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Fusion gene ID: 34823 |
FusionGeneSummary for SMARCC1_ITGB4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SMARCC1_ITGB4 | Fusion gene ID: 34823 | Hgene | Tgene | Gene symbol | SMARCC1 | ITGB4 | Gene ID | 6599 | 3691 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 | integrin subunit beta 4 | |
| Synonyms | BAF155|CRACC1|Rsc8|SRG3|SWI3 | CD104|GP150 | |
| Cytomap | 3p21.31 | 17q25.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | SWI/SNF complex subunit SMARCC1BRG1-associated factor 155SWI/SNF complex 155 kDa subunitSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1chromatin remodeling complex BAF155 subunitmammalian chromatin remode | integrin beta-4CD104 antigen | |
| Modification date | 20180523 | 20180527 | |
| UniProtAcc | Q92922 | P16144 | |
| Ensembl transtripts involved in fusion gene | ENST00000254480, ENST00000425518, | ENST00000579662, ENST00000339591, ENST00000200181, ENST00000450894, ENST00000449880, ENST00000584558, | |
| Fusion gene scores | * DoF score | 13 X 10 X 9=1170 | 4 X 4 X 5=80 |
| # samples | 17 | 5 | |
| ** MAII score | log2(17/1170*10)=-2.78290187833307 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: SMARCC1 [Title/Abstract] AND ITGB4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, in-frame but not retained their 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 |
| Hgene | SMARCC1 | GO:0006337 | nucleosome disassembly | 8895581 |
| Hgene | SMARCC1 | GO:0006338 | chromatin remodeling | 10078207|11018012|11726552 |
| Hgene | SMARCC1 | GO:0045893 | positive regulation of transcription, DNA-templated | 11018012 |
| Tgene | ITGB4 | GO:0009611 | response to wounding | 19403692 |
| Tgene | ITGB4 | GO:0031581 | hemidesmosome assembly | 12482924 |
| 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 | LD | GBM | TCGA-27-2526-01A | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| * 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 | ENST00000254480 | ENST00000579662 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| In-frame | ENST00000254480 | ENST00000339591 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| In-frame | ENST00000254480 | ENST00000200181 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| In-frame | ENST00000254480 | ENST00000450894 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| In-frame | ENST00000254480 | ENST00000449880 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5CDS-intron | ENST00000254480 | ENST00000584558 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-3CDS | ENST00000425518 | ENST00000579662 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-3CDS | ENST00000425518 | ENST00000339591 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-3CDS | ENST00000425518 | ENST00000200181 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-3CDS | ENST00000425518 | ENST00000450894 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-3CDS | ENST00000425518 | ENST00000449880 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
| 5UTR-intron | ENST00000425518 | ENST00000584558 | SMARCC1 | chr3 | 47676680 | - | ITGB4 | chr17 | 73744922 | + |
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FusionProtFeatures for SMARCC1_ITGB4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SMARCC1 | ITGB4 |