|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 5576 |
FusionGeneSummary for CASC3_THRA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CASC3_THRA | Fusion gene ID: 5576 | Hgene | Tgene | Gene symbol | CASC3 | THRA | Gene ID | 22794 | 7067 |
| Gene name | CASC3, exon junction complex subunit | thyroid hormone receptor alpha | |
| Synonyms | BTZ|MLN51 | AR7|CHNG6|EAR7|ERB-T-1|ERBA|ERBA1|NR1A1|THRA1|THRA2|c-ERBA-1 | |
| Cytomap | 17q21.1 | 17q21.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | protein CASC3MLN 51barentszcancer susceptibility 3cancer susceptibility candidate 3cancer susceptibility candidate gene 3 proteinmetastatic lymph node 51metastatic lymph node gene 51 proteinprotein barentsz | thyroid hormone receptor alphaEAR-7ERBA-related 7V-erbA-related protein 7c-erbA-alphanuclear receptor subfamily 1 group A member 1thyroid hormone receptor alpha 1thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homo | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | O15234 | P10827 | |
| Ensembl transtripts involved in fusion gene | ENST00000264645, | ENST00000394121, ENST00000264637, ENST00000584985, ENST00000450525, ENST00000546243, | |
| Fusion gene scores | * DoF score | 15 X 7 X 8=840 | 6 X 5 X 5=150 |
| # samples | 17 | 8 | |
| ** MAII score | log2(17/840*10)=-2.30485458152842 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/150*10)=-0.906890595608519 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CASC3 [Title/Abstract] AND THRA [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Oncogene involved fusion gene, in-frame and retained their domain. Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. Transcription factor involved fusion gene, inframe and retained DNA-binding domain. | ||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | THRA | GO:0006357 | regulation of transcription by RNA polymerase II | 18052923 |
| Tgene | THRA | GO:0006366 | transcription by RNA polymerase II | 8710870|9653119 |
| Tgene | THRA | GO:0009755 | hormone-mediated signaling pathway | 18052923 |
| Tgene | THRA | GO:0017055 | negative regulation of RNA polymerase II transcriptional preinitiation complex assembly | 8524305 |
| Tgene | THRA | GO:0045892 | negative regulation of transcription, DNA-templated | 8710870 |
| Tgene | THRA | GO:2000143 | negative regulation of DNA-templated transcription, initiation | 8524305 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | CHOL | TCGA-ZH-A8Y4-01A | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| In-frame | ENST00000264645 | ENST00000394121 | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
| Frame-shift | ENST00000264645 | ENST00000264637 | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
| 5CDS-intron | ENST00000264645 | ENST00000584985 | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
| 5CDS-intron | ENST00000264645 | ENST00000450525 | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
| 5CDS-intron | ENST00000264645 | ENST00000546243 | CASC3 | chr17 | 38324670 | + | THRA | chr17 | 38249273 | + |
Top |
FusionProtFeatures for CASC3_THRA |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CASC3 | THRA |
| Core component of the splicing-dependent multiproteinexon junction complex (EJC) deposited at splice junctions onmRNAs. The EJC is a dynamic structure consisting of core proteinsand several peripheral nuclear and cytoplasmic associated factorsthat join the complex only transiently either during EJC assemblyor during subsequent mRNA metabolism. The EJC marks the positionof the exon-exon junction in the mature mRNA for the geneexpression machinery and the core components remain bound tospliced mRNAs throughout all stages of mRNA metabolism therebyinfluencing downstream processes including nuclear mRNA export,subcellular mRNA localization, translation efficiency andnonsense-mediated mRNA decay (NMD). Stimulates the ATPase and RNA-helicase activities of EIF4A3. Plays a role in the stress responseby participating in cytoplasmic stress granules assembly and byfavoring cell recovery following stress. Component of thedendritic ribonucleoprotein particles (RNPs) in hippocampalneurons. May play a role in mRNA transport. Binds spliced mRNA insequence-independent manner, 20-24 nucleotides upstream of mRNAexon-exon junctions. Binds poly(G) and poly(U) RNA homopolymer.{ECO:0000269|PubMed:17375189, ECO:0000269|PubMed:17652158}. | Isoform Alpha-1: Nuclear hormone receptor that can actas a repressor or activator of transcription. High affinityreceptor for thyroid hormones, including triiodothyronine andthyroxine. {ECO:0000269|PubMed:12699376,ECO:0000269|PubMed:14673100, ECO:0000269|PubMed:18237438,ECO:0000269|PubMed:19926848}. Isoform Alpha-2: Does not bind thyroid hormone andfunctions as a weak dominant negative inhibitor of thyroid hormoneaction. {ECO:0000269|PubMed:8910441}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 95_131 | 655 | 1130 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 392_395 | 655 | 1130 | Compositional bias | Note=Poly-Pro |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 41_46 | 655 | 1130 | Compositional bias | Note=Poly-Gly |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 425_428 | 655 | 1130 | Compositional bias | Note=Poly-Pro |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 643_648 | 655 | 1130 | Compositional bias | Note=Poly-Pro |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 204_210 | 655 | 1130 | Motif | Nuclear localization signal 1 |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 254_262 | 655 | 1130 | Motif | Nuclear localization signal 2 |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 462_466 | 655 | 1130 | Motif | Note=Nuclear export signal |
