 CABP4 calcium binding protein 4 2 2
MIRT453215 CERS1 ceramide synthase 1 2 2
MIRT453259 PARP11 poly(ADP-ribose) polymerase family member 11 2 2
MIRT453449 GLG1 golgi glycoprotein 1 2 2
MIRT453479 PITPNM3 PITPNM family member 3 2 2
MIRT453663 CD207 CD207 molecule 2 6
MIRT453724 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 2 2
MIRT453760 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT454181 AP1S3 adaptor related protein complex 1 sigma 3 subunit 2 6
MIRT454330 PPARA peroxisome proliferator activated receptor alpha 2 2
MIRT454338 CDKL1 cyclin dependent kinase like 1 2 2
MIRT454427 GTF2F1 general transcription factor IIF subunit 1 2 2
MIRT454665 FBXL18 F-box and leucine rich repeat protein 18 2 2
MIRT454825 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT455130 TBC1D25 TBC1 domain family member 25 2 2
MIRT455166 SUV39H1 suppressor of variegation 3-9 homolog 1 2 2
MIRT455416 RXRB retinoid X receptor beta 2 2
MIRT455668 GLO1 glyoxalase I 2 2
MIRT455999 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 2
MIRT456446 TMEM81 transmembrane protein 81 2 2
MIRT456642 NOS1AP nitric oxide synthase 1 adaptor protein 2 2
MIRT456728 TMEM239 transmembrane protein 239 2 2
MIRT457131 ASPH aspartate beta-hydroxylase 2 2
MIRT457157 MXRA7 matrix remodeling associated 7 2 2
MIRT457358 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT457458 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT457619 UPK3BL uroplakin 3B like 1 2 2
MIRT457692 ZNF587 zinc finger protein 587 2 2
MIRT457727 SMOX spermine oxidase 2 2
MIRT457788 VWA1 von Willebrand factor A domain containing 1 2 2
MIRT457875 THEM6 thioesterase superfamily member 6 2 4
MIRT457909 ZNF212 zinc finger protein 212 2 2
MIRT458395 ABCF1 ATP binding cassette subfamily F member 1 2 2
MIRT458496 MARVELD2 MARVEL domain containing 2 2 2
MIRT458544 CYP2B6 cytochrome P450 family 2 subfamily B member 6 2 2
MIRT458577 TCOF1 treacle ribosome biogenesis factor 1 2 2
MIRT458732 CES2 carboxylesterase 2 2 2
MIRT458814 ZNF843 zinc finger protein 843 2 2
MIRT458931 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459341 ZNF17 zinc finger protein 17 2 2
MIRT459365 MPLKIP M-phase specific PLK1 interacting protein 2 6
MIRT459572 NLGN2 neuroligin 2 2 2
MIRT460015 DTX3L deltex E3 ubiquitin ligase 3L 2 4
MIRT460144 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460653 IGFBP4 insulin like growth factor binding protein 4 2 2
MIRT460798 VPS33A VPS33A, CORVET/HOPS core subunit 2 2
MIRT461058 KCNK6 potassium two pore domain channel subfamily K member 6 2 4
MIRT461458 SLC19A3 solute carrier family 19 member 3 2 2
MIRT461572 SCO1 SCO1, cytochrome c oxidase assembly protein 2 4
MIRT461927 TNFSF14 TNF superfamily member 14 2 2
MIRT461953 C3 complement C3 2 2
MIRT462278 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT462744 EFNB1 ephrin B1 2 2
MIRT463136 ZNF451 zinc finger protein 451 2 4
MIRT463566 ZBTB39 zinc finger and BTB domain containing 39 2 6
MIRT463866 WNT7B Wnt family member 7B 2 2
MIRT464326 UST uronyl 2-sulfotransferase 2 2
MIRT464796 UBE2F ubiquitin conjugating enzyme E2 F (putative) 2 2
MIRT465034 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT466207 TMED10 transmembrane p24 trafficking protein 10 2 2
MIRT467007 SSBP2 single stranded DNA binding protein 2 2 2
MIRT467029 SRSF1 serine and arginine rich splicing factor 1 2 4
MIRT468001 SKI SKI proto-oncogene 2 2
MIRT468031 SIKE1 suppressor of IKBKE 1 2 6
MIRT468575 SERBP1 SERPINE1 mRNA binding protein 1 2 6
MIRT468834 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT468970 RPRD2 regulation of nuclear pre-mRNA domain containing 2 2 2
MIRT469450 REL REL proto-oncogene, NF-kB subunit 2 6
MIRT470888 PLXND1 plexin D1 2 2
MIRT470953 PKM pyruvate kinase, muscle 2 2
MIRT471828 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT472590 NACC1 nucleus accumbens associated 1 2 2
