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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:BRAF-CUL1 (FusionGDB2 ID:10120) |
Fusion Gene Summary for BRAF-CUL1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: BRAF-CUL1 | Fusion gene ID: 10120 | Hgene | Tgene | Gene symbol | BRAF | CUL1 | Gene ID | 673 | 8454 |
| Gene name | B-Raf proto-oncogene, serine/threonine kinase | cullin 1 | |
| Synonyms | B-RAF1|B-raf|BRAF1|NS7|RAFB1 | - | |
| Cytomap | 7q34 | 7q36.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | serine/threonine-protein kinase B-raf94 kDa B-raf proteinB-Raf proto-oncogene serine/threonine-protein kinase (p94)B-Raf serine/threonine-proteinmurine sarcoma viral (v-raf) oncogene homolog B1proto-oncogene B-Rafv-raf murine sarcoma viral oncogene | cullin-1CUL-1 | |
| Modification date | 20200329 | 20200327 | |
| UniProtAcc | P15056 | Q13616 | |
| Ensembl transtripts involved in fusion gene | ENST00000288602, | ENST00000325222, ENST00000409469, ENST00000602748, | |
| Fusion gene scores | * DoF score | 28 X 21 X 11=6468 | 7 X 9 X 4=252 |
| # samples | 32 | 11 | |
| ** MAII score | log2(32/6468*10)=-4.3371758685863 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(11/252*10)=-1.19592020997526 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: BRAF [Title/Abstract] AND CUL1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | BRAF(140549911)-CUL1(148427054), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | BRAF | GO:0000186 | activation of MAPKK activity | 29433126 |
| Hgene | BRAF | GO:0006468 | protein phosphorylation | 17563371 |
| Hgene | BRAF | GO:0010828 | positive regulation of glucose transmembrane transport | 23010278 |
| Hgene | BRAF | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19667065 |
| Hgene | BRAF | GO:0043066 | negative regulation of apoptotic process | 19667065 |
| Hgene | BRAF | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 22065586 |
| Hgene | BRAF | GO:0071277 | cellular response to calcium ion | 18567582 |
| Hgene | BRAF | GO:0090150 | establishment of protein localization to membrane | 23010278 |
| Tgene | CUL1 | GO:0016567 | protein ubiquitination | 15103331 |
| Tgene | CUL1 | GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | 15103331 |
| Fusion gene breakpoints across BRAF (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across CUL1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | KIRP | TCGA-5P-A9JZ-01A | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148427054 | + |
| ChimerDB4 | KIRP | TCGA-5P-A9JZ | BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + |
| ChimerDB4 | KIRP | TCGA-5P-A9JZ | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148391242 | + |
| ChimerDB4 | KIRP | TCGA-5P-A9JZ | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148427054 | + |
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Fusion Gene ORF analysis for BRAF-CUL1 |
| 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 |
| 5CDS-5UTR | ENST00000288602 | ENST00000325222 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148427054 | + |
| 5CDS-5UTR | ENST00000288602 | ENST00000325222 | BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + |
| 5CDS-5UTR | ENST00000288602 | ENST00000409469 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148427054 | + |
| 5CDS-5UTR | ENST00000288602 | ENST00000409469 | BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + |
| 5CDS-5UTR | ENST00000288602 | ENST00000602748 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148427054 | + |
| 5CDS-5UTR | ENST00000288602 | ENST00000602748 | BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + |
| 5CDS-intron | ENST00000288602 | ENST00000325222 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148391242 | + |
| 5CDS-intron | ENST00000288602 | ENST00000409469 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148391242 | + |
| 5CDS-intron | ENST00000288602 | ENST00000602748 | BRAF | chr7 | 140549911 | - | CUL1 | chr7 | 148391242 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for BRAF-CUL1 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + | 8.34E-07 | 0.99999917 |
| BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + | 8.34E-07 | 0.99999917 |
| BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + | 8.34E-07 | 0.99999917 |
| BRAF | chr7 | 140549910 | - | CUL1 | chr7 | 148427053 | + | 8.34E-07 | 0.99999917 |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for BRAF-CUL1 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:140549911/:148427054) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| BRAF | CUL1 |
| FUNCTION: Protein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus (Probable). Phosphorylates MAP2K1, and thereby activates the MAP kinase signal transduction pathway (PubMed:21441910, PubMed:29433126). May play a role in the postsynaptic responses of hippocampal neurons (PubMed:1508179). {ECO:0000269|PubMed:1508179, ECO:0000269|PubMed:21441910, ECO:0000269|PubMed:29433126, ECO:0000305}. | FUNCTION: Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. SCF complexes and ARIH1 collaborate in tandem to mediate ubiquitination of target proteins (PubMed:27565346). In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and exchange of the substrate recognition component is mediated by TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(BTRC) and/or SCF(FBXW11) direct ubiquitination of CEP68 (PubMed:25704143, PubMed:25503564). SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of CCNE1, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO1) directs ubiquitination of BCL6 and DTL but does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(CCNF) directs ubiquitination of CCP110. SCF(FBXL3) and SCF(FBXL21) direct ubiquitination of CRY1 and CRY2. SCF(FBXO9) directs ubiquitination of TTI1 and TELO2. SCF(FBXO10) directs ubiquitination of BCL2. {ECO:0000269|PubMed:15531760, ECO:0000269|PubMed:15640526, ECO:0000269|PubMed:18644861, ECO:0000269|PubMed:19679664, ECO:0000269|PubMed:22113614, ECO:0000269|PubMed:22405651, ECO:0000269|PubMed:23263282, ECO:0000269|PubMed:23431138, ECO:0000269|PubMed:25503564, ECO:0000269|PubMed:25704143, ECO:0000269|PubMed:27565346, ECO:0000269|PubMed:9663463}. |
| 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 |
| - 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 |
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Fusion Gene Sequence for BRAF-CUL1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for BRAF-CUL1 |
| 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 |
| - 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 |
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Related Drugs for BRAF-CUL1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for BRAF-CUL1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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