ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MKNK1

Gene summary

Gene information	Gene symbol	MKNK1
	Gene ID	8569
	Gene name	MAP kinase interacting serine/threonine kinase 1
	Synonyms	MNK1
	Cytomap	1p33
	Type of gene	protein-coding
	Description	MAP kinase-interacting serine/threonine-protein kinase 1MAP kinase signal-integrating kinase 1MAPK signal-integrating kinase 1
	Modification date	20180523
	UniProtAcc	Q9BUB5
	Context	PubMed: MKNK1 [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
MKNK1	GO:0006468	protein phosphorylation	9155018
MKNK1	GO:0018105	peptidyl-serine phosphorylation	17130135
MKNK1	GO:0035556	intracellular signal transduction	9155018

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Exon skipping events across known transcript of Ensembl for MKNK1 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 MKNK1

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 MKNK1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_26372	1	47024427:47024472:47025905:47025949:47027149:47027314	47025905:47025949	ENSG00000079277.15	ENST00000342571.3,ENST00000371946.4,ENST00000371944.4,ENST00000371945.4
exon_skip_26373	1	47024427:47024472:47027149:47027314:47028320:47028515	47027149:47027314	ENSG00000079277.15	ENST00000341183.5,ENST00000528077.1,ENST00000532897.1,ENST00000428112.2
exon_skip_26375	1	47024427:47024472:47028320:47028515:47030712:47030735	47028320:47028515	ENSG00000079277.15	ENST00000524749.1
exon_skip_26376	1	47027243:47027314:47028320:47028515:47030712:47030735	47028320:47028515	ENSG00000079277.15	ENST00000341183.5,ENST00000342571.3,ENST00000371946.4,ENST00000528077.1,ENST00000371944.4,ENST00000371945.4,ENST00000532897.1,ENST00000428112.2,ENST00000470237.1
exon_skip_26377	1	47034127:47034170:47037088:47037211:47037734:47037839	47037088:47037211	ENSG00000079277.15	ENST00000371946.4
exon_skip_26378	1	47034127:47034170:47037734:47037839:47040618:47040692	47037734:47037839	ENSG00000079277.15	ENST00000532783.1,ENST00000496619.1,ENST00000341183.5,ENST00000531355.1,ENST00000371945.4,ENST00000428112.2
exon_skip_26379	1	47034127:47034170:47037734:47037839:47042246:47042326	47037734:47037839	ENSG00000079277.15	ENST00000342571.3,ENST00000528077.1,ENST00000371944.4
exon_skip_26388	1	47037829:47037839:47040618:47040692:47042246:47042326	47040618:47040692	ENSG00000079277.15	ENST00000532783.1,ENST00000496619.1,ENST00000341183.5,ENST00000528237.1,ENST00000371946.4,ENST00000531355.1,ENST00000526513.1,ENST00000371945.4,ENST00000428112.2
exon_skip_26394	1	47042260:47042326:47046201:47046299:47048899:47048999	47046201:47046299	ENSG00000079277.15	ENST00000532783.1,ENST00000496619.1,ENST00000480531.1,ENST00000531769.1,ENST00000341183.5,ENST00000342571.3,ENST00000528237.1,ENST00000371946.4,ENST00000486716.1,ENST00000528077.1,ENST00000371944.4,ENST00000371945.4,ENST00000428112.2,ENST00000545730.1,ENS
exon_skip_26396	1	47042260:47042326:47048899:47049001:47059784:47059878	47048899:47049001	ENSG00000079277.15	ENST00000531355.1
exon_skip_26397	1	47046267:47046299:47048485:47048577:47048899:47048999	47048485:47048577	ENSG00000079277.15	ENST00000484301.1
exon_skip_26398	1	47046267:47046299:47048485:47048595:47048899:47048999	47048485:47048595	ENSG00000079277.15	ENST00000526513.1
exon_skip_26405	1	47048899:47049001:47051545:47051646:47051905:47051931	47051545:47051646	ENSG00000079277.15	ENST00000528237.1
exon_skip_26406	1	47048899:47049001:47051545:47051646:47059784:47059878	47051545:47051646	ENSG00000079277.15	ENST00000484301.1,ENST00000474868.1
