miRTarBase - #MIRT364023


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pre-miRNA Information
pre-miRNA hsa-mir-3119-1   
Genomic Coordinates chr1: 170151378 - 170151462
Description Homo sapiens miR-3119-1 stem-loop
Comment None
RNA Secondary Structure
pre-miRNA hsa-mir-3119-2   
Genomic Coordinates chr1: 170151378 - 170151462
Description Homo sapiens miR-3119-2 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3119
Sequence 9| UGGCUUUUAACUUUGAUGGC |28
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs976695651 1 dbSNP
rs924732934 1 dbSNP
rs537840374 2 dbSNP
rs1264087496 6 dbSNP
rs1484055858 9 dbSNP
rs1467832924 10 dbSNP
rs1198335970 11 dbSNP
rs1431115212 12 dbSNP
rs1176953550 16 dbSNP
Putative Targets

Gene Information
Gene Symbol SDCBP   
Synonyms MDA-9, MDA9, ST1, SYCL, TACIP18
Description syndecan binding protein
Transcript NM_001007067   
Other Transcripts NM_001007068 , NM_001007069 , NM_001007070 , NM_005625   
Expression
Putative miRNA Targets on SDCBP
3'UTR of SDCBP
(miRNA target sites are highlighted)		 
>SDCBP|NM_001007067|3'UTR
   1 AATTCACGGCACCATGGAAATGTAGCTGAACGTCTCCAGTTTCCTTCTTTGGCAACTTCTGTATTATGCACGTGAAGCCT
  81 TCCCGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATCTTACATTATGGCTGGGAATCTTACTCTTTCATCTGAT
 161 ACCTTGTTCAGATTTCAAAATAGTTGTAGCCTTATCCTGGTTTTACAGATGTGAAACTTTCAAGAGATTTACTGACTTTC
 241 CTAGAATAGTTTCTCTACTGGAAACCTGATGCTTTTATAAGCCATTGTGATTAGGATGACTGTTACAGGCTTAGCTTTGT
 321 GTGAAAACCAGTCACCTTTCTCCTAGGTAATGAGTAGTGCTGTTCATATTACTTTAGTTCTATAGCATACTTGCATCTTT
 401 AACATGCTATCATAGTACATTTAGAATGATTGCCTTTGATTTTTTTTTTAAATTCTGTGTGTGTGTGTGTAAAATGCCAA
 481 TTAAGAACACTGGTTTCATTCCATGTAAGCATTAAACAGTGTATGTAGGTTTCAAGAGATTGTGATGATTCTTAAATTTT
 561 AACTACCTTCACTTAATATGCTTGAACTGTCGCCTTAACTATGTTAAGCATCTAGACTAAAAGCCAAAATATAATTATTG
 641 CTGCCTTTCTAAAAACCCAAAATGTAGTTCTCTATTAACCTGAAATGTACACTAGCCCAGAACAGTTTAATGGTACTTAC
 721 TGAGCTATAGCATAGCTGCTTAGTTGTTTTTGAGATTTTTTAGTCAACACATAATGGAAACTTCTTTCTTCTAAAAGTTG
 801 CCAGTGCCACTTTTAAGAAGTGAATCACTATATGTGATGTAAAAGTTATTACACTAAACAGGATAAACTTTTGACTCCCC
 881 TTTTGTTCATTTGTGGATTAAGTGGTATAATACTTAATTTTGGCATTTGACTCTTAAGATTATGTAACCTAGCTACTTTG
 961 GGATGGTCTTAGAATATTTTTCTGATAACTTGTTCCTTTTCCTGACTCCTCCTTGCAAACAAAATGATAGTTGACACTTT
1041 ATCCTGATTTTTTTCTTCTTTTTGGTTTATGTCTATTCTAATTAAATATGTATAAATAAAGTTACATTTTAGTCTGTCTA
1121 AAAAAA
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' cgGUAGUUUCAAUUUUCGGu 5'
            |||| |:  |||||||| 
Target 5' agCATCTAGACTAAAAGCCa 3'
 607 - 626 162.00 -14.60
2 
miRNA  3' cgguaguuucAAUUUUCGGu 5'
                    ||| ||||| 
Target 5' cctgatgcttTTATAAGCCa 3'
 265 - 284 118.00 -6.66
3 
miRNA  3' cgguaguuuCAAUUUUCGGu 5'
                   || ||| ||| 
Target 5' tgtgtgtgtGTAAAATGCCa 3'
 460 - 479 115.00 -5.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31602067 6 COSMIC
COSN30146901 17 COSMIC
COSN30499191 28 COSMIC
COSN31502728 46 COSMIC
COSN30151787 67 COSMIC
COSN4881510 94 COSMIC
COSN1366505 100 COSMIC
COSN31573400 120 COSMIC
COSN30100623 125 COSMIC
COSN31542374 254 COSMIC
COSN30068211 431 COSMIC
COSN31527801 451 COSMIC
COSN31595109 458 COSMIC
COSN20105528 471 COSMIC
