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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for RAF1 |
 Gene summary |
| Gene information | Gene symbol | RAF1 | Gene ID | 5894 |
| Gene name | Raf-1 proto-oncogene, serine/threonine kinase | |
| Synonyms | CMD1NN|CRAF|NS5|Raf-1|c-Raf | |
| Cytomap | 3p25.2 | |
| Type of gene | protein-coding | |
| Description | RAF proto-oncogene serine/threonine-protein kinaseC-Raf proto-oncogene, serine/threonine kinaseOncogene RAF1proto-oncogene c-RAFraf proto-oncogene serine/threonine protein kinasev-raf-1 murine leukemia viral oncogene homolog 1v-raf-1 murine leukemia | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| RAF1 | GO:0000186 | activation of MAPKK activity | 10644344 |
| RAF1 | GO:0007190 | activation of adenylate cyclase activity | 15385642 |
| RAF1 | GO:0008285 | negative regulation of cell proliferation | 9765203 |
| RAF1 | GO:0031333 | negative regulation of protein complex assembly | 19667065 |
| RAF1 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19667065 |
| RAF1 | GO:0043066 | negative regulation of apoptotic process | 19667065 |
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Gene structures and expression levels for RAF1 |
| 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. |
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ENSG00000132155
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000416093.1 | RAF1-202:nonsense_mediated_decay:RAF1 | 5.023219e+01 | 1.126305e+00 | 3.234690e-14 | 9.100756e-12 |
| CB | UP | ENST00000491290.1 | RAF1-210:retained_intron:RAF1 | 5.448836e+00 | 8.038412e-01 | 1.394866e-06 | 1.988697e-05 |
| CB | DOWN | ENST00000546084.5 | TRAF1-203:protein_coding:TRAF1 | 8.355914e+01 | -1.598748e+00 | 1.764383e-06 | 2.430583e-05 |
| CB | UP | ENST00000460610.1 | RAF1-206:retained_intron:RAF1 | 5.088723e+00 | 1.337585e+00 | 4.080075e-03 | 1.663889e-02 |
| TC | DOWN | ENST00000546084.5 | TRAF1-203:protein_coding:TRAF1 | 2.128952e+02 | -1.004850e+00 | 4.752938e-06 | 1.430010e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RAF1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_124655 | chr3 | 12609234:12609335:12611950:12612062:12618515:12618747 | 12611950:12612062 |
| exon_skip_125152 | chr3 | 12591708:12591792:12599113:12599225:12599691:12599755 | 12599113:12599225 |
| exon_skip_13809 | chr3 | 12600388:12600415:12604136:12604289:12608766:12608867 | 12604136:12604289 |
| exon_skip_141498 | chr3 | 12591708:12591792:12599113:12599225:12599691:12599808 | 12599113:12599225 |
| exon_skip_152587 | chr3 | 12599691:12599808:12600152:12600279:12600388:12600415 | 12600152:12600279 |
| exon_skip_15983 | chr3 | 12604136:12604289:12606201:12606299:12608766:12608867 | 12606201:12606299 |
| exon_skip_172532 | chr3 | 12587591:12587637:12590798:12590974:12591708:12591789 | 12590798:12590974 |
| exon_skip_21480 | chr3 | 12611950:12612062:12618515:12618747:12663813:12664125 | 12618515:12618747 |
| exon_skip_6487 | chr3 | 12600388:12600415:12603478:12603537:12604136:12604213 | 12603478:12603537 |
| exon_skip_78903 | chr3 | 12591708:12591792:12599113:12599225:12599691:12599806 | 12599113:12599225 |
| exon_skip_82438 | chr3 | 12600152:12600279:12600388:12600415:12604136:12604213 | 12600388:12600415 |
| exon_skip_85027 | chr3 | 12609233:12609335:12611950:12612062:12618515:12618747 | 12611950:12612062 |
| 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 |
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Open reading frame (ORF) annotation in the exon skipping event for RAF1 |
| 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 |
| ENST00000251849 | 12611950 | 12612062 | Frame-shift |
| ENST00000251849 | 12606201 | 12606299 | 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 |
| ENST00000251849 | 12611950 | 12612062 | Frame-shift |
| ENST00000251849 | 12606201 | 12606299 | 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 |
| ENST00000251849 | 12600152 | 12600279 | Frame-shift |
| ENST00000251849 | 12600388 | 12600415 | Frame-shift |
| ENST00000251849 | 12611950 | 12612062 | Frame-shift |
| ENST00000251849 | 12590798 | 12590974 | In-frame |
| ENST00000251849 | 12606201 | 12606299 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RAF1 |
p-ENSG00000132155_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 |
| ENST00000251849 | 3317 | 648 | 12606201 | 12606299 | 1022 | 1119 | 194 | 226 |
| 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 |
| ENST00000251849 | 3317 | 648 | 12606201 | 12606299 | 1022 | 1119 | 194 | 226 |
| 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 |
| ENST00000251849 | 3317 | 648 | 12606201 | 12606299 | 1022 | 1119 | 194 | 226 |
| ENST00000251849 | 3317 | 648 | 12590798 | 12590974 | 1634 | 1809 | 398 | 456 |
| 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 |
| P04049 | 194 | 226 | 1 | 648 | Chain | ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase |
| 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 |
| P04049 | 194 | 226 | 1 | 648 | Chain | ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase |
| 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 |
| P04049 | 194 | 226 | 1 | 648 | Chain | ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase |
| P04049 | 398 | 456 | 1 | 648 | Chain | ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase |
| P04049 | 398 | 456 | 349 | 609 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RAF1 |
| 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 |
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SNVs in the skipped exons for RAF1 |
| - 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 |
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AD stage-associated exon skippint events for RAF1 |
| 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAF1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for RAF1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | TARDBP | exon_skip_85027 | 4.444945e-01 | 1.779637e-02 |
| IFG | RBM25 | exon_skip_85027 | 5.242256e-01 | 4.189834e-03 |
| IFG | SFPQ | exon_skip_85027 | 4.042121e-01 | 3.289471e-02 |
| IFG | CNOT4 | exon_skip_85027 | 5.911425e-01 | 9.244100e-04 |
| IFG | MBNL1 | exon_skip_85027 | 4.806096e-01 | 9.632545e-03 |
| IFG | CELF1 | exon_skip_85027 | 4.036565e-01 | 3.315878e-02 |
| IFG | PABPC1 | exon_skip_85027 | 4.413600e-01 | 1.871535e-02 |
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RelatedDrugs for RAF1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P04049 | approved|investigational | DB00398 | Sorafenib | small molecule | P04049 |
| P04049 | approved|investigational | DB08862 | Cholecystokinin | small molecule | P04049 |
| P04049 | approved | DB08896 | Regorafenib | small molecule | P04049 |
| P04049 | approved|investigational | DB08912 | Dabrafenib | small molecule | P04049 |
| P04049 | approved|investigational | DB12010 | Fostamatinib | small molecule | P04049 |
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RelatedDiseases for RAF1 |
| 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)
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