ExonSkipDB: functional annotation of exon skipping event in human

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	20180523
	UniProtAcc	P04049
	Context	PubMed: RAF1 [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
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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Exon skipping events across known transcript of Ensembl for RAF1 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 RAF1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for RAF1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_381339	3	12625844:12626156:12626345:12626480:12626620:12626752	12626345:12626480	ENSG00000132155.7	ENST00000251849.4,ENST00000534997.1,ENST00000542177.1,ENST00000471449.1,ENST00000423275.1,ENST00000442415.2,ENST00000432427.2
exon_skip_381347	3	12629089:12629136:12632296:12632473:12633206:12633291	12632296:12632473	ENSG00000132155.7	ENST00000251849.4,ENST00000534997.1,ENST00000542177.1,ENST00000465826.1,ENST00000475353.1,ENST00000423275.1,ENST00000442415.2,ENST00000432427.2
exon_skip_381350	3	12633206:12633291:12640611:12640724:12641189:12641254	12640611:12640724	ENSG00000132155.7	ENST00000465826.1
exon_skip_381355	3	12641189:12641307:12641650:12641778:12641886:12641914	12641650:12641778	ENSG00000132155.7	ENST00000251849.4,ENST00000534997.1,ENST00000542177.1,ENST00000465826.1,ENST00000423275.1,ENST00000442415.2,ENST00000432427.2
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENSG00000132155.7	ENST00000442415.2
exon_skip_381359	3	12641886:12641914:12645634:12645788:12650264:12650366	12645634:12645788	ENSG00000132155.7	ENST00000534997.1,ENST00000432427.2
exon_skip_381361	3	12645634:12645788:12647699:12647798:12650264:12650366	12647699:12647798	ENSG00000132155.7	ENST00000491290.1,ENST00000251849.4,ENST00000542177.1,ENST00000423275.1,ENST00000442415.2
exon_skip_381363	3	12650731:12650834:12653448:12653561:12660013:12660246	12653448:12653561	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2
exon_skip_381366	3	12650731:12650834:12660013:12660246:12705311:12705616	12660013:12660246	ENSG00000132155.7	ENST00000542177.1,ENST00000423275.1,ENST00000416093.1
exon_skip_381367	3	12653448:12653561:12660013:12660246:12705311:12705616	12660013:12660246	ENSG00000132155.7	ENST00000442415.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RAF1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_381339	3	12625844:12626156:12626345:12626480:12626620:12626752	12626345:12626480	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2,ENST00000432427.2,ENST00000534997.1,ENST00000423275.1,ENST00000542177.1,ENST00000471449.1
exon_skip_381347	3	12629089:12629136:12632296:12632473:12633206:12633291	12632296:12632473	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2,ENST00000432427.2,ENST00000534997.1,ENST00000423275.1,ENST00000542177.1,ENST00000465826.1,ENST00000475353.1
exon_skip_381350	3	12633206:12633291:12640611:12640724:12641189:12641254	12640611:12640724	ENSG00000132155.7	ENST00000465826.1
exon_skip_381355	3	12641189:12641307:12641650:12641778:12641886:12641914	12641650:12641778	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2,ENST00000432427.2,ENST00000534997.1,ENST00000423275.1,ENST00000542177.1,ENST00000465826.1
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENSG00000132155.7	ENST00000442415.2
exon_skip_381359	3	12641886:12641914:12645634:12645788:12650264:12650366	12645634:12645788	ENSG00000132155.7	ENST00000432427.2,ENST00000534997.1
exon_skip_381361	3	12645634:12645788:12647699:12647798:12650264:12650366	12647699:12647798	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2,ENST00000423275.1,ENST00000542177.1,ENST00000491290.1
exon_skip_381363	3	12650731:12650834:12653448:12653561:12660013:12660246	12653448:12653561	ENSG00000132155.7	ENST00000251849.4,ENST00000442415.2
exon_skip_381366	3	12650731:12650834:12660013:12660246:12705311:12705616	12660013:12660246	ENSG00000132155.7	ENST00000423275.1,ENST00000542177.1,ENST00000416093.1
exon_skip_381367	3	12653448:12653561:12660013:12660246:12705311:12705616	12660013:12660246	ENSG00000132155.7	ENST00000442415.2

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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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 TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000251849	12641650	12641778	Frame-shift
ENST00000251849	12653448	12653561	Frame-shift
ENST00000251849	12626345	12626480	In-frame
ENST00000251849	12632296	12632473	In-frame
ENST00000251849	12647699	12647798	In-frame

