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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for BRAF |
 Gene summary |
| Gene information | Gene symbol | BRAF | Gene ID | 673 |
| Gene name | B-Raf proto-oncogene, serine/threonine kinase | |
| Synonyms | B-RAF1|B-raf|BRAF1|NS7|RAFB1 | |
| Cytomap | 7q34 | |
| Type of gene | 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 | |
| Modification date | 20180527 | |
| UniProtAcc | P15056 | |
| Context | PubMed: BRAF [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| BRAF | GO:0006468 | protein phosphorylation | 17563371 |
| BRAF | GO:0010828 | positive regulation of glucose transmembrane transport | 23010278 |
| BRAF | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19667065 |
| BRAF | GO:0043066 | negative regulation of apoptotic process | 19667065 |
| BRAF | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 22065586 |
| BRAF | GO:0071277 | cellular response to calcium ion | 18567582 |
| BRAF | GO:0090150 | establishment of protein localization to membrane | 23010278 |
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Exon skipping events across known transcript of Ensembl for BRAF from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for BRAF |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for BRAF |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_479931 | 7 | 140419126:140426316:140434416:140434570:140439611:140439746 | 140434416:140434570 | ENSG00000157764.8 | ENST00000496384.2 |
| exon_skip_479932 | 7 | 140439611:140439746:140447165:140447247:140449086:140449218 | 140447165:140447247 | ENSG00000157764.8 | ENST00000479537.1 |
| exon_skip_479936 | 7 | 140507759:140507862:140508036:140508116:140508691:140508795 | 140508036:140508116 | ENSG00000157764.8 | ENST00000497784.1 |
| exon_skip_479938 | 7 | 140508691:140508795:140534408:140534672:140549910:140550012 | 140534408:140534672 | ENSG00000157764.8 | ENST00000288602.6,ENST00000497784.1 |
| exon_skip_479939 | 7 | 140534408:140534672:140549910:140550012:140624365:140624458 | 140549910:140550012 | ENSG00000157764.8 | ENST00000469930.1,ENST00000288602.6,ENST00000497784.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for BRAF |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_479931 | 7 | 140419126:140426316:140434416:140434570:140439611:140439746 | 140434416:140434570 | ENSG00000157764.8 | ENST00000496384.2 |
| exon_skip_479932 | 7 | 140439611:140439746:140447165:140447247:140449086:140449218 | 140447165:140447247 | ENSG00000157764.8 | ENST00000479537.1 |
| exon_skip_479936 | 7 | 140507759:140507862:140508036:140508116:140508691:140508795 | 140508036:140508116 | ENSG00000157764.8 | ENST00000497784.1 |
| exon_skip_479938 | 7 | 140508691:140508795:140534408:140534672:140549910:140550012 | 140534408:140534672 | ENSG00000157764.8 | ENST00000288602.6,ENST00000497784.1 |
| exon_skip_479939 | 7 | 140534408:140534672:140549910:140550012:140624365:140624458 | 140549910:140550012 | ENSG00000157764.8 | ENST00000288602.6,ENST00000497784.1,ENST00000469930.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for BRAF |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
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Infer the effects of exon skipping event on protein functional features for BRAF |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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SNVs in the skipped exons for BRAF |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_479931 | 140434417 | 140434570 | 140434525 | 140434525 | Frame_Shift_Del | G | - | p.H725fs |
| KIRC | TCGA-A3-3363-01 | exon_skip_479938 | 140534409 | 140534672 | 140534611 | 140534612 | Frame_Shift_Ins | - | G | p.I101fs |
| CESC | TCGA-EK-A2RK-01 | exon_skip_479939 | 140549911 | 140550012 | 140550007 | 140550007 | Nonsense_Mutation | C | T | p.W48* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 140534409 | 140534672 | 140534480 | 140534481 | Frame_Shift_Del | CC | - | p.A145fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 140534409 | 140534672 | 140534482 | 140534483 | Frame_Shift_Ins | - | TG | p.V144fs |