exon_skip_26409	1	47050330:47050475:47051545:47051646:47059784:47059878	47051545:47051646	ENSG00000079277.15	ENST00000525888.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MKNK1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_26372	1	47024427:47024472:47025905:47025949:47027149:47027314	47025905:47025949	ENSG00000079277.15	ENST00000342571.3,ENST00000371946.4,ENST00000371945.4,ENST00000371944.4
exon_skip_26373	1	47024427:47024472:47027149:47027314:47028320:47028515	47027149:47027314	ENSG00000079277.15	ENST00000341183.5,ENST00000528077.1,ENST00000428112.2,ENST00000532897.1
exon_skip_26375	1	47024427:47024472:47028320:47028515:47030712:47030735	47028320:47028515	ENSG00000079277.15	ENST00000524749.1
exon_skip_26376	1	47027243:47027314:47028320:47028515:47030712:47030735	47028320:47028515	ENSG00000079277.15	ENST00000342571.3,ENST00000371946.4,ENST00000371945.4,ENST00000371944.4,ENST00000341183.5,ENST00000528077.1,ENST00000428112.2,ENST00000532897.1,ENST00000470237.1
exon_skip_26377	1	47034127:47034170:47037088:47037211:47037734:47037839	47037088:47037211	ENSG00000079277.15	ENST00000371946.4
exon_skip_26378	1	47034127:47034170:47037734:47037839:47040618:47040692	47037734:47037839	ENSG00000079277.15	ENST00000371945.4,ENST00000341183.5,ENST00000428112.2,ENST00000531355.1,ENST00000532783.1,ENST00000496619.1
exon_skip_26379	1	47034127:47034170:47037734:47037839:47042246:47042326	47037734:47037839	ENSG00000079277.15	ENST00000342571.3,ENST00000371944.4,ENST00000528077.1
exon_skip_26388	1	47037829:47037839:47040618:47040692:47042246:47042326	47040618:47040692	ENSG00000079277.15	ENST00000371946.4,ENST00000371945.4,ENST00000341183.5,ENST00000428112.2,ENST00000531355.1,ENST00000532783.1,ENST00000496619.1,ENST00000528237.1,ENST00000526513.1
exon_skip_26394	1	47042260:47042326:47046201:47046299:47048899:47048999	47046201:47046299	ENSG00000079277.15	ENST00000342571.3,ENST00000371946.4,ENST00000371945.4,ENST00000371944.4,ENST00000341183.5,ENST00000528077.1,ENST00000428112.2,ENST00000532783.1,ENST00000496619.1,ENST00000528237.1,ENST00000545730.1,ENST00000486716.1,ENST00000480531.1,ENST00000529170.1,ENS
exon_skip_26396	1	47042260:47042326:47048899:47049001:47059784:47059878	47048899:47049001	ENSG00000079277.15	ENST00000531355.1
exon_skip_26397	1	47046267:47046299:47048485:47048577:47048899:47048999	47048485:47048577	ENSG00000079277.15	ENST00000484301.1
exon_skip_26398	1	47046267:47046299:47048485:47048595:47048899:47048999	47048485:47048595	ENSG00000079277.15	ENST00000526513.1
exon_skip_26405	1	47048899:47049001:47051545:47051646:47051905:47051931	47051545:47051646	ENSG00000079277.15	ENST00000528237.1
exon_skip_26406	1	47048899:47049001:47051545:47051646:47059784:47059878	47051545:47051646	ENSG00000079277.15	ENST00000484301.1,ENST00000474868.1
exon_skip_26409	1	47050330:47050475:47051545:47051646:47059784:47059878	47051545:47051646	ENSG00000079277.15	ENST00000525888.1

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 MKNK1

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
ENST00000371946	47025905	47025949	Frame-shift
ENST00000371946	47040618	47040692	Frame-shift
ENST00000371946	47046201	47046299	Frame-shift
ENST00000371946	47028320	47028515	In-frame
ENST00000371946	47037088	47037211	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
ENST00000371946	47025905	47025949	Frame-shift
ENST00000371946	47040618	47040692	Frame-shift
ENST00000371946	47046201	47046299	Frame-shift
ENST00000371946	47028320	47028515	In-frame
ENST00000371946	47037088	47037211	In-frame

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Infer the effects of exon skipping event on protein functional features for MKNK1