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
ENST00000251849	12641650	12641778	Frame-shift
ENST00000251849	12653448	12653561	Frame-shift
ENST00000251849	12626345	12626480	In-frame
ENST00000251849	12632296	12632473	In-frame
ENST00000251849	12647699	12647798	In-frame

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Infer the effects of exon skipping event on protein functional features for RAF1

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

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
ENST00000251849	3317	648	12647699	12647798	1022	1120	194	226
ENST00000251849	3317	648	12632296	12632473	1634	1810	398	456
ENST00000251849	3317	648	12626345	12626480	2109	2243	556	601

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
ENST00000251849	3317	648	12647699	12647798	1022	1120	194	226
ENST00000251849	3317	648	12632296	12632473	1634	1810	398	456
ENST00000251849	3317	648	12626345	12626480	2109	2243	556	601

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
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
P04049	556	601	1	648	Chain	ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase
P04049	556	601	349	609	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P04049	556	601	563	563	Modified residue	Note=Symmetric dimethylarginine%3B by PRMT5;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21917714;Dbxref=PMID:21917714
P04049	556	601	563	563	Mutagenesis	Note=Loss of methylation. Increased stability and catalytic activity in response to EGF treatment. R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21917714;Dbxref=PMID:21917714

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
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
P04049	556	601	1	648	Chain	ID=PRO_0000086596;Note=RAF proto-oncogene serine/threonine-protein kinase
P04049	556	601	349	609	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P04049	556	601	563	563	Modified residue	Note=Symmetric dimethylarginine%3B by PRMT5;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21917714;Dbxref=PMID:21917714
P04049	556	601	563	563	Mutagenesis	Note=Loss of methylation. Increased stability and catalytic activity in response to EGF treatment. R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21917714;Dbxref=PMID:21917714

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SNVs in the skipped exons for RAF1

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- 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-BC-A3KG-01	exon_skip_381339	12626346	12626480	12626352	12626352	Frame_Shift_Del	A	-	p.F599fs
LIHC	TCGA-DD-A3A0-01	exon_skip_381339	12626346	12626480	12626352	12626352	Frame_Shift_Del	A	-	p.F599fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_381339	12626346	12626480	12626352	12626352	Frame_Shift_Del	A	-	p.F599fs
LIHC	TCGA-DD-A1EG-01	exon_skip_381355	12641651	12641778	12641658	12641658	Frame_Shift_Del	T	-	p.N328fs
KIRP	TCGA-GL-A59R-01	exon_skip_381363	12653449	12653561	12653543	12653543	Frame_Shift_Del	T	-	p.M76fs
LIHC	TCGA-DD-A3A0-01	exon_skip_381366 exon_skip_381367	12660014	12660246	12660176	12660176	Frame_Shift_Del	A	-	p.F15fs
LGG	TCGA-HT-7694-01	exon_skip_381363	12653449	12653561	12653552	12653552	Nonsense_Mutation	G	A	p.R73*

- 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
RCCJF_KIDNEY	12626346	12626480	12626386	12626386	Missense_Mutation	C	T	p.C588Y
WM35_SKIN	12632297	12632473	12632350	12632350	Missense_Mutation	C	A	p.K439N
EFO27_OVARY	12632297	12632473	12632459	12632459	Missense_Mutation	A	G	p.V403A
BICR18_UPPER_AERODIGESTIVE_TRACT	12641651	12641778	12641679	12641679	Missense_Mutation	A	C	p.V321G
BICR18_UPPER_AERODIGESTIVE_TRACT	12645635	12645788	12645657	12645657	Missense_Mutation	G	T	p.P271H
C99_LARGE_INTESTINE	12645635	12645788	12645687	12645687	Missense_Mutation	G	C	p.P261R
UPCISCC152_UPPER_AERODIGESTIVE_TRACT	12645635	12645788	12645693	12645693	Missense_Mutation	G	A	p.S259F
NO10_CENTRAL_NERVOUS_SYSTEM	12645635	12645788	12645693	12645693	Missense_Mutation	G	A	p.S259F
SCC90_UPPER_AERODIGESTIVE_TRACT	12645635	12645788	12645693	12645693	Missense_Mutation	G	A	p.S259F
HCC2998_LARGE_INTESTINE	12645635	12645788	12645699	12645699	Missense_Mutation	G	A	p.S257L
MZ2MEL_SKIN	12645635	12645788	12645699	12645699	Missense_Mutation	G	A	p.S257L
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12645635	12645788	12645760	12645760	Missense_Mutation	C	T	p.A237T
CHAGOK1_LUNG	12647700	12647798	12647704	12647704	Missense_Mutation	C	T	p.V226I
SW684_SOFT_TISSUE	12647700	12647798	12647761	12647761	Missense_Mutation	G	A	p.P207S
BICR18_UPPER_AERODIGESTIVE_TRACT	12653449	12653561	12653460	12653460	Missense_Mutation	G	C	p.H103Q
LOVO_LARGE_INTESTINE	12653449	12653561	12653476	12653476	Missense_Mutation	A	G	p.V98A
CAOV4_OVARY	12660014	12660246	12660096	12660097	Missense_Mutation	GC	AT	p.A42I
MESSA_SOFT_TISSUE	12660014	12660246	12660151	12660151	Missense_Mutation	C	T	p.G24S
BICR18_UPPER_AERODIGESTIVE_TRACT	12660014	12660246	12660172	12660172	Missense_Mutation	A	G	p.F17L
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12660014	12660246	12660172	12660172	Missense_Mutation	A	G	p.F17L
HEC59_ENDOMETRIUM	12632297	12632473	12632403	12632403	Nonsense_Mutation	G	A	p.Q422*
RL952_ENDOMETRIUM	12653449	12653561	12653552	12653552	Nonsense_Mutation	G	A	p.R73*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAF1

