ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SYK

Gene summary

Gene information	Gene symbol	SYK
	Gene ID	6850
	Gene name	spleen associated tyrosine kinase
	Synonyms	p72-Syk
	Cytomap	9q22.2
	Type of gene	protein-coding
	Description	tyrosine-protein kinase SYKspleen tyrosine kinase
	Modification date	20180523
	UniProtAcc	P43405
	Context	PubMed: SYK [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
SYK	GO:0006468	protein phosphorylation	17681949
SYK	GO:0007159	leukocyte cell-cell adhesion	12885943
SYK	GO:0030593	neutrophil chemotaxis	12885943

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Exon skipping events across known transcript of Ensembl for SYK 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 SYK

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 SYK

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_497057	9	93627329:93627379:93629412:93629481:93636485:93636573	93629412:93629481	ENSG00000165025.10	ENST00000375754.4,ENST00000375746.1
exon_skip_497060	9	93627329:93627379:93636485:93636573:93636953:93637131	93636485:93636573	ENSG00000165025.10	ENST00000375751.4,ENST00000375747.1
exon_skip_497063	9	93641045:93641235:93650030:93650171:93650796:93650909	93650030:93650171	ENSG00000165025.10	ENST00000375754.4,ENST00000375751.4,ENST00000375746.1,ENST00000375747.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SYK

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_497057	9	93627329:93627379:93629412:93629481:93636485:93636573	93629412:93629481	ENSG00000165025.10	ENST00000375754.4,ENST00000375746.1
exon_skip_497060	9	93627329:93627379:93636485:93636573:93636953:93637131	93636485:93636573	ENSG00000165025.10	ENST00000375751.4,ENST00000375747.1
exon_skip_497063	9	93641045:93641235:93650030:93650171:93650796:93650909	93650030:93650171	ENSG00000165025.10	ENST00000375754.4,ENST00000375751.4,ENST00000375747.1,ENST00000375746.1

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 SYK

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
ENST00000375746	93629412	93629481	In-frame
ENST00000375754	93629412	93629481	In-frame
ENST00000375746	93650030	93650171	In-frame
ENST00000375754	93650030	93650171	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
ENST00000375746	93629412	93629481	In-frame
ENST00000375754	93629412	93629481	In-frame
ENST00000375746	93650030	93650171	In-frame
ENST00000375754	93650030	93650171	In-frame

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

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
ENST00000375746	5007	635	93629412	93629481	980	1048	282	305
ENST00000375754	5022	635	93629412	93629481	995	1063	282	305
ENST00000375746	5007	635	93650030	93650171	1715	1855	527	574
ENST00000375754	5022	635	93650030	93650171	1730	1870	527	574

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
ENST00000375746	5007	635	93629412	93629481	980	1048	282	305
ENST00000375754	5022	635	93629412	93629481	995	1063	282	305
ENST00000375746	5007	635	93650030	93650171	1715	1855	527	574
ENST00000375754	5022	635	93650030	93650171	1730	1870	527	574

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
P43405	282	305	283	305	Alternative sequence	ID=VSP_005010;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P43405	282	305	283	305	Alternative sequence	ID=VSP_005010;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P43405	282	305	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	282	305	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	282	305	295	295	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	295	295	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	296	296	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	296	296	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Mutagenesis	Note=Abolishes YWHAG binding. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Mutagenesis	Note=Abolishes YWHAG binding. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	260	370	Region	Note=Interdomain B
P43405	282	305	260	370	Region	Note=Interdomain B
P43405	527	574	524	527	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	524	527	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	548	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	548	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	527	574	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	527	574	371	631	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P43405	527	574	371	631	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P43405	527	574	536	538	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	536	538	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	541	546	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	541	546	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	551	566	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	551	566	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	530	530	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	527	574	530	530	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	527	574	546	546	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P48025
P43405	527	574	546	546	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P48025
P43405	527	574	567	569	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	567	569	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	572	575	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	572	575	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR

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
P43405	282	305	283	305	Alternative sequence	ID=VSP_005010;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P43405	282	305	283	305	Alternative sequence	ID=VSP_005010;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P43405	282	305	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	282	305	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	282	305	295	295	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	295	295	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	296	296	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	296	296	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Mutagenesis	Note=Abolishes YWHAG binding. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	297	297	Mutagenesis	Note=Abolishes YWHAG binding. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	282	305	260	370	Region	Note=Interdomain B
P43405	282	305	260	370	Region	Note=Interdomain B
P43405	527	574	524	527	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	524	527	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	548	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	548	550	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	527	574	1	635	Chain	ID=PRO_0000088165;Note=Tyrosine-protein kinase SYK
P43405	527	574	371	631	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P43405	527	574	371	631	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P43405	527	574	536	538	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	536	538	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	541	546	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	541	546	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	551	566	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	551	566	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	530	530	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	527	574	530	530	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21469132;Dbxref=PMID:21469132
P43405	527	574	546	546	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P48025
P43405	527	574	546	546	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P48025
P43405	527	574	567	569	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	567	569	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	572	575	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR
P43405	527	574	572	575	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4YJR

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SNVs in the skipped exons for SYK

- 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
BLCA	TCGA-CF-A47X-01	exon_skip_497057	93629413	93629481	93629438	93629438	Nonsense_Mutation	C	G	p.S291*
HNSC	TCGA-CV-A468-01	exon_skip_497063	93650031	93650171	93650034	93650034	Nonsense_Mutation	C	T	p.Q529*
LUAD	TCGA-67-3771-01	exon_skip_497063	93650031	93650171	93650153	93650153	Nonsense_Mutation	T	G	p.Y568*
READ	TCGA-AG-A002-01	exon_skip_497063	93650031	93650171	93650169	93650169	Nonsense_Mutation	C	T	p.R551X
READ	TCGA-F5-6814-01	exon_skip_497063	93650031	93650171	93650169	93650169	Nonsense_Mutation	C	T	p.R551X

- 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
MEWO_SKIN	93636486	93636573	93636513	93636513	Missense_Mutation	G	A	p.E315K
KM12_LARGE_INTESTINE	93636486	93636573	93636560	93636560	Missense_Mutation	G	T	p.W330C
PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	93650031	93650171	93650071	93650071	Missense_Mutation	C	A	p.P541Q
NCIH650_LUNG	93650031	93650171	93650151	93650151	Missense_Mutation	T	C	p.Y568H
HS944T_SKIN	93650031	93650171	93650051	93650051	Nonsense_Mutation	G	A	p.W534*

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

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 SYK

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

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RelatedDrugs for SYK

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
	P43405	DB12010	Fostamatinib	Tyrosine-protein kinase SYK	small molecule	approved\|investigational

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RelatedDiseases for SYK

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SYK	C0025202	melanoma	1	CTD_human
SYK	C0025500	Mesothelioma	1	CTD_human

	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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