COSN31532538 477 COSMIC
COSN20091817 593 COSMIC
COSN26564014 604 COSMIC
COSN6700817 873 COSMIC
COSN31486118 1080 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs370633085 8 dbSNP
rs577430106 9 dbSNP
rs1300348606 16 dbSNP
rs189167178 18 dbSNP
rs1347569550 23 dbSNP
rs370076491 25 dbSNP
rs759067145 26 dbSNP
rs371949686 29 dbSNP
rs563050111 30 dbSNP
rs137927039 32 dbSNP
rs763938746 33 dbSNP
rs753770369 35 dbSNP
rs201667562 42 dbSNP
rs1199149694 48 dbSNP
rs765048220 49 dbSNP
rs1803072 59 dbSNP
rs1453826244 64 dbSNP
rs1271663307 65 dbSNP
rs373695046 72 dbSNP
rs1362665865 73 dbSNP
rs1420584782 75 dbSNP
rs181823693 85 dbSNP
rs953368080 86 dbSNP
rs1347224268 99 dbSNP
rs1006182348 102 dbSNP
rs1016946760 103 dbSNP
rs962349435 104 dbSNP
rs972707143 109 dbSNP
rs1803071 117 dbSNP
rs1402595230 118 dbSNP
rs547354370 123 dbSNP
rs570780186 129 dbSNP
rs1176048204 133 dbSNP
rs1468543638 133 dbSNP
rs1041933920 141 dbSNP
rs918124282 148 dbSNP
rs970860972 158 dbSNP
rs1232866662 161 dbSNP
rs981162496 175 dbSNP
rs1239795984 176 dbSNP
rs2997 178 dbSNP
rs927004776 180 dbSNP
rs1355369766 181 dbSNP
rs937018775 211 dbSNP
rs1224061810 218 dbSNP
rs1054097197 224 dbSNP
rs914210939 234 dbSNP
rs946011291 235 dbSNP
rs1337368904 240 dbSNP
rs1224275091 245 dbSNP
rs539674908 246 dbSNP
rs901712937 251 dbSNP
rs11550278 256 dbSNP
rs368807103 257 dbSNP
rs569977497 271 dbSNP
rs997317174 273 dbSNP
rs1337817936 290 dbSNP
rs1468463717 293 dbSNP
rs1409818948 299 dbSNP
rs1417978240 305 dbSNP
rs756998326 307 dbSNP
rs548637514 319 dbSNP
rs1050503956 324 dbSNP
rs771864245 334 dbSNP
rs187436234 337 dbSNP
rs1181322503 338 dbSNP
rs555626507 350 dbSNP
rs1243453372 352 dbSNP
rs565762692 355 dbSNP
rs1406067214 358 dbSNP
rs755940317 360 dbSNP
rs1435920482 366 dbSNP
rs1398700473 368 dbSNP
rs1274999159 373 dbSNP
rs993744036 380 dbSNP
rs1215128078 385 dbSNP
rs1025146544 391 dbSNP
rs1342910142 395 dbSNP
rs534721260 406 dbSNP
rs1325306580 413 dbSNP
rs3739326 414 dbSNP
rs577568381 431 dbSNP
rs546434818 438 dbSNP
rs1303702918 439 dbSNP
rs202058764 440 dbSNP
rs990290122 440 dbSNP
rs1331416537 445 dbSNP
rs935993008 450 dbSNP
rs1364348110 451 dbSNP
rs556569919 451 dbSNP
rs1278546727 452 dbSNP
rs1348121610 453 dbSNP
rs1385453807 454 dbSNP
rs1234423961 456 dbSNP
rs373068871 456 dbSNP
rs375487262 456 dbSNP
rs748166947 458 dbSNP
rs1490169761 464 dbSNP
rs1291046070 467 dbSNP
rs1274240066 470 dbSNP
rs1361745022 481 dbSNP
rs1313672685 483 dbSNP
rs760832121 489 dbSNP
rs772247252 504 dbSNP
rs1371572855 505 dbSNP
rs1212430197 511 dbSNP
rs117089964 521 dbSNP
rs542004174 522 dbSNP
rs1345425543 527 dbSNP
rs1050224241 532 dbSNP
rs1425977480 534 dbSNP
rs1365701544 546 dbSNP
rs1157861645 554 dbSNP
rs1398615459 563 dbSNP
rs142419216 564 dbSNP
rs942167334 565 dbSNP
rs771166767 566 dbSNP
rs1201556459 568 dbSNP
rs776924987 577 dbSNP
rs1490850133 580 dbSNP
rs1038183095 581 dbSNP
rs1215263752 587 dbSNP
rs527753119 588 dbSNP
rs117485213 592 dbSNP
rs770186549 593 dbSNP
rs1473926836 594 dbSNP
rs1345325682 599 dbSNP
rs906762927 602 dbSNP
rs1407329240 614 dbSNP
rs1367634529 616 dbSNP
rs1287795284 620 dbSNP
rs1428133151 623 dbSNP