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
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	CESC	rs2596828	chr3:12645007	C/T	9.72e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	COAD	rs2596828	chr3:12645007	C/T	1.00e-03
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	BLCA	rs2596828	chr3:12645007	C/T	8.76e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	ESCA	rs2596828	chr3:12645007	C/T	8.06e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	HNSC	rs2596828	chr3:12645007	C/T	1.17e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	BRCA	rs2596828	chr3:12645007	C/T	6.95e-09
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	BRCA	rs2596828	chr3:12645007	C/T	4.02e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	LGG	rs2596828	chr3:12645007	C/T	3.76e-12
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	LGG	rs2596828	chr3:12645007	C/T	4.51e-06
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	KIRC	rs2596828	chr3:12645007	C/T	1.03e-03
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	LUAD	rs2596828	chr3:12645007	C/T	5.23e-05
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	OV	rs2596828	chr3:12645007	C/T	9.09e-07
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	PRAD	rs2596828	chr3:12645007	C/T	4.09e-06
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	PRAD	rs2596828	chr3:12645007	C/T	1.87e-03
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	THYM	rs2596828	chr3:12645007	C/T	4.45e-04
exon_skip_381356	3	12641886:12641914:12644976:12645036:12645634:12645712	12644976:12645036	ENST00000442415.2	STAD	rs2596828	chr3:12645007	C/T	1.31e-05

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAF1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAF1

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RelatedDrugs for RAF1

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
	P04049	DB08896	Regorafenib	RAF proto-oncogene serine/threonine-protein kinase	small molecule	approved
	P04049	DB00398	Sorafenib	RAF proto-oncogene serine/threonine-protein kinase	small molecule	approved\|investigational
	P04049	DB08862	Cholecystokinin	RAF proto-oncogene serine/threonine-protein kinase	small molecule	approved\|investigational
	P04049	DB08912	Dabrafenib	RAF proto-oncogene serine/threonine-protein kinase	small molecule	approved\|investigational
	P04049	DB12010	Fostamatinib	RAF proto-oncogene serine/threonine-protein kinase	small molecule	approved\|investigational

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RelatedDiseases for RAF1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
RAF1	C1969057	Noonan Syndrome 5	3	CTD_human;UNIPROT
RAF1	C0007194	Hypertrophic Cardiomyopathy	2	CTD_human;HPO
RAF1	C0028326	Noonan Syndrome	2	CTD_human;ORPHANET
RAF1	C0007131	Non-Small Cell Lung Carcinoma	1	CTD_human
RAF1	C0007193	Cardiomyopathy, Dilated	1	CTD_human;HPO
RAF1	C0017638	Glioma	1	CTD_human
RAF1	C0020429	Hyperalgesia	1	CTD_human
RAF1	C0022665	Kidney Neoplasm	1	CTD_human
RAF1	C0023903	Liver neoplasms	1	CTD_human
RAF1	C0024121	Lung Neoplasms	1	CTD_human
RAF1	C0175704	LEOPARD Syndrome	1	CTD_human;ORPHANET
RAF1	C0345967	Malignant mesothelioma	1	CTD_human
RAF1	C1458155	Mammary Neoplasms	1	CTD_human
RAF1	C4014656	CARDIOMYOPATHY, DILATED, 1NN	1	UNIPROT

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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