ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CASK

Gene summary

Gene information	Gene symbol	CASK
	Gene ID	8573
	Gene name	calcium/calmodulin dependent serine protein kinase
	Synonyms	CAGH39\|CAMGUK\|CMG\|FGS4\|LIN2\|MICPCH\|MRXSNA\|TNRC8\|hCASK
	Cytomap	Xp11.4
	Type of gene	protein-coding
	Description	peripheral plasma membrane protein CASKcalcium/calmodulin-dependent serin protein kinasecalcium/calmodulin-dependent serine protein kinase (MAGUK family)calcium/calmodulin-dependent serine protein kinase membrane-associated guanylate kinaseprotein lin
	Modification date	20200327
	UniProtAcc	A0A0B6XJY0, A0A2R8Y3B3, A0A2R8Y472, A0A2R8Y4K4, A0A2R8Y6D8, A0A2R8Y6F8, A0A2R8Y7X6, A0A2R8YE77, A0A2R8YEJ7, A0A2R8YEK3, A0A2R8YFN5, A0A2R8YGH2, A0A2U3TZM1, A0A2U3TZM4, A0A2U3TZN6, B7ZKY2, O14936, P07498, Q5JS72, Q5JS79,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
CASK	GO:0010839	negative regulation of keratinocyte proliferation	18664494

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Gene structures and expression levels for CASK

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.

ENSG00000147044

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
PCC	UP	ENST00000642499.1	CASK-215:retained_intron:CASK	8.362073e+00	8.937297e-01	2.960556e-03	4.978585e-02
PG	DOWN	ENST00000378168.7	CASK-205:protein_coding:CASK	8.887039e+00	-8.113143e-01	9.665332e-04	1.423560e-02
CB	UP	ENST00000442742.7	CASK-208:protein_coding:CASK	1.756602e+01	3.380755e+00	6.365475e-07	1.021146e-05
CB	UP	ENST00000378154.2	CASK-201:protein_coding:CASK	3.894591e+01	1.057390e+00	1.469393e-05	1.460483e-04
CB	DOWN	ENST00000642361.1	CASK-214:protein_coding:CASK	2.225468e+00	-8.091206e-01	1.792986e-03	8.419939e-03
CB	UP	ENST00000378158.6	CASK-202:protein_coding:CASK	1.962046e+00	3.181432e+00	1.845037e-03	8.623837e-03
CB	UP	ENST00000645986.1	CASK-227:protein_coding:CASK	1.205861e+01	1.666738e+00	2.496400e-03	1.107681e-02
TC	DOWN	ENST00000642499.1	CASK-215:retained_intron:CASK	2.518717e+01	-1.565934e+00	2.380604e-04	3.208004e-03
TC	UP	ENST00000378163.6	CASK-203:protein_coding:CASK	1.728284e+01	1.174593e+00	5.468360e-03	3.585689e-02

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 CASK

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_117025	chrX	41553719:41553915:41555600:41555635:41559779:41559847	41555600:41555635
exon_skip_158930	chrX	41745524:41745601:41787178:41787283:41853115:41853227	41787178:41787283
exon_skip_164321	chrX	41520333:41520596:41523951:41524034:41529529:41529648	41523951:41524034
exon_skip_185162	chrX	41553719:41553915:41557032:41557100:41559779:41559847	41557032:41557100
exon_skip_201513	chrX	41520333:41520596:41522999:41523025:41523951:41524034	41522999:41523025
exon_skip_215219	chrX	41609985:41610025:41622617:41622634:41626604:41626703	41622617:41622634
exon_skip_274173	chrX	41553719:41553915:41555600:41555635:41557032:41557100	41555600:41555635
exon_skip_279291	chrX	41555600:41555635:41557032:41557100:41559779:41559847	41557032:41557100
exon_skip_283318	chrX	41520333:41520596:41523951:41524034:41531007:41531209	41523951:41524034
exon_skip_291016	chrX	41542691:41542806:41553719:41553915:41559779:41559847	41553719:41553915
exon_skip_295359	chrX	41523951:41524034:41529529:41529648:41531007:41531209	41529529:41529648

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
exon_skip_215219	MSBB_PG	4.312712e-01	5.918367e-01	-1.605655e-01	3.821416e-02

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Open reading frame (ORF) annotation in the exon skipping event for CASK

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
ENST00000378163	41787178	41787283	Frame-shift
ENST00000378163	41555600	41555635	In-frame
ENST00000378163	41557032	41557100	In-frame
ENST00000378163	41622617	41622634	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
ENST00000378163	41555600	41555635	In-frame
ENST00000378163	41557032	41557100	In-frame
ENST00000378163	41622617	41622634	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
ENST00000378163	41787178	41787283	Frame-shift
ENST00000378163	41523951	41524034	In-frame
ENST00000378163	41555600	41555635	In-frame
ENST00000378163	41557032	41557100	In-frame
ENST00000378163	41622617	41622634	In-frame

