ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for YAP1

Gene summary

Gene information	Gene symbol	YAP1
	Gene ID	10413
	Gene name	Yes1 associated transcriptional regulator
	Synonyms	COB1\|YAP\|YAP2\|YAP65\|YKI
	Cytomap	11q22.1
	Type of gene	protein-coding
	Description	transcriptional coactivator YAP165 kDa Yes-associated proteinYes associated protein 1protein yorkie homologyes-associated protein 1yes-associated protein 2yes-associated protein YAP65 homologyorkie homolog
	Modification date	20200329
	UniProtAcc	A0A024R3E4, H0YCI3, K0KVU2, P46937,
	Context	- 28923553(A systematic integrated analysis of brain expression profiles reveals YAP1 and other prioritized hub genes as important upstream regulators 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
YAP1	GO:0006974	cellular response to DNA damage stimulus	18280240
YAP1	GO:0008283	cell proliferation	17974916
YAP1	GO:0032570	response to progesterone	16772533
YAP1	GO:0033148	positive regulation of intracellular estrogen receptor signaling pathway	16772533
YAP1	GO:0045893	positive regulation of transcription, DNA-templated	20368466
YAP1	GO:0045944	positive regulation of transcription by RNA polymerase II	25796446
YAP1	GO:0050767	regulation of neurogenesis	25433207
YAP1	GO:0050847	progesterone receptor signaling pathway	16772533
YAP1	GO:0060242	contact inhibition	17974916
YAP1	GO:0065003	protein-containing complex assembly	20368466
YAP1	GO:0071480	cellular response to gamma radiation	18280240
YAP1	GO:0072091	regulation of stem cell proliferation	25433207

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Gene structures and expression levels for YAP1

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.

ENSG00000137693

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
TC	UP	2.092159e+03	8.402762e-01	4.964698e-13	8.679796e-11

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	ENST00000531439.5	YAP1-208:protein_coding:YAP1	2.793601e+01	1.171671e+00	7.666816e-04	3.341648e-02
PG	DOWN	ENST00000581602.1	ADCYAP1-204:retained_intron:ADCYAP1	2.190559e+01	-9.614758e-01	1.449294e-05	6.618429e-04
PG	UP	ENST00000537274.5	YAP1-209:protein_coding:YAP1	2.033285e+02	1.064522e+00	2.226669e-04	4.930609e-03
PG	UP	ENST00000629586.2	YAP1-211:protein_coding:YAP1	2.200038e+00	4.076823e+00	1.565909e-03	2.008441e-02
CB	UP	ENST00000531439.5	YAP1-208:protein_coding:YAP1	3.627843e+01	8.436489e-01	8.337325e-06	9.062638e-05
TC	UP	ENST00000531439.5	YAP1-208:protein_coding:YAP1	5.855602e+01	1.290712e+00	2.265027e-12	7.435990e-10
TC	UP	ENST00000282441.10	YAP1-201:protein_coding:YAP1	8.307433e+02	8.238340e-01	4.457836e-08	3.152710e-06
TC	DOWN	ENST00000581602.1	ADCYAP1-204:retained_intron:ADCYAP1	9.233184e+01	-9.992059e-01	2.988380e-05	6.151894e-04
TC	UP	ENST00000526343.5	YAP1-204:protein_coding:YAP1	3.029341e+00	1.719429e+00	5.958031e-03	3.815525e-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 YAP1

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_104101	chr11	102223622:102223752:102227469:102227581:102229702:102229940	102227469:102227581
exon_skip_177926	chr11	102162456:102162571:102186018:102186131:102205893:102206074	102186018:102186131
exon_skip_1847	chr11	102205893:102206074:102209517:102209564:102223622:102223752	102209517:102209564
exon_skip_21555	chr11	102205893:102206086:102209517:102209564:102223622:102223752	102209517:102209564

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 YAP1

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
ENST00000282441	102227469	102227581	Frame-shift
ENST00000282441	102186018	102186131	In-frame
ENST00000282441	102209517	102209564	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
ENST00000282441	102186018	102186131	In-frame
ENST00000282441	102209517	102209564	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
ENST00000282441	102227469	102227581	Frame-shift
ENST00000282441	102186018	102186131	In-frame
ENST00000282441	102209517	102209564	In-frame

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Infer the effects of exon skipping event on protein functional features for YAP1

p-ENSG00000137693_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
ENST00000282441	5403	504	102186018	102186131	1078	1190	230	267
ENST00000282441	5403	504	102209517	102209564	1374	1420	328	344

