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Fusion gene ID: 30483 |
FusionGeneSummary for RARA_SKAP1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RARA_SKAP1 | Fusion gene ID: 30483 | Hgene | Tgene | Gene symbol | RARA | SKAP1 | Gene ID | 5914 | 8631 |
| Gene name | retinoic acid receptor alpha | src kinase associated phosphoprotein 1 | |
| Synonyms | NR1B1|RAR | HEL-S-81p|SCAP1|SKAP55 | |
| Cytomap | 17q21.2 | 17q21.32 | |
| Type of gene | protein-coding | protein-coding | |
| Description | retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2 | src kinase-associated phosphoprotein 1SKAP-55epididymis secretory sperm binding protein Li 81ppp55src family-associated phosphoprotein 1src kinase-associated phosphoprotein of 55 kDa | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P10276 | Q86WV1 | |
| Ensembl transtripts involved in fusion gene | ENST00000254066, ENST00000394089, ENST00000425707, ENST00000394086, ENST00000394081, ENST00000420042, | ENST00000336915, ENST00000584924, | |
| Fusion gene scores | * DoF score | 29 X 12 X 7=2436 | 22 X 8 X 9=1584 |
| # samples | 42 | 22 | |
| ** MAII score | log2(42/2436*10)=-2.53605290024021 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(22/1584*10)=-2.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RARA [Title/Abstract] AND SKAP1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Oncogene involved fusion gene, in-frame and 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 | RARA | GO:0007165 | signal transduction | 2825025 |
| Hgene | RARA | GO:0030853 | negative regulation of granulocyte differentiation | 19917671 |
| Hgene | RARA | GO:0032689 | negative regulation of interferon-gamma production | 18416830 |
| Hgene | RARA | GO:0032720 | negative regulation of tumor necrosis factor production | 18416830 |
| Hgene | RARA | GO:0032736 | positive regulation of interleukin-13 production | 18416830 |
| Hgene | RARA | GO:0032753 | positive regulation of interleukin-4 production | 18416830 |
| Hgene | RARA | GO:0032754 | positive regulation of interleukin-5 production | 18416830 |
| Hgene | RARA | GO:0045630 | positive regulation of T-helper 2 cell differentiation | 18416830 |
| Hgene | RARA | GO:0045892 | negative regulation of transcription, DNA-templated | 20080953 |
| Hgene | RARA | GO:0045893 | positive regulation of transcription, DNA-templated | 18845237|19850744|20080953 |
| Hgene | RARA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19850744 |
| Hgene | RARA | GO:0071300 | cellular response to retinoic acid | 19917671 |
| Hgene | RARA | GO:0071391 | cellular response to estrogen stimulus | 20080953 |
| Tgene | SKAP1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 11909961 |
| 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 | BRCA | TCGA-B6-A0IN-01A | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| * 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 | ENST00000254066 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| Frame-shift | ENST00000254066 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| In-frame | ENST00000394089 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| Frame-shift | ENST00000394089 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| In-frame | ENST00000425707 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| Frame-shift | ENST00000425707 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000394086 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000394086 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000394081 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000394081 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000420042 | ENST00000336915 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
| intron-3CDS | ENST00000420042 | ENST00000584924 | RARA | chr17 | 38487648 | + | SKAP1 | chr17 | 46214699 | - |
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FusionProtFeatures for RARA_SKAP1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RARA | SKAP1 |