ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TEK

Gene summary

Gene information	Gene symbol	TEK
	Gene ID	7010
	Gene name	TEK receptor tyrosine kinase
	Synonyms	CD202B\|GLC3E\|TIE-2\|TIE2\|VMCM\|VMCM1
	Cytomap	9p21.2
	Type of gene	protein-coding
	Description	angiopoietin-1 receptorTEK tyrosine kinase, endothelialendothelial tyrosine kinasetunica interna endothelial cell kinasetyrosine kinase with Ig and EGF homology domains-2tyrosine-protein kinase receptor TEKtyrosine-protein kinase receptor TIE-2
	Modification date	20200322
	UniProtAcc	B5A953, B5A954, D9MND0, D9MND2, E5RIV9, Q02763,
	Context	- 24762948(Hidden risk genes with high-order intragenic epistasis in 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
TEK	GO:0001934	positive regulation of protein phosphorylation	15284220
TEK	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	15284220
TEK	GO:0010595	positive regulation of endothelial cell migration	15284220
TEK	GO:0018108	peptidyl-tyrosine phosphorylation	11513602
TEK	GO:0045766	positive regulation of angiogenesis	15284220
TEK	GO:0046777	protein autophosphorylation	11513602
TEK	GO:0048014	Tie signaling pathway	15284220\|19223473
TEK	GO:0051897	positive regulation of protein kinase B signaling	19615361
TEK	GO:0070374	positive regulation of ERK1 and ERK2 cascade	19615361

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Gene structures and expression levels for TEK

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.

ENSG00000120156

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

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 TEK

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_200813	chr9	27109141:27109642:27157831:27158142:27168495:27168605	27157831:27158142
exon_skip_237323	chr9	27190529:27190690:27192489:27192623:27197315:27197599	27192489:27192623
exon_skip_246594	chr9	27173222:27173362:27180240:27180368:27183459:27183610	27180240:27180368
exon_skip_268108	chr9	27190529:27190690:27191929:27191965:27192489:27192623	27191929:27191965
exon_skip_37713	chr9	27217688:27217758:27218777:27218817:27220049:27220145	27218777:27218817
exon_skip_45060	chr9	27185485:27185629:27190529:27190690:27192489:27192623	27190529:27190690

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

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

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
ENST00000380036	27218777	27218817	Frame-shift
ENST00000380036	27157831	27158142	In-frame
ENST00000380036	27180240	27180368	In-frame
ENST00000380036	27190529	27190690	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
ENST00000380036	27180240	27180368	In-frame
ENST00000380036	27190529	27190690	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
ENST00000380036	27218777	27218817	Frame-shift
ENST00000380036	27180240	27180368	In-frame
ENST00000380036	27190529	27190690	In-frame
ENST00000380036	27192489	27192623	In-frame

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

p-ENSG00000120156_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
ENST00000380036	4777	1124	27157831	27158142	496	806	18	121
ENST00000380036	4777	1124	27180240	27180368	1345	1472	301	343
ENST00000380036	4777	1124	27190529	27190690	1771	1931	443	496

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
ENST00000380036	4777	1124	27180240	27180368	1345	1472	301	343
ENST00000380036	4777	1124	27190529	27190690	1771	1931	443	496

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
ENST00000380036	4777	1124	27180240	27180368	1345	1472	301	343
ENST00000380036	4777	1124	27190529	27190690	1771	1931	443	496
ENST00000380036	4777	1124	27192489	27192623	1933	2066	497	541

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
Q02763	18	121	18	121	Alternative sequence	ID=VSP_042137;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q02763	18	121	26	29	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	33	35	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	40	46	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	64	66	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	74	76	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	80	88	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	98	106	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	109	119	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	18	121	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	18	121	44	102	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	18	121	44	123	Domain	Note=Ig-like C2-type 1
Q02763	18	121	19	210	Natural variant	ID=VAR_078045;Note=In GLC3E%3B formation of protein aggregates. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27270174;Dbxref=PMID:27270174
Q02763	18	121	117	117	Natural variant	ID=VAR_035714;Note=In breast cancer samples%3B infiltrating ductal carcinoma%3B somatic mutation. K->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16959974,ECO:0000269\|PubMed:17344846;Dbxref=PMID:16959974,PMID:17344846
Q02763	18	121	1	22	Signal peptide	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15340161;Dbxref=PMID:15340161
Q02763	18	121	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	18	121	61	63	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	300	342	Alternative sequence	ID=VSP_042138;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q02763	301	343	322	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	328	330	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	301	343	302	311	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	315	323	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	317	329	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	331	340	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	301	341	Domain	Note=EGF-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
Q02763	301	343	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	301	343	325	327	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	443	496	446	449	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	452	456	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	469	472	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	476	485	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	493	504	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	443	496	447	541	Domain	Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316
Q02763	443	496	464	464	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	443	496	486	486	Natural variant	ID=VAR_024578;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs1334811,PMID:17344846
Q02763	443	496	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q02763	301	343	300	342	Alternative sequence	ID=VSP_042138;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q02763	301	343	322	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	328	330	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	301	343	302	311	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	315	323	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	317	329	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	331	340	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	301	341	Domain	Note=EGF-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
Q02763	301	343	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	301	343	325	327	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	443	496	446	449	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	452	456	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	469	472	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	476	485	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	493	504	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	443	496	447	541	Domain	Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316
Q02763	443	496	464	464	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	443	496	486	486	Natural variant	ID=VAR_024578;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs1334811,PMID:17344846
Q02763	443	496	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q02763	301	343	300	342	Alternative sequence	ID=VSP_042138;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q02763	301	343	322	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	328	330	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	301	343	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	301	343	302	311	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	315	323	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	317	329	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	331	340	Disulfide bond	Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16732286;Dbxref=PMID:16732286
Q02763	301	343	301	341	Domain	Note=EGF-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
Q02763	301	343	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	301	343	325	327	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GY5
Q02763	443	496	446	449	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	452	456	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	461	464	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	469	472	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	476	485	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	493	504	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	443	496	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	443	496	447	541	Domain	Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316
Q02763	443	496	464	464	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	443	496	486	486	Natural variant	ID=VAR_024578;Note=V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs1334811,PMID:17344846
Q02763	443	496	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q02763	497	541	493	504	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	497	541	512	521	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	497	541	534	537	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5UTK
Q02763	497	541	23	1124	Chain	ID=PRO_0000024474;Note=Angiopoietin-1 receptor
Q02763	497	541	447	541	Domain	Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316
Q02763	497	541	536	536	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q02763	497	541	23	748	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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

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 TEK

- 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 TEK

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 TEK

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
CB	exon_skip_45060	rs1322051	chr9:27185103	8.952252e-05	1.586476e-02
CB	exon_skip_45060	rs1334811	chr9:27190657	8.952252e-05	1.586476e-02

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Correlation with RNA binding proteins (RBPs) for TEK

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for TEK

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Q02763	approved\|vet_approved	DB00415	Ampicillin	small molecule	Q02763
Q02763	approved	DB05294	Vandetanib	small molecule	Q02763
Q02763	approved	DB08896	Regorafenib	small molecule	Q02763
Q02763	approved\|investigational	DB08901	Ponatinib	small molecule	Q02763
Q02763	approved\|investigational	DB12010	Fostamatinib	small molecule	Q02763

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RelatedDiseases for TEK

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 TEK

Gene structures and expression levels for TEK

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

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

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

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

SNVs in the skipped exons for TEK

AD stage-associated exon skippint events for TEK

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

Correlation with RNA binding proteins (RBPs) for TEK

RelatedDrugs for TEK

RelatedDiseases for TEK