ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for MINK1

Gene summary

Gene information	Gene symbol	MINK1
	Gene ID	50488
	Gene name	misshapen like kinase 1
	Synonyms	B55\|MAP4K6\|MINK\|YSK2\|ZC3
	Cytomap	17p13.2
	Type of gene	protein-coding
	Description	misshapen-like kinase 1GCK family kinase MINKMAPK/ERK kinase kinase kinase 6MEK kinase kinase 6MEKKK 6misshapen/NIK-related kinasemitogen-activated protein kinase kinase kinase kinase 6
	Modification date	20200320
	UniProtAcc	A0A590UJE1, I3L1U1, I3L203, I3L2I2, I3L4T2, Q8N4C8,
	Context	- 30413934(Dissecting the genetic relationship between cardiovascular risk factors and Alzheimer's disease)

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

Gene	GO ID	GO term	PubMed ID
MINK1	GO:0046777	protein autophosphorylation	15469942

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Gene structures and expression levels for MINK1

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.

ENSG00000141503

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
STG	UP	ENST00000572629.1	MINK1-208:retained_intron:MINK1	1.721192e+01	9.082296e-01	3.370622e-05	5.901345e-03
PG	UP	ENST00000574453.5	MINK1-209:nonsense_mediated_decay:MINK1	5.348908e+01	1.412552e+00	1.850494e-04	4.308400e-03
PG	UP	ENST00000576037.1	MINK1-212:protein_coding:MINK1	3.160642e+00	1.741793e+00	2.550791e-04	5.443171e-03

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 MINK1

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_106429	chr17	4892149:4892234:4892402:4892512:4892656:4892684	4892402:4892512
exon_skip_10788	chr17	4892979:4893067:4893286:4893309:4893434:4893495	4893286:4893309
exon_skip_131502	chr17	4890951:4891124:4891516:4891716:4892149:4892234	4891516:4891716
exon_skip_133510	chr17	4892998:4893067:4893286:4893309:4893434:4893597	4893286:4893309
exon_skip_143847	chr17	4885911:4885965:4886120:4886198:4886451:4886617	4886120:4886198
exon_skip_147279	chr17	4890951:4891124:4891456:4891716:4892149:4892234	4891456:4891716
exon_skip_167170	chr17	4889647:4889763:4890222:4890308:4890517:4890735	4890222:4890308
exon_skip_175838	chr17	4833621:4833640:4878317:4878382:4880984:4881040	4878317:4878382
exon_skip_180121	chr17	4884469:4884473:4884912:4885002:4885483:4885613	4884912:4885002
exon_skip_222195	chr17	4894525:4894633:4895075:4895242:4895350:4895493	4895075:4895242
exon_skip_229121	chr17	4895350:4895493:4895698:4895832:4896003:4896103	4895698:4895832
exon_skip_240955	chr17	4833621:4833640:4859213:4859328:4878317:4878348	4859213:4859328
exon_skip_24223	chr17	4894174:4894311:4894525:4894633:4895075:4895242	4894525:4894633
exon_skip_245046	chr17	4833413:4833640:4859213:4859328:4878317:4878382	4859213:4859328
exon_skip_252414	chr17	4892979:4893067:4893286:4893309:4893434:4893514	4893286:4893309
exon_skip_266895	chr17	4889653:4889763:4890222:4890308:4890517:4890735	4890222:4890308
exon_skip_277400	chr17	4890517:4890735:4890951:4891124:4891456:4891716	4890951:4891124
exon_skip_279431	chr17	4892149:4892234:4892402:4892512:4892656:4892768	4892402:4892512
exon_skip_295879	chr17	4892979:4893067:4893286:4893309:4893434:4893597	4893286:4893309
exon_skip_35325	chr17	4889647:4889763:4890222:4890308:4890517:4890536	4890222:4890308
exon_skip_63853	chr17	4878317:4878382:4880984:4881040:4881132:4881257	4880984:4881040
exon_skip_95772	chr17	4833621:4833640:4859213:4859328:4878317:4878382	4859213:4859328

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_295879	MSBB_PG	4.785496e-01	6.542857e-01	-1.757361e-01	2.362124e-03

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Open reading frame (ORF) annotation in the exon skipping event for MINK1

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
ENST00000355280	4886120	4886198	Frame-shift
ENST00000355280	4890951	4891124	In-frame
ENST00000355280	4891456	4891716	In-frame
ENST00000355280	4892402	4892512	In-frame
ENST00000355280	4895075	4895242	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
ENST00000355280	4890951	4891124	In-frame
ENST00000355280	4892402	4892512	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
ENST00000355280	4884912	4885002	Frame-shift
ENST00000355280	4886120	4886198	Frame-shift
ENST00000355280	4894525	4894633	Frame-shift
ENST00000355280	4880984	4881040	In-frame
ENST00000355280	4890951	4891124	In-frame
ENST00000355280	4892402	4892512	In-frame
ENST00000355280	4895698	4895832	In-frame

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Infer the effects of exon skipping event on protein functional features for MINK1

p-ENSG00000141503_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
ENST00000355280	4978	1332	4890951	4891124	1764	1936	522	580
ENST00000355280	4978	1332	4891456	4891716	1938	2197	580	667
ENST00000355280	4978	1332	4892402	4892512	2285	2394	696	732
ENST00000355280	4978	1332	4895075	4895242	3115	3281	973	1028

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
ENST00000355280	4978	1332	4890951	4891124	1764	1936	522	580
ENST00000355280	4978	1332	4892402	4892512	2285	2394	696	732