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
ENST00000371946	2736	465	47037088	47037211	658	780	164	205
ENST00000371946	2736	465	47028320	47028515	933	1127	256	321

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
ENST00000371946	2736	465	47037088	47037211	658	780	164	205
ENST00000371946	2736	465	47028320	47028515	933	1127	256	321

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
Q9BUB5	164	205	165	205	Alternative sequence	ID=VSP_007352;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15350534,ECO:0000303\|PubMed:9155018;Dbxref=PMID:15350534,PMID:9155018
Q9BUB5	164	205	1	465	Chain	ID=PRO_0000086334;Note=MAP kinase-interacting serine/threonine-protein kinase 1
Q9BUB5	164	205	49	374	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9BUB5	256	321	271	274	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HW6
Q9BUB5	256	321	1	465	Chain	ID=PRO_0000086334;Note=MAP kinase-interacting serine/threonine-protein kinase 1
Q9BUB5	256	321	49	374	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9BUB5	256	321	277	296	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HW6
Q9BUB5	256	321	308	308	Natural variant	ID=VAR_040803;Note=D->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs55791614,PMID:17344846

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
Q9BUB5	164	205	165	205	Alternative sequence	ID=VSP_007352;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15350534,ECO:0000303\|PubMed:9155018;Dbxref=PMID:15350534,PMID:9155018
Q9BUB5	164	205	1	465	Chain	ID=PRO_0000086334;Note=MAP kinase-interacting serine/threonine-protein kinase 1
Q9BUB5	164	205	49	374	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9BUB5	256	321	271	274	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HW6
Q9BUB5	256	321	1	465	Chain	ID=PRO_0000086334;Note=MAP kinase-interacting serine/threonine-protein kinase 1
Q9BUB5	256	321	49	374	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9BUB5	256	321	277	296	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HW6
Q9BUB5	256	321	308	308	Natural variant	ID=VAR_040803;Note=D->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs55791614,PMID:17344846

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SNVs in the skipped exons for MKNK1

- 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
OV	TCGA-13-0723-01	exon_skip_26405 exon_skip_26406 exon_skip_26409	47051546	47051646	47051647	47051647	Splice_Site	C	C	e1-1

- 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
CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47025906	47025949	47025921	47025921	Missense_Mutation	G	A	p.P386L
NCIH1755_LUNG	47025906	47025949	47025937	47025937	Missense_Mutation	T	C	p.K381E
NCIH2810_PLEURA	47027150	47027314	47027185	47027185	Missense_Mutation	C	T	p.A365T
SNGM_ENDOMETRIUM	47037089	47037211	47037172	47037172	Missense_Mutation	G	A	p.A178V
LB2518EBV_MATCHED_NORMAL_TISSUE	47037735	47037839	47037756	47037756	Missense_Mutation	G	C	p.L158V
LB2518MEL_SKIN	47037735	47037839	47037756	47037756	Missense_Mutation	G	C	p.L158V
MDAMB453_BREAST	47040619	47040692	47040634	47040634	Missense_Mutation	C	G	p.E125Q
HCC44_LUNG	47040619	47040692	47040636	47040636	Missense_Mutation	A	T	p.F124Y
HT55_LARGE_INTESTINE	47040619	47040692	47040641	47040641	Missense_Mutation	C	A	p.L122F
GOTO_AUTONOMIC_GANGLIA	47040619	47040692	47040656	47040656	Missense_Mutation	G	T	p.D117E
VMRCMELG_SKIN	47046202	47046299	47046237	47046237	Missense_Mutation	C	T	p.V67M
SUM159PT_BREAST	47046202	47046299	47046250	47046250	Missense_Mutation	T	G	p.K62N
KOSC2_UPPER_AERODIGESTIVE_TRACT	47048900	47049001	47048969	47048969	Missense_Mutation	C	A	p.D23Y
BICR18_UPPER_AERODIGESTIVE_TRACT	47037735	47037839	47037838	47037838	Splice_Site	A	G	p.G130G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MKNK1

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 MKNK1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MKNK1

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RelatedDrugs for MKNK1

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
	Q9BUB5	DB12010	Fostamatinib	MAP kinase-interacting serine/threonine-protein kinase 1	small molecule	approved\|investigational

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RelatedDiseases for MKNK1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MKNK1	C0236969	Substance-Related Disorders	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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