|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
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 | 20200329 | |
| UniProtAcc | A0A0C4LC38, A0A1X9T4I6, A0A2R8Y467, A0A2R8Y492, A0A2R8Y679, | |
| Context |
| 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:0000186 | activation of MAPKK activity | 29433126 |
| 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 |
Top |
Gene structures and expression levels for BRAF |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
 |
ENSG00000157764
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000647434.1 | BRAF-221:nonsense_mediated_decay:BRAF | 7.044589e+00 | 1.733085e+00 | 4.540677e-09 | 1.549417e-07 |
| CB | UP | ENST00000642228.1 | BRAF-206:nonsense_mediated_decay:BRAF | 1.781780e+00 | 1.386463e+00 | 6.572634e-04 | 3.630932e-03 |
| CB | UP | ENST00000642808.1 | BRAF-208:lncRNA:BRAF | 4.512381e-01 | 1.039194e+00 | 1.093339e-02 | 3.739018e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for BRAF |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_110648 | chr7 | 140739812:140739946:140749287:140749418:140776912:140777088 | 140749287:140749418 |
| exon_skip_129870 | chr7 | 140747366:140747447:140748932:140749052:140749287:140749418 | 140748932:140749052 |
| exon_skip_134385 | chr7 | 140777991:140778075:140779807:140779928:140781576:140781693 | 140779807:140779928 |
| exon_skip_175944 | chr7 | 140808892:140808995:140834609:140834872:140850111:140850212 | 140834609:140834872 |
| exon_skip_180956 | chr7 | 140783021:140783157:140787548:140787584:140794308:140794415 | 140787548:140787584 |
| exon_skip_19329 | chr7 | 140783021:140783157:140785689:140785808:140787548:140787584 | 140785689:140785808 |
| exon_skip_200845 | chr7 | 140726369:140726516:140734617:140734770:140739812:140739946 | 140734617:140734770 |
| exon_skip_213971 | chr7 | 140739812:140739946:140747366:140747447:140749287:140749418 | 140747366:140747447 |
| exon_skip_2229 | chr7 | 140807960:140808062:140808892:140808995:140834609:140834703 | 140808892:140808995 |
| exon_skip_225594 | chr7 | 140749287:140749418:140753275:140754233:140776912:140777088 | 140753275:140754233 |
| exon_skip_235113 | chr7 | 140808892:140808995:140834609:140834703:140850111:140850212 | 140834609:140834703 |
| exon_skip_267505 | chr7 | 140807960:140808062:140808883:140808995:140834609:140834703 | 140808883:140808995 |
| exon_skip_280765 | chr7 | 140777991:140778075:140779807:140779928:140781576:140781677 | 140779807:140779928 |
| exon_skip_291682 | chr7 | 140807960:140808062:140808237:140808316:140808892:140808995 | 140808237:140808316 |
| exon_skip_66094 | chr7 | 140739812:140739946:140747366:140747447:140748932:140749052 | 140747366:140747447 |
| exon_skip_84865 | chr7 | 140834609:140834872:140850111:140850212:140924566:140924703 | 140850111:140850212 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
Top |
Open reading frame (ORF) annotation in the exon skipping event for BRAF |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000646891 | 140834609 | 140834872 | In-frame |
| ENST00000646891 | 140850111 | 140850212 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000646891 | 140834609 | 140834872 | In-frame |
| ENST00000646891 | 140850111 | 140850212 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000646891 | 140787548 | 140787584 | Frame-shift |
| ENST00000646891 | 140808892 | 140808995 | Frame-shift |
| ENST00000646891 | 140850111 | 140850212 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for BRAF |