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

p-ENSG00000147044_img4.png
boxplot

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
ENST00000378163	4440	926	41557032	41557100	2225	2292	579	601
ENST00000378163	4440	926	41555600	41555635	2294	2328	602	613

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
ENST00000378163	4440	926	41557032	41557100	2225	2292	579	601
ENST00000378163	4440	926	41555600	41555635	2294	2328	602	613

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
ENST00000378163	4440	926	41557032	41557100	2225	2292	579	601
ENST00000378163	4440	926	41555600	41555635	2294	2328	602	613
ENST00000378163	4440	926	41523951	41524034	3008	3090	840	867

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
O14936	579	601	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	579	601	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	579	601	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938
O14936	602	613	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	602	613	603	614	Alternative sequence	ID=VSP_024425;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O14936	602	613	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	602	613	612	682	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O14936	602	613	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938

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
O14936	579	601	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	579	601	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	579	601	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938
O14936	602	613	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	602	613	603	614	Alternative sequence	ID=VSP_024425;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O14936	602	613	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	602	613	612	682	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O14936	602	613	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938

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
O14936	579	601	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	579	601	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	579	601	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938
O14936	602	613	580	602	Alternative sequence	ID=VSP_024424;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11003712,ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2,ECO:0000303\|Ref.3;Dbxref=PMID:11003712,PMI
O14936	602	613	603	614	Alternative sequence	ID=VSP_024425;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O14936	602	613	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	602	613	612	682	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O14936	602	613	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938
O14936	840	867	852	858	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1KGD
O14936	840	867	1	926	Chain	ID=PRO_0000094568;Note=Peripheral plasma membrane protein CASK
O14936	840	867	739	911	Domain	Note=Guanylate kinase-like;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00100
O14936	840	867	839	841	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1KGD
O14936	840	867	842	845	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1KGD
O14936	840	867	19	926	Natural variant	ID=VAR_078710;Note=Probable disease-associated mutation found in a patient with epilepsy and pontocerebellar hypoplasia. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23662938;Dbxref=PMID:23662938
O14936	840	867	848	850	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1KGD

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3'-UTR located exon skipping events that lost miRNA binding sites in CASK

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 CASK

- 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 CASK

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 CASK

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 CASK

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_117025	-5.319475e-01	8.105286e-12
FL	SRSF2	exon_skip_215219	4.023382e-01	2.589832e-08
HCC	SAMD4A	exon_skip_295359	-6.024722e-01	5.762999e-28
HCC	HNRNPA2B1	exon_skip_295359	-4.431679e-01	2.282066e-14
HCC	PTBP1	exon_skip_295359	-5.911412e-01	9.700234e-27
HCC	HNRNPF	exon_skip_295359	-5.632351e-01	6.448994e-24
HCC	SRSF11	exon_skip_215219	-4.540103e-01	6.235012e-15
IFG	SAMD4A	exon_skip_295359	-4.797856e-01	1.132369e-02
IFG	TRA2A	exon_skip_295359	-4.994019e-01	7.999537e-03
IFG	PTBP1	exon_skip_295359	-4.841048e-01	1.050728e-02
IFG	HNRNPH2	exon_skip_295359	5.693558e-01	1.937665e-03
IFG	ELAVL1	exon_skip_279291	5.027645e-01	7.521724e-03
IFG	IGF2BP3	exon_skip_279291	4.676001e-01	1.391638e-02
IFG	ENOX1	exon_skip_279291	5.086707e-01	6.740525e-03
PCC	SRSF11	exon_skip_215219	-4.212585e-01	4.291899e-10
TC	SRSF2	exon_skip_215219	5.023057e-01	9.035537e-11
TC	SRSF9	exon_skip_215219	4.045966e-01	3.722369e-07
TC	SRSF5	exon_skip_215219	4.052371e-01	3.553404e-07

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RelatedDrugs for CASK

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
O14936	approved\|investigational	DB12010	Fostamatinib	small molecule	O14936
P07498	approved\|investigational	DB12010	Fostamatinib	small molecule	P07498

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RelatedDiseases for CASK

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for CASK

Gene structures and expression levels for CASK

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CASK

Open reading frame (ORF) annotation in the exon skipping event for CASK

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

3'-UTR located exon skipping events that lost miRNA binding sites in CASK

SNVs in the skipped exons for CASK

AD stage-associated exon skippint events for CASK

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

Correlation with RNA binding proteins (RBPs) for CASK

RelatedDrugs for CASK

RelatedDiseases for CASK