| OC316_OVARY | 140434417 | 140434570 | 140434458 | 140434458 | Missense_Mutation | G | A | p.A747V |
| OC314_OVARY | 140434417 | 140434570 | 140434458 | 140434458 | Missense_Mutation | G | A | p.A747V |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 140434417 | 140434570 | 140434515 | 140434515 | Missense_Mutation | G | A | p.A728V |
| MFE319_ENDOMETRIUM | 140434417 | 140434570 | 140434519 | 140434519 | Missense_Mutation | T | C | p.S727G |
| SNU407_LARGE_INTESTINE | 140434417 | 140434570 | 140434522 | 140434522 | Missense_Mutation | G | A | p.R726C |
| KM12_LARGE_INTESTINE | 140434417 | 140434570 | 140434564 | 140434564 | Missense_Mutation | C | T | p.A712T |
| CCFSTTG1_CENTRAL_NERVOUS_SYSTEM | 140534409 | 140534672 | 140534476 | 140534476 | Missense_Mutation | C | T | p.R146Q |
| SNU1040_LARGE_INTESTINE | 140534409 | 140534672 | 140534555 | 140534555 | Missense_Mutation | C | T | p.V120I |
| HT29_LARGE_INTESTINE | 140534409 | 140534672 | 140534557 | 140534557 | Missense_Mutation | G | C | p.T119S |
| C33A_CERVIX | 140534409 | 140534672 | 140534569 | 140534569 | Missense_Mutation | G | A | p.A115V |
| SNU1040_LARGE_INTESTINE | 140549911 | 140550012 | 140549925 | 140549925 | Missense_Mutation | A | G | p.S76P |
| MDAMB415_BREAST | 140549911 | 140550012 | 140549931 | 140549931 | Missense_Mutation | G | C | p.P74A |
| GMEL_SKIN | 140434417 | 140434570 | 140434423 | 140434423 | Nonsense_Mutation | C | A | p.G759* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BRAF |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRAF |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BRAF |
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RelatedDrugs for BRAF |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P15056 | DB08881 | Vemurafenib | Serine/threonine-protein kinase B-raf | small molecule | approved | |
| P15056 | DB08896 | Regorafenib | Serine/threonine-protein kinase B-raf | small molecule | approved | |
| P15056 | DB00398 | Sorafenib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational | |
| P15056 | DB08912 | Dabrafenib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational | |
| P15056 | DB11718 | Encorafenib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational | |
| P15056 | DB12010 | Fostamatinib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational |
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RelatedDiseases for BRAF |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| BRAF | C0025202 | melanoma | 21 | CTD_human |
| BRAF | C1527249 | Colorectal Cancer | 8 | UNIPROT |
| BRAF | C1275081 | Cardio-facio-cutaneous syndrome | 6 | CTD_human;ORPHANET;UNIPROT |
| BRAF | C0009404 | Colorectal Neoplasms | 4 | CTD_human |
| BRAF | C0040136 | Thyroid Neoplasm | 4 | CTD_human |
| BRAF | C0024305 | Lymphoma, Non-Hodgkin | 3 | UNIPROT |
| BRAF | C0684249 | Carcinoma of lung | 3 | UNIPROT |
| BRAF | C3150970 | NOONAN SYNDROME 7 | 3 | CTD_human;UNIPROT |
| BRAF | C0152013 | Adenocarcinoma of lung (disorder) | 2 | CTD_human |
| BRAF | C0002448 | Ameloblastoma | 1 | CTD_human |
| BRAF | C0004114 | Astrocytoma | 1 | CTD_human |
| BRAF | C0010276 | Craniopharyngioma | 1 | CTD_human;ORPHANET |
| BRAF | C0017638 | Glioma | 1 | CTD_human |
| BRAF | C0022665 | Kidney Neoplasm | 1 | CTD_human |
| BRAF | C0023903 | Liver neoplasms | 1 | CTD_human |
| BRAF | C0024694 | Mandibular Neoplasms | 1 | CTD_human |
| BRAF | C0028326 | Noonan Syndrome | 1 | CTD_human;ORPHANET |
| BRAF | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| BRAF | C0036920 | Sezary Syndrome | 1 | CTD_human |
| BRAF | C0079773 | Lymphoma, T-Cell, Cutaneous | 1 | CTD_human |
| BRAF | C0206686 | Adrenocortical carcinoma | 1 | CTD_human |
| BRAF | C0206754 | Neuroendocrine Tumors | 1 | CTD_human |
| BRAF | C0238463 | Papillary thyroid carcinoma | 1 | CTD_human;ORPHANET |
| BRAF | C0587248 | Costello syndrome (disorder) | 1 | CTD_human |
| BRAF | C0596263 | Carcinogenesis | 1 | CTD_human |
| BRAF | C0920269 | Microsatellite Instability | 1 | CTD_human |
| BRAF | C2239176 | Liver carcinoma | 1 | CTD_human |
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