p-ENSG00000157764_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000646891 | 6475 | 766 | 140850111 | 140850212 | 364 | 464 | 46 | 79 |
| ENST00000646891 | 6475 | 766 | 140834609 | 140834872 | 466 | 728 | 80 | 167 |
| Loci of skipped exons in MSBB 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 |
| ENST00000646891 | 6475 | 766 | 140850111 | 140850212 | 364 | 464 | 46 | 79 |
| ENST00000646891 | 6475 | 766 | 140834609 | 140834872 | 466 | 728 | 80 | 167 |
| Loci of skipped exons in Mayo 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 |
| ENST00000646891 | 6475 | 766 | 140850111 | 140850212 | 364 | 464 | 46 | 79 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| P15056 | 46 | 79 | 2 | 766 | Chain | ID=PRO_0000085665;Note=Serine/threonine-protein kinase B-raf |
| P15056 | 46 | 79 | 43 | 68 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 46 | 79 | 76 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 80 | 167 | 156 | 161 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| P15056 | 80 | 167 | 165 | 170 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| P15056 | 80 | 167 | 2 | 766 | Chain | ID=PRO_0000085665;Note=Serine/threonine-protein kinase B-raf |
| P15056 | 80 | 167 | 122 | 129 | Compositional bias | Note=Poly-Ser |
| P15056 | 80 | 167 | 155 | 227 | Domain | Note=RBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00262 |
| P15056 | 80 | 167 | 76 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 80 | 167 | 151 | 151 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569 |
| P15056 | 80 | 167 | 162 | 164 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| P15056 | 46 | 79 | 2 | 766 | Chain | ID=PRO_0000085665;Note=Serine/threonine-protein kinase B-raf |
| P15056 | 46 | 79 | 43 | 68 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 46 | 79 | 76 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 80 | 167 | 156 | 161 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| P15056 | 80 | 167 | 165 | 170 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| P15056 | 80 | 167 | 2 | 766 | Chain | ID=PRO_0000085665;Note=Serine/threonine-protein kinase B-raf |
| P15056 | 80 | 167 | 122 | 129 | Compositional bias | Note=Poly-Ser |
| P15056 | 80 | 167 | 155 | 227 | Domain | Note=RBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00262 |
| P15056 | 80 | 167 | 76 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 80 | 167 | 151 | 151 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569 |
| P15056 | 80 | 167 | 162 | 164 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NY5 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| P15056 | 46 | 79 | 2 | 766 | Chain | ID=PRO_0000085665;Note=Serine/threonine-protein kinase B-raf |
| P15056 | 46 | 79 | 43 | 68 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
| P15056 | 46 | 79 | 76 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5VYK |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in BRAF |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Top |
SNVs in the skipped exons for BRAF |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
Top |
AD stage-associated exon skippint events for BRAF |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BRAF |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for BRAF |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_225594 | -4.751862e-01 | 6.572292e-09 |
| CB | PCBP4 | exon_skip_225594 | 4.272931e-01 | 2.618403e-07 |
| CB | TRA2A | exon_skip_225594 | -5.010188e-01 | 7.027896e-10 |
| CB | RBM45 | exon_skip_225594 | 5.695891e-01 | 6.869589e-13 |