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
ENST00000282441	5403	504	102186018	102186131	1078	1190	230	267
ENST00000282441	5403	504	102209517	102209564	1374	1420	328	344

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
ENST00000282441	5403	504	102186018	102186131	1078	1190	230	267
ENST00000282441	5403	504	102209517	102209564	1374	1420	328	344

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
P46937	230	267	230	267	Alternative sequence	ID=VSP_039053;Note=In isoform 3%2C isoform 5%2C isoform 6 and isoform 7. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:22939869,ECO:0000303\|Ref.3;Dbxref=PMID:22939869
P46937	230	267	233	235	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	238	241	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	245	250	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	255	259	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	230	267	230	263	Domain	Note=WW 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00224
P46937	230	267	242	244	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	251	254	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	328	344	328	343	Alternative sequence	ID=VSP_039054;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12807903;Dbxref=PMID:12807903
P46937	328	344	328	328	Alternative sequence	ID=VSP_053483;Note=In isoform 7 and isoform 9. Q->QVRPQ;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	329	343	Alternative sequence	ID=VSP_039055;Note=In isoform 3 and isoform 8. AMRNINPSTANSPKC->VRP;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	328	344	298	359	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P46937	328	344	330	330	Natural variant	ID=VAR_071127;Note=M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24462371;Dbxref=dbSNP:rs777949318,PMID:24462371
P46937	328	344	291	504	Region	Note=Transactivation domain

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
P46937	230	267	230	267	Alternative sequence	ID=VSP_039053;Note=In isoform 3%2C isoform 5%2C isoform 6 and isoform 7. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:22939869,ECO:0000303\|Ref.3;Dbxref=PMID:22939869
P46937	230	267	233	235	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	238	241	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	245	250	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	255	259	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	230	267	230	263	Domain	Note=WW 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00224
P46937	230	267	242	244	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	251	254	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	328	344	328	343	Alternative sequence	ID=VSP_039054;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12807903;Dbxref=PMID:12807903
P46937	328	344	328	328	Alternative sequence	ID=VSP_053483;Note=In isoform 7 and isoform 9. Q->QVRPQ;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	329	343	Alternative sequence	ID=VSP_039055;Note=In isoform 3 and isoform 8. AMRNINPSTANSPKC->VRP;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	328	344	298	359	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P46937	328	344	330	330	Natural variant	ID=VAR_071127;Note=M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24462371;Dbxref=dbSNP:rs777949318,PMID:24462371
P46937	328	344	291	504	Region	Note=Transactivation domain

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
P46937	230	267	230	267	Alternative sequence	ID=VSP_039053;Note=In isoform 3%2C isoform 5%2C isoform 6 and isoform 7. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:22939869,ECO:0000303\|Ref.3;Dbxref=PMID:22939869
P46937	230	267	233	235	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	238	241	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	245	250	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	255	259	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	230	267	230	263	Domain	Note=WW 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00224
P46937	230	267	242	244	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	230	267	251	254	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LAW
P46937	328	344	328	343	Alternative sequence	ID=VSP_039054;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12807903;Dbxref=PMID:12807903
P46937	328	344	328	328	Alternative sequence	ID=VSP_053483;Note=In isoform 7 and isoform 9. Q->QVRPQ;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	329	343	Alternative sequence	ID=VSP_039055;Note=In isoform 3 and isoform 8. AMRNINPSTANSPKC->VRP;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22939869;Dbxref=PMID:22939869
P46937	328	344	1	504	Chain	ID=PRO_0000076071;Note=Transcriptional coactivator YAP1
P46937	328	344	298	359	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
P46937	328	344	330	330	Natural variant	ID=VAR_071127;Note=M->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24462371;Dbxref=dbSNP:rs777949318,PMID:24462371
P46937	328	344	291	504	Region	Note=Transactivation domain

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3'-UTR located exon skipping events that lost miRNA binding sites in YAP1

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 YAP1

- 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 YAP1

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 YAP1

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 YAP1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for YAP1

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for YAP1

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 YAP1

Gene structures and expression levels for YAP1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for YAP1

Open reading frame (ORF) annotation in the exon skipping event for YAP1

Infer the effects of exon skipping event on protein functional features for YAP1

3'-UTR located exon skipping events that lost miRNA binding sites in YAP1

SNVs in the skipped exons for YAP1

AD stage-associated exon skippint events for YAP1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YAP1

Correlation with RNA binding proteins (RBPs) for YAP1

RelatedDrugs for YAP1

RelatedDiseases for YAP1