MIRT472805 MTMR12 myotubularin related protein 12 2 2
MIRT472818 MTMR10 myotubularin related protein 10 2 6
MIRT472914 MSN moesin 2 2
MIRT474558 KLHDC3 kelch domain containing 3 2 2
MIRT474716 KIF13A kinesin family member 13A 2 6
MIRT475279 TOR1AIP2 torsin 1A interacting protein 2 2 2
MIRT475300 IFNLR1 interferon lambda receptor 1 2 2
MIRT475759 HDLBP high density lipoprotein binding protein 2 2
MIRT475786 HDGF heparin binding growth factor 2 2
MIRT475933 GXYLT2 glucoside xylosyltransferase 2 2 8
MIRT476212 GNS glucosamine (N-acetyl)-6-sulfatase 2 2
MIRT476238 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 2 4
MIRT476799 FNDC3B fibronectin type III domain containing 3B 2 2
MIRT477988 DNAL1 dynein axonemal light chain 1 2 2
MIRT478317 DDN dendrin 2 2
MIRT479257 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT479344 CEP97 centrosomal protein 97 2 2
MIRT479522 CDCA4 cell division cycle associated 4 2 2
MIRT479906 CCDC117 coiled-coil domain containing 117 2 6
MIRT481147 AVL9 AVL9 cell migration associated 2 6
MIRT481735 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT482089 ALG8 ALG8, alpha-1,3-glucosyltransferase 2 2
MIRT482389 AEN apoptosis enhancing nuclease 2 2
MIRT483093 TFPI tissue factor pathway inhibitor 2 2
MIRT484246 ANK1 ankyrin 1 2 2
MIRT484342 EPN1 epsin 1 2 4
MIRT489141 C5orf38 chromosome 5 open reading frame 38 2 2
MIRT489163 MRPL12 mitochondrial ribosomal protein L12 2 4
MIRT489547 SOX11 SRY-box 11 2 4
MIRT489780 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT489799 KRT80 keratin 80 2 6
MIRT490535 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT492198 SOCS1 suppressor of cytokine signaling 1 2 2
MIRT492283 SHISA6 shisa family member 6 2 4
MIRT501059 SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 2 4
MIRT501094 SLC5A6 solute carrier family 5 member 6 2 4
MIRT503870 CBS cystathionine-beta-synthase 2 2
MIRT507981 BCL2L13 BCL2 like 13 2 4
MIRT508125 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT508205 SLC35E1 solute carrier family 35 member E1 2 2
MIRT508385 SPTBN2 spectrin beta, non-erythrocytic 2 2 4
MIRT510308 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT510462 ZDHHC18 zinc finger DHHC-type containing 18 2 2
MIRT512227 ATXN3 ataxin 3 2 8
MIRT512665 STEAP3 STEAP3 metalloreductase 2 2
MIRT514184 PGPEP1 pyroglutamyl-peptidase I 2 2
MIRT515053 EBNA1BP2 EBNA1 binding protein 2 2 2
MIRT515138 ZNF799 zinc finger protein 799 2 4
MIRT515452 ZNF747 zinc finger protein 747 2 2
MIRT515791 COL4A3BP collagen type IV alpha 3 binding protein 2 2
MIRT515905 AGTPBP1 ATP/GTP binding protein 1 2 2
MIRT516129 MRPS16 mitochondrial ribosomal protein S16 2 6
MIRT516679 ZNF860 zinc finger protein 860 2 4
MIRT516750 ZNF100 zinc finger protein 100 2 2
MIRT516971 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT517491 NPAP1 nuclear pore associated protein 1 2 2
MIRT517774 PROM2 prominin 2 2 2
MIRT517938 ZNF431 zinc finger protein 431 2 4
MIRT518386 ZNF250 zinc finger protein 250 2 2
MIRT520621 TMEM41B transmembrane protein 41B 2 2
MIRT521028 SLC30A5 solute carrier family 30 member 5 2 2
MIRT521454 RAD51 RAD51 recombinase 2 2
MIRT521564 PTPLB 3-hydroxyacyl-CoA dehydratase 2 1 1
MIRT521581 PTBP2 polypyrimidine tract binding protein 2 2 2
MIRT522263 NKRF NFKB repressing factor 2 2
MIRT522410 MXI1 MAX interactor 1, dimerization protein 2 2
MIRT522543 MED28 mediator complex subunit 28 2 6
MIRT522915 KCNE3 potassium voltage-gated channel subfamily E regulatory subunit 3 2 2
MIRT523029 IGF1 insulin like growth factor 1 2 2
MIRT523854 ESPL1 extra spindle pole bodies like 1, separase 2 4
MIRT524184 DFFA DNA fragmentation factor subunit alpha 2 2
MIRT524520 CDK19 cyclin dependent kinase 19 2 2
MIRT524674 C12orf5 TP53 induced glycolysis regulatory phosphatase 2 2