| CB | NUP42 | exon_skip_225594 | 4.487767e-01 | 5.376346e-08 |
| FL | ELAVL4 | exon_skip_291682 | -5.190968e-01 | 6.453560e-15 |
| FL | RBM24 | exon_skip_291682 | -5.030386e-01 | 5.740735e-14 |
| FL | RALYL | exon_skip_291682 | -4.576869e-01 | 1.536764e-11 |
| FL | CELF1 | exon_skip_291682 | -4.276509e-01 | 4.059277e-10 |
| HCC | RALYL | exon_skip_225594 | 4.526734e-01 | 3.096388e-14 |
| HCC | EIF4B | exon_skip_225594 | 4.672011e-01 | 3.548586e-15 |
| HCC | ESRP2 | exon_skip_225594 | -4.096035e-01 | 1.073182e-11 |
| HCC | RALYL | exon_skip_291682 | -4.580999e-01 | 6.804697e-15 |
| IFG | MSI1 | exon_skip_200845 | 5.250209e-01 | 4.925373e-03 |
| IFG | RBM6 | exon_skip_200845 | 4.141793e-01 | 3.172790e-02 |
| IFG | TIA1 | exon_skip_200845 | 4.289056e-01 | 2.559151e-02 |
| IFG | IGF2BP3 | exon_skip_200845 | 4.617420e-01 | 1.532748e-02 |
| IFG | RBFOX2 | exon_skip_225594 | 4.272599e-01 | 2.334525e-02 |
| IFG | IGF2BP3 | exon_skip_225594 | -4.264290e-01 | 2.364488e-02 |
| IFG | RBM47 | exon_skip_225594 | -4.375708e-01 | 1.987810e-02 |
| IFG | RBM24 | exon_skip_225594 | 4.028058e-01 | 3.356642e-02 |
| IFG | TARDBP | exon_skip_291682 | -4.527769e-01 | 1.554547e-02 |
| IFG | ELAVL4 | exon_skip_291682 | -4.822460e-01 | 9.353925e-03 |
| IFG | HNRNPD | exon_skip_291682 | -5.066893e-01 | 5.931499e-03 |
| IFG | RALYL | exon_skip_291682 | -4.525015e-01 | 1.561633e-02 |
| IFG | CELF1 | exon_skip_291682 | -4.348752e-01 | 2.074083e-02 |
| PCC | RBM3 | exon_skip_225594 | 4.313494e-01 | 5.194434e-10 |
| PCC | PUM1 | exon_skip_225594 | 4.027192e-01 | 8.398657e-09 |
| PCC | HNRNPD | exon_skip_225594 | 4.136182e-01 | 3.002049e-09 |
| PCC | RALYL | exon_skip_225594 | 4.194414e-01 | 1.706327e-09 |
| PCC | SRSF9 | exon_skip_225594 | 4.140921e-01 | 2.868301e-09 |
| PCC | ESRP2 | exon_skip_225594 | -4.545767e-01 | 4.451545e-11 |
| PCC | MSI1 | exon_skip_291682 | 4.230323e-01 | 1.082676e-09 |
| PCC | ELAVL4 | exon_skip_291682 | -5.014054e-01 | 1.488070e-13 |
| PCC | ILF2 | exon_skip_291682 | -4.297176e-01 | 5.521822e-10 |
| PCC | HNRNPD | exon_skip_291682 | -4.274910e-01 | 6.921261e-10 |
| PCC | RALYL | exon_skip_291682 | -5.612379e-01 | 3.038458e-17 |
| PCC | PTBP1 | exon_skip_291682 | 4.604383e-01 | 2.057941e-11 |
| PG | RBFOX2 | exon_skip_225594 | 4.187274e-01 | 1.326905e-08 |
| PG | ELAVL4 | exon_skip_225594 | 4.025919e-01 | 5.253416e-08 |
| PG | ELAVL4 | exon_skip_291682 | -5.399708e-01 | 7.787794e-17 |
| PG | ELAVL1 | exon_skip_291682 | -4.154317e-01 | 6.466916e-10 |
| PG | RBM24 | exon_skip_291682 | -4.650049e-01 | 2.437482e-12 |
| PG | RALYL | exon_skip_291682 | -5.348141e-01 | 1.726927e-16 |
| PG | CELF1 | exon_skip_291682 | -4.540585e-01 | 9.042713e-12 |
| STG | HNRNPA0 | exon_skip_225594 | 4.386485e-01 | 3.754373e-05 |
| STG | ELAVL4 | exon_skip_291682 | -4.036827e-01 | 9.616292e-05 |
| STG | RALYL | exon_skip_291682 | -4.010621e-01 | 1.077740e-04 |
Top |
RelatedDrugs for BRAF |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P15056 | approved|investigational | DB00398 | Sorafenib | small molecule | P15056 |
| P15056 | approved | DB08881 | Vemurafenib | small molecule | P15056 |
| P15056 | approved | DB08896 | Regorafenib | small molecule | P15056 |
| P15056 | approved|investigational | DB08912 | Dabrafenib | small molecule | P15056 |
| P15056 | approved|investigational | DB11718 | Encorafenib | small molecule | P15056 |
| P15056 | approved|investigational | DB12010 | Fostamatinib | small molecule | P15056 |
Top |
RelatedDiseases for BRAF |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|