ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for MARK2

Gene summary

Gene information	Gene symbol	MARK2
	Gene ID	2011
	Gene name	microtubule affinity regulating kinase 2
	Synonyms	EMK-1\|EMK1\|PAR-1\|Par-1b\|Par1b
	Cytomap	11q13.1
	Type of gene	protein-coding
	Description	serine/threonine-protein kinase MARK2ELKL motif kinase 1MAP/microtubule affinity-regulating kinase 2PAR1 homolog bSer/Thr protein kinase PAR-1Bserine/threonine protein kinase EMKtesticular tissue protein Li 117
	Modification date	20200329
	UniProtAcc	A0A024R555, A0A024R5B2, A0A1B0GXH6, E7ETY4, E9PC69, F5H4F6, F5H4J8, F5H6N2, Q7KZI7,
	Context	- 30930738(Genetic Overlap Between Alzheimer's Disease and Bipolar Disorder Implicates the MARK2 and VAC14 Genes)

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

Gene	GO ID	GO term	PubMed ID
MARK2	GO:0006468	protein phosphorylation	14976552
MARK2	GO:0010976	positive regulation of neuron projection development	12429843
MARK2	GO:0018105	peptidyl-serine phosphorylation	10542369\|16717194
MARK2	GO:0030010	establishment of cell polarity	12429843
MARK2	GO:0035556	intracellular signal transduction	14976552
MARK2	GO:0045197	establishment or maintenance of epithelial cell apical/basal polarity	15324659
MARK2	GO:0070507	regulation of microtubule cytoskeleton organization	10542369

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Gene structures and expression levels for MARK2

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.

ENSG00000072518

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	ENST00000350490.11	MARK2-201:protein_coding:MARK2	2.696761e+02	8.311876e-01	5.519004e-13	9.127737e-11

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 MARK2

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_116275	chr11	63903061:63903158:63903986:63904147:63904786:63904921	63903986:63904147
exon_skip_117686	chr11	63904786:63905043:63906088:63906114:63908260:63908304	63906088:63906114
exon_skip_177197	chr11	63902198:63902330:63902604:63902782:63903061:63903132	63902604:63902782
exon_skip_216159	chr11	63898232:63898280:63898608:63898673:63898763:63898793	63898608:63898673
exon_skip_225232	chr11	63906088:63906114:63908260:63908304:63908877:63909237	63908260:63908304
exon_skip_239346	chr11	63902198:63902330:63902601:63902782:63903061:63903132	63902601:63902782
exon_skip_281693	chr11	63900780:63900879:63900957:63901069:63902198:63902330	63900957:63901069
exon_skip_286481	chr11	63895580:63895633:63898232:63898280:63898608:63898673	63898232:63898280
exon_skip_289284	chr11	63903061:63903158:63903986:63904147:63904786:63905043	63903986:63904147
exon_skip_78331	chr11	63904786:63905043:63908260:63908304:63908877:63909237	63908260:63908304
exon_skip_91246	chr11	63904786:63905043:63906088:63906114:63908877:63909237	63906088:63906114

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_78331	Mayo_CB	3.352439e-01	4.923377e-01	-1.570938e-01	1.197614e-05

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Open reading frame (ORF) annotation in the exon skipping event for MARK2

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
ENST00000402010	63900957	63901069	Frame-shift
ENST00000402010	63902601	63902782	Frame-shift
ENST00000402010	63903986	63904147	In-frame
ENST00000402010	63906088	63906114	In-frame
ENST00000402010	63908260	63908304	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
ENST00000402010	63903986	63904147	In-frame
ENST00000402010	63906088	63906114	In-frame
ENST00000402010	63908260	63908304	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
ENST00000402010	63898232	63898280	Frame-shift
ENST00000402010	63900957	63901069	Frame-shift
ENST00000402010	63902601	63902782	Frame-shift
ENST00000402010	63898608	63898673	In-frame
ENST00000402010	63903986	63904147	In-frame
ENST00000402010	63906088	63906114	In-frame
ENST00000402010	63908260	63908304	In-frame

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Infer the effects of exon skipping event on protein functional features for MARK2

p-ENSG00000072518_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
ENST00000402010	4745	788	63903986	63904147	2095	2255	505	558
ENST00000402010	4745	788	63908260	63908304	2542	2585	654	668

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
ENST00000402010	4745	788	63903986	63904147	2095	2255	505	558
ENST00000402010	4745	788	63908260	63908304	2542	2585	654	668

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
ENST00000402010	4745	788	63898608	63898673	918	982	113	134
ENST00000402010	4745	788	63903986	63904147	2095	2255	505	558
ENST00000402010	4745	788	63908260	63908304	2542	2585	654	668