MIRT530257 ZNF620 zinc finger protein 620 2 2
MIRT540691 BMP3 bone morphogenetic protein 3 2 2
MIRT540976 C17orf85 nuclear cap binding subunit 3 2 2
MIRT545505 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT545631 GGCX gamma-glutamyl carboxylase 2 2
MIRT547358 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT550701 MPL MPL proto-oncogene, thrombopoietin receptor 2 4
MIRT550717 PMPCA peptidase, mitochondrial processing alpha subunit 2 4
MIRT551203 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT553999 SRGAP1 SLIT-ROBO Rho GTPase activating protein 1 2 4
MIRT561081 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT563523 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT564463 SLC35E2 solute carrier family 35 member E2 2 2
MIRT565233 TRAF6 TNF receptor associated factor 6 2 2
MIRT566618 NKAP NFKB activating protein 2 2
MIRT569527 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569639 QPCT glutaminyl-peptide cyclotransferase 2 2
MIRT570253 SSPN sarcospan 2 2
MIRT570570 OTUD7B OTU deubiquitinase 7B 2 2
MIRT570621 MTF2 metal response element binding transcription factor 2 2 2
MIRT571098 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 2 2
MIRT575196 Entpd4 ectonucleoside triphosphate diphosphohydrolase 4 2 2
MIRT575554 Cd99 CD99 antigen 2 2
MIRT575634 Gnl3l guanine nucleotide binding protein-like 3 (nucleolar)-like 2 2
MIRT608267 NOP14 NOP14 nucleolar protein 2 2
MIRT609314 FXYD6 FXYD domain containing ion transport regulator 6 2 2
MIRT627670 RPL28 ribosomal protein L28 2 2
MIRT631185 TSPAN14 tetraspanin 14 2 2
MIRT631964 YIPF5 Yip1 domain family member 5 2 2
MIRT632885 GINM1 glycoprotein integral membrane 1 2 2
MIRT642618 CDKN3 cyclin dependent kinase inhibitor 3 2 2
MIRT645609 TSPAN6 tetraspanin 6 2 2
MIRT662227 PGBD4 piggyBac transposable element derived 4 2 2
MIRT662329 MYLK3 myosin light chain kinase 3 2 2
MIRT662725 LRRC3C leucine rich repeat containing 3C 2 2
MIRT665520 USP14 ubiquitin specific peptidase 14 2 2
MIRT666634 RBMS2 RNA binding motif single stranded interacting protein 2 2 2
MIRT668969 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT670925 DESI1 desumoylating isopeptidase 1 2 2
MIRT673939 ZNF500 zinc finger protein 500 2 2
MIRT674675 PLCE1 phospholipase C epsilon 1 2 2
MIRT675230 MAK male germ cell associated kinase 2 2
MIRT680864 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT681047 ZDBF2 zinc finger DBF-type containing 2 2 2
MIRT681105 CEP57L1 centrosomal protein 57 like 1 2 2
MIRT683553 HAVCR1 hepatitis A virus cellular receptor 1 2 2
MIRT684508 C1orf174 chromosome 1 open reading frame 174 2 2
MIRT684812 BRIX1 BRX1, biogenesis of ribosomes 2 2
MIRT685981 CCDC77 coiled-coil domain containing 77 2 2
MIRT686709 TBC1D19 TBC1 domain family member 19 2 2
MIRT686867 SLC25A32 solute carrier family 25 member 32 2 2
MIRT688908 C11orf84 chromosome 11 open reading frame 84 2 2
MIRT691208 KLHL30 kelch like family member 30 2 2
MIRT692298 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 2 2
MIRT694380 MTA1 metastasis associated 1 2 2
MIRT696497 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT700686 POLR3D RNA polymerase III subunit D 2 2
MIRT701088 PAPOLG poly(A) polymerase gamma 2 2
MIRT703373 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT706189 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT706648 SMIM19 small integral membrane protein 19 2 2
MIRT709466 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT709699 DMWD DM1 locus, WD repeat containing 2 2
MIRT710693 LYRM4 LYR motif containing 4 2 2
MIRT713457 DNAJC11 DnaJ heat shock protein family (Hsp40) member C11 2 2
MIRT722409 RARS2 arginyl-tRNA synthetase 2, mitochondrial 2 2
MIRT725391 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT725548 DNMT3A DNA methyltransferase 3 alpha 2 2

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