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
ENST00000355280	4978	1332	4880984	4881040	321	376	41	60
ENST00000355280	4978	1332	4890951	4891124	1764	1936	522	580
ENST00000355280	4978	1332	4892402	4892512	2285	2394	696	732
ENST00000355280	4978	1332	4895698	4895832	3427	3560	1077	1121

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
Q8N4C8	522	580	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	522	580	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	580	667	581	600	Alternative sequence	ID=VSP_041871;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15469942;Dbxref=PMID:15469942
Q8N4C8	580	667	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	580	667	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	580	667	641	641	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18691976,PMID:23186163
Q8N4C8	696	732	696	732	Alternative sequence	ID=VSP_007059;Note=In isoform 1%2C isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10708748;Dbxref=PMID:10708748
Q8N4C8	696	732	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	696	732	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	696	732	701	701	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8N4C8	973	1028	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	973	1028	1019	1306	Domain	Note=CNH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00795
Q8N4C8	973	1028	1010	1010	Natural variant	ID=VAR_046061;Note=In a gastric adenocarcinoma sample%3B somatic mutation. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
Q8N4C8	973	1028	866	1332	Region	Note=Mediates interaction with RAP2A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930710;Dbxref=PMID:18930710

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
Q8N4C8	522	580	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	522	580	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	696	732	696	732	Alternative sequence	ID=VSP_007059;Note=In isoform 1%2C isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10708748;Dbxref=PMID:10708748
Q8N4C8	696	732	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	696	732	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	696	732	701	701	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163

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
Q8N4C8	41	60	54	54	Binding site	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8N4C8	41	60	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	41	60	25	289	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8N4C8	522	580	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	522	580	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	696	732	696	732	Alternative sequence	ID=VSP_007059;Note=In isoform 1%2C isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10708748;Dbxref=PMID:10708748
Q8N4C8	696	732	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	696	732	542	729	Compositional bias	Note=Pro-rich
Q8N4C8	696	732	701	701	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8N4C8	1077	1121	1	1332	Chain	ID=PRO_0000086329;Note=Misshapen-like kinase 1
Q8N4C8	1077	1121	1019	1306	Domain	Note=CNH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00795
Q8N4C8	1077	1121	866	1332	Region	Note=Mediates interaction with RAP2A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930710;Dbxref=PMID:18930710

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3'-UTR located exon skipping events that lost miRNA binding sites in MINK1

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 MINK1

- 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 MINK1

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

ADstage

ROSMAP

PCC

exon_skip_295879

-3.041377e-01

5.580000e-06

chr17

4892979

4893067

4893286

4893309

4893434

4893597

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MINK1

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 MINK1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_143847	-5.055731e-01	1.067823e-11
CB	RBM4	exon_skip_143847	-5.273482e-01	9.225907e-13
CB	SRSF11	exon_skip_266895	4.065105e-01	1.055650e-07
CB	SRSF1	exon_skip_266895	4.815054e-01	1.317342e-10
CB	SRSF4	exon_skip_266895	6.006333e-01	5.815353e-17
CB	SRSF9	exon_skip_266895	4.206453e-01	3.378748e-08
CB	SNRPA	exon_skip_66381	4.175094e-01	4.370176e-08
CB	SRSF4	exon_skip_66381	5.937157e-01	1.611562e-16
DLPFC	MBNL1	exon_skip_266895	4.809987e-01	3.804630e-21
DLPFC	RC3H1	exon_skip_266895	5.409778e-01	2.585893e-27
FL	MBNL1	exon_skip_295879	4.195409e-01	9.312799e-10
HCC	RBMS2	exon_skip_266895	-4.361139e-01	5.219501e-14
PCC	RBMS2	exon_skip_266895	-4.681386e-01	7.793672e-13
PG	ILF2	exon_skip_279431	-4.254153e-01	9.989263e-09
PG	HNRNPK	exon_skip_279431	-4.163178e-01	2.196844e-08
PG	RBM45	exon_skip_279431	-4.386816e-01	3.033441e-09
PG	MBNL1	exon_skip_295879	6.014952e-01	8.775169e-20
TC	MBNL1	exon_skip_35325	4.617804e-01	7.933734e-10
TC	RC3H1	exon_skip_35325	4.031935e-01	1.248912e-07
TC	HNRNPD	exon_skip_35325	4.910430e-01	4.326824e-11
TC	SRSF1	exon_skip_35325	4.102709e-01	7.125100e-08
TC	SRSF4	exon_skip_35325	4.287849e-01	1.541419e-08
TC	SRSF9	exon_skip_35325	4.421623e-01	4.808889e-09
TC	ESRP1	exon_skip_35325	5.613847e-01	1.145122e-14
TC	MBNL1	exon_skip_10788	4.597852e-01	9.579619e-10

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RelatedDrugs for MINK1

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Q8N4C8	approved\|investigational	DB12010	Fostamatinib	small molecule	Q8N4C8

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RelatedDiseases for MINK1

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 MINK1

Gene structures and expression levels for MINK1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MINK1

Open reading frame (ORF) annotation in the exon skipping event for MINK1

Infer the effects of exon skipping event on protein functional features for MINK1

3'-UTR located exon skipping events that lost miRNA binding sites in MINK1

SNVs in the skipped exons for MINK1

AD stage-associated exon skippint events for MINK1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MINK1

Correlation with RNA binding proteins (RBPs) for MINK1

RelatedDrugs for MINK1

RelatedDiseases for MINK1