| Hgene | CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 137_283 | 655 | 1130 | Region | Note=Sufficient to form the EJC |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000450525 | + | 0 | 9 | 53_127 | -164 | 411 | DNA binding | Nuclear receptor |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000546243 | + | 0 | 9 | 53_127 | -134 | 411 | DNA binding | Nuclear receptor |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000584985 | + | 0 | 10 | 53_127 | -194 | 452 | DNA binding | Nuclear receptor |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000450525 | + | 0 | 9 | 163_407 | -164 | 411 | Domain | NR LBD |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000546243 | + | 0 | 9 | 163_407 | -134 | 411 | Domain | NR LBD |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000584985 | + | 0 | 10 | 163_407 | -194 | 452 | Domain | NR LBD |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000450525 | + | 0 | 9 | 1_52 | -164 | 411 | Region | Note=Modulating |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000546243 | + | 0 | 9 | 1_52 | -134 | 411 | Region | Note=Modulating |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000584985 | + | 0 | 10 | 1_52 | -194 | 452 | Region | Note=Modulating |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000450525 | + | 0 | 9 | 53_73 | -164 | 411 | Zinc finger | NR C4-type |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000450525 | + | 0 | 9 | 91_115 | -164 | 411 | Zinc finger | NR C4-type |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000546243 | + | 0 | 9 | 53_73 | -134 | 411 | Zinc finger | NR C4-type |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000546243 | + | 0 | 9 | 91_115 | -134 | 411 | Zinc finger | NR C4-type |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000584985 | + | 0 | 10 | 53_73 | -194 | 452 | Zinc finger | NR C4-type |
| Tgene | >THRA | chr17:38324670 | chr17:38249273 | ENST00000584985 | + | 0 | 10 | 91_115 | -194 | 452 | Zinc finger | NR C4-type |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | >CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 692_695 | 655 | 1130 | Compositional bias | Note=Poly-Pro |
| Hgene | >CASC3 | chr17:38324670 | chr17:38249273 | ENST00000264645 | + | 11 | 14 | 377_703 | 655 | 1130 | Region | Note=Necessary for localization in cytoplasmic stress granules |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000264637 | + | 8 | 10 | 53_127 | 370 | 491 | DNA binding | Nuclear receptor |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000394121 | + | 8 | 10 | 53_127 | 370 | 491 | DNA binding | Nuclear receptor |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000264637 | + | 8 | 10 | 163_407 | 370 | 491 | Domain | NR LBD |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000394121 | + | 8 | 10 | 163_407 | 370 | 491 | Domain | NR LBD |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000264637 | + | 8 | 10 | 1_52 | 370 | 491 | Region | Note=Modulating |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000394121 | + | 8 | 10 | 1_52 | 370 | 491 | Region | Note=Modulating |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000264637 | + | 8 | 10 | 53_73 | 370 | 491 | Zinc finger | NR C4-type |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000264637 | + | 8 | 10 | 91_115 | 370 | 491 | Zinc finger | NR C4-type |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000394121 | + | 8 | 10 | 53_73 | 370 | 491 | Zinc finger | NR C4-type |
| Tgene | THRA | chr17:38324670 | chr17:38249273 | ENST00000394121 | + | 8 | 10 | 91_115 | 370 | 491 | Zinc finger | NR C4-type |
Top |
FusionGeneSequence for CASC3_THRA |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
Top |
FusionGenePPI for CASC3_THRA |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| CASC3 | ELAVL1, CAND1, EIF4A3, MAGOH, CDK6, GRB2, NXF1, BMI1, VTI1B, TRA2A, PRR11, LUC7L, LUC7L2, SNIP1, UPF3B, AKT1, APC, CASP8, CDKN2A, ESR2, FGFR4, NBN, PHB, PTPN1, PTPRJ, EWSR1, XPO1, LLGL2, RBM8A, MED12, CHST15, KDM1B, UPF3A, WIBG, PNN, ELAVL2, GSPT2, U2AF2, CDX1, APOBEC3D, C11orf57, CLK2, PRDM5, CELF5, RBM3 | THRA | NCOA6, TDG, CCND1, MEF2A, EP300, YWHAQ, ITGB3BP, POU2F1, DAP3, NR0B2, NRIP1, HR, AKAP13, MED12, MED16, MED6, MED24, CDK8, MED21, TRIM24, COPS2, TRIP11, RXRA, MED1, FUS, HDAC3, NCOR1, ZBTB3, SUV39H1, PARP1, NCOA1, NCOA2, NCOA3, TAF11, TAF7, GRIP1, NCOR2, EMD, PRKDC, SMC1A, LIG3, XRCC5, XRCC6, HSPA4, TBL1XR1, GPS2, TBL1X, CUL1, RGN, SEPP1, CDK7, MED25, ARID5A, GTF2B, C1D, THRA, CLIC1, FOXJ1, BUB3, PTGES3, RANBP9, AMOTL2, L3MBTL3, ENO1, MOV10, NXF1, UBE2I, CEP76, TRIM63, A2ML1, HAL, CST6, MTNR1B |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
Top |
RelatedDrugs for CASC3_THRA |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | THRA | P10827 | DB00451 | Levothyroxine | Thyroid hormone receptor alpha | small molecule | approved |
| Tgene | THRA | P10827 | DB00509 | Dextrothyroxine | Thyroid hormone receptor alpha | small molecule | approved|investigational |
| Tgene | THRA | P10827 | DB01118 | Amiodarone | Thyroid hormone receptor alpha | small molecule | approved|investigational |
| Tgene | THRA | P10827 | DB00279 | Liothyronine | Thyroid hormone receptor alpha | small molecule | approved|vet_approved |
Top |
RelatedDiseases for CASC3_THRA |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | THRA | C3280817 | HYPOTHYROIDISM, CONGENITAL, NONGOITROUS, 6 | 2 | UNIPROT |
| Tgene | THRA | C0014175 | Endometriosis | 1 | CTD_human |
| Tgene | THRA | C0019284 | Diaphragmatic Hernia | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|