rs1418395998 647 dbSNP
rs1346591237 652 dbSNP
rs776113853 653 dbSNP
rs1469074042 658 dbSNP
rs1033878348 667 dbSNP
rs1426982039 673 dbSNP
rs1178443068 674 dbSNP
rs1480732204 677 dbSNP
rs190601179 687 dbSNP
rs144694795 695 dbSNP
rs1484964921 701 dbSNP
rs1244035361 704 dbSNP
rs1209637412 706 dbSNP
rs1323221309 711 dbSNP
rs1261689422 714 dbSNP
rs1313301831 719 dbSNP
rs1402407719 719 dbSNP
rs1409988922 734 dbSNP
rs989951755 736 dbSNP
rs1363503229 742 dbSNP
rs1333589378 747 dbSNP
rs1451486966 756 dbSNP
rs1021761069 762 dbSNP
rs550197473 771 dbSNP
rs1466415171 772 dbSNP
rs182846496 777 dbSNP
rs1426783709 778 dbSNP
rs1421783715 782 dbSNP
rs761497147 784 dbSNP
rs1355156621 791 dbSNP
rs1231850314 795 dbSNP
rs34213860 799 dbSNP
rs933254201 799 dbSNP
rs529235568 804 dbSNP
rs1260507323 805 dbSNP
rs986043362 811 dbSNP
rs1203071111 817 dbSNP
rs1308695325 818 dbSNP
rs1297711076 824 dbSNP
rs1244697466 827 dbSNP
rs1380112856 831 dbSNP
rs375546473 839 dbSNP
rs556904207 841 dbSNP
rs1396375168 850 dbSNP
rs1395562032 865 dbSNP
rs1296341833 875 dbSNP
rs1463485334 881 dbSNP
rs1383024068 888 dbSNP
rs941823627 890 dbSNP
rs1037793250 892 dbSNP
rs767280461 894 dbSNP
rs375338364 899 dbSNP
rs1383603681 914 dbSNP
rs148339226 925 dbSNP
rs879148668 930 dbSNP
rs565902159 934 dbSNP
rs1424720546 945 dbSNP
rs1250284103 953 dbSNP
rs1257078982 963 dbSNP
rs1474732370 986 dbSNP
rs929319503 1015 dbSNP
rs1481907918 1016 dbSNP
rs745541451 1023 dbSNP
rs1276055789 1045 dbSNP
rs1221070585 1047 dbSNP
rs1356701008 1048 dbSNP
rs556672357 1048 dbSNP
rs1245109637 1049 dbSNP
rs1475730475 1053 dbSNP
rs1166796613 1055 dbSNP
rs753271575 1056 dbSNP
rs1044304 1059 dbSNP
rs1304620628 1060 dbSNP
rs1436048815 1069 dbSNP
rs1313047057 1074 dbSNP
rs1374497858 1079 dbSNP
rs1413279447 1093 dbSNP
rs1280533956 1094 dbSNP
rs534657293 1097 dbSNP
rs1362632584 1099 dbSNP
rs1002452438 1100 dbSNP
rs1165168466 1112 dbSNP
rs1034340334 1118 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

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

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000260130.4 | 3UTR | CCAAAAUAUAAUUAUUGCUGCCUUUCUAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
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-3119 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT130164 TXNIP thioredoxin interacting protein 2 4
MIRT364023 SDCBP syndecan binding protein 2 2
MIRT383920 BTG2 BTG anti-proliferation factor 2 2 2
MIRT397609 RACGAP1 Rac GTPase activating protein 1 2 2
MIRT404072 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT443202 ECHDC3 enoyl-CoA hydratase domain containing 3 2 2
MIRT446469 THUMPD3 THUMP domain containing 3 2 2
MIRT446489 PRELP proline and arginine rich end leucine rich repeat protein 2 2
MIRT446849 FIBIN fin bud initiation factor homolog (zebrafish) 2 2
MIRT463282 ZFX zinc finger protein, X-linked 2 4
MIRT478441 DAZAP2 DAZ associated protein 2 2 2
MIRT480447 C16orf72 chromosome 16 open reading frame 72 2 2
MIRT480632 BTBD3 BTB domain containing 3 2 6
MIRT487460 ANKRD42 ankyrin repeat domain 42 2 2
MIRT487497 IL1F10 interleukin 1 family member 10 2 4