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
Q7KZI7	505	558	505	558	Alternative sequence	ID=VSP_051706;Note=In isoform 2%2C isoform 4%2C isoform 5%2C isoform 7%2C isoform 9%2C isoform 10%2C isoform 13%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:00
Q7KZI7	505	558	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2
Q7KZI7	654	668	645	668	Alternative sequence	ID=VSP_041853;Note=In isoform 15. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q7KZI7	654	668	654	668	Alternative sequence	ID=VSP_051708;Note=In isoform 5%2C isoform 11%2C isoform 10 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:0000303\|PubMed:9730619,ECO:0000303\|Ref.2;Dbxref=PMID:11433294,PMID:9730619
Q7KZI7	654	668	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2

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
Q7KZI7	505	558	505	558	Alternative sequence	ID=VSP_051706;Note=In isoform 2%2C isoform 4%2C isoform 5%2C isoform 7%2C isoform 9%2C isoform 10%2C isoform 13%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:00
Q7KZI7	505	558	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2
Q7KZI7	654	668	645	668	Alternative sequence	ID=VSP_041853;Note=In isoform 15. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q7KZI7	654	668	654	668	Alternative sequence	ID=VSP_051708;Note=In isoform 5%2C isoform 11%2C isoform 10 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:0000303\|PubMed:9730619,ECO:0000303\|Ref.2;Dbxref=PMID:11433294,PMID:9730619
Q7KZI7	654	668	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2

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
Q7KZI7	113	134	115	120	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3IEC
Q7KZI7	113	134	122	129	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3IEC
Q7KZI7	113	134	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2
Q7KZI7	113	134	53	304	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q7KZI7	505	558	505	558	Alternative sequence	ID=VSP_051706;Note=In isoform 2%2C isoform 4%2C isoform 5%2C isoform 7%2C isoform 9%2C isoform 10%2C isoform 13%2C isoform 15 and isoform 16. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:00
Q7KZI7	505	558	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2
Q7KZI7	654	668	645	668	Alternative sequence	ID=VSP_041853;Note=In isoform 15. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q7KZI7	654	668	654	668	Alternative sequence	ID=VSP_051708;Note=In isoform 5%2C isoform 11%2C isoform 10 and isoform 12. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11433294,ECO:0000303\|PubMed:9730619,ECO:0000303\|Ref.2;Dbxref=PMID:11433294,PMID:9730619
Q7KZI7	654	668	1	788	Chain	ID=PRO_0000086301;Note=Serine/threonine-protein kinase MARK2

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3'-UTR located exon skipping events that lost miRNA binding sites in MARK2

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 MARK2

- 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 MARK2

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 MARK2

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 MARK2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_116275	-4.336543e-01	1.129423e-08
CB	PCBP4	exon_skip_116275	4.648662e-01	6.698872e-10
CB	TRA2A	exon_skip_91246	-4.679452e-01	4.990538e-10
CB	NUP42	exon_skip_91246	4.631784e-01	7.862343e-10
CB	TARDBP	exon_skip_78331	-4.342362e-01	1.074237e-08
CB	TRA2A	exon_skip_78331	-6.177972e-01	4.156659e-18
CB	NUP42	exon_skip_78331	4.983905e-01	2.307250e-11
HCC	SFPQ	exon_skip_289284	-4.446892e-01	1.817010e-14
HCC	RBM6	exon_skip_289284	-4.253032e-01	3.049649e-13
HCC	EIF4G2	exon_skip_289284	-4.181902e-01	8.211360e-13
IFG	PCBP4	exon_skip_289284	-4.520912e-01	1.572240e-02
IFG	TARDBP	exon_skip_78331	-5.846955e-01	1.360194e-03
IFG	RBM5	exon_skip_78331	-5.190165e-01	5.536647e-03
IFG	TRA2A	exon_skip_78331	-4.957997e-01	8.539413e-03
TC	NOVA1	exon_skip_116275	4.721114e-01	2.931105e-10

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RelatedDrugs for MARK2

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Q7KZI7	approved\|investigational	DB12010	Fostamatinib	small molecule	Q7KZI7

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RelatedDiseases for MARK2

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 MARK2

Gene structures and expression levels for MARK2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MARK2

Open reading frame (ORF) annotation in the exon skipping event for MARK2

Infer the effects of exon skipping event on protein functional features for MARK2

3'-UTR located exon skipping events that lost miRNA binding sites in MARK2

SNVs in the skipped exons for MARK2

AD stage-associated exon skippint events for MARK2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MARK2

Correlation with RNA binding proteins (RBPs) for MARK2

RelatedDrugs for MARK2

RelatedDiseases for MARK2