MIRT491967 USP37 ubiquitin specific peptidase 37 2 2
MIRT495620 PPP1R1C protein phosphatase 1 regulatory inhibitor subunit 1C 2 2
MIRT496151 RPS15A ribosomal protein S15a 2 2
MIRT498042 SNX5 sorting nexin 5 2 6
MIRT500546 XBP1P1 X-box binding protein 1 pseudogene 1 2 8
MIRT503902 ZSCAN25 zinc finger and SCAN domain containing 25 2 2
MIRT513157 BIRC5 baculoviral IAP repeat containing 5 2 6
MIRT519070 KCNK6 potassium two pore domain channel subfamily K member 6 2 2
MIRT519741 ZNF394 zinc finger protein 394 2 4
MIRT522733 LRP8 LDL receptor related protein 8 2 4
MIRT539402 ADIPOR2 adiponectin receptor 2 2 2
MIRT551660 KIAA1143 KIAA1143 2 4
MIRT559131 BTG3 BTG anti-proliferation factor 3 2 4
MIRT559307 ATXN1 ataxin 1 2 2
MIRT559515 ARHGEF26 Rho guanine nucleotide exchange factor 26 2 2
MIRT560771 RRP7A ribosomal RNA processing 7 homolog A 2 2
MIRT562210 HMGB2 high mobility group box 2 2 2
MIRT562734 ZNF468 zinc finger protein 468 2 2
MIRT563070 EMC8 ER membrane protein complex subunit 8 2 2
MIRT563731 ZNF107 zinc finger protein 107 2 4
MIRT576719 Wars tryptophanyl-tRNA synthetase 2 2
MIRT612872 IGFBP5 insulin like growth factor binding protein 5 2 4
MIRT613214 CCDC85C coiled-coil domain containing 85C 2 4
MIRT613591 THSD7A thrombospondin type 1 domain containing 7A 2 2
MIRT614332 NANOS1 nanos C2HC-type zinc finger 1 2 4
MIRT614929 MARCH3 membrane associated ring-CH-type finger 3 2 2
MIRT616257 KANK4 KN motif and ankyrin repeat domains 4 2 2
MIRT617087 FPR1 formyl peptide receptor 1 2 2
MIRT617167 SLC16A5 solute carrier family 16 member 5 2 2
MIRT620350 WDR75 WD repeat domain 75 2 2
MIRT621041 SOX30 SRY-box 30 2 2
MIRT625936 SCYL3 SCY1 like pseudokinase 3 2 2
MIRT636872 BCORL1 BCL6 corepressor like 1 2 2
MIRT637019 CLASP1 cytoplasmic linker associated protein 1 2 2
MIRT637299 ACTN2 actinin alpha 2 2 2
MIRT639734 MAP2K2 mitogen-activated protein kinase kinase 2 2 2
MIRT640811 ZMAT1 zinc finger matrin-type 1 2 2
MIRT642879 SAMD1 sterile alpha motif domain containing 1 2 2
MIRT648116 ADAT1 adenosine deaminase, tRNA specific 1 2 2
MIRT655769 NPTX1 neuronal pentraxin 1 2 2
MIRT655801 NOVA2 NOVA alternative splicing regulator 2 2 2
MIRT659142 DDR2 discoidin domain receptor tyrosine kinase 2 2 2
MIRT660327 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT662150 IPO11 importin 11 2 2
MIRT664741 METTL16 methyltransferase like 16 2 2
MIRT670134 HOXD12 homeobox D12 2 2
MIRT679027 ZNF419 zinc finger protein 419 2 2
MIRT695596 TMEM199 transmembrane protein 199 2 2
MIRT703345 GATAD2B GATA zinc finger domain containing 2B 2 2
MIRT704097 DST dystonin 2 2
MIRT711833 AMOTL2 angiomotin like 2 2 2
MIRT715820 ZNF598 zinc finger protein 598 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3119 Imatinib 5291 NSC743414 approved sensitive High Gastrointestinal Stromal Tumor cell line (882R-NC, 882R-OE, 882R-KD)
hsa-miR-3119 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3119 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-3119 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)

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