ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for WAC

Gene summary

Gene information	Gene symbol	WAC
	Gene ID	51322
	Gene name	WW domain containing adaptor with coiled-coil
	Synonyms	BM-016\|DESSH\|PRO1741\|Wwp4
	Cytomap	10p12.1\|10p12.1-p11.2
	Type of gene	protein-coding
	Description	WW domain-containing adapter protein with coiled-coil
	Modification date	20200313
	UniProtAcc	A0A0A0MRT2, A0A494C0B7, A0A494C0C1, A0A494C0S5, C9JD58, C9JMU2, C9JVK6, E9PMZ7, J3QT76, J3QTA0, Q9BTA9, Q9P1G8,
	Context

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for WAC

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.

ENSG00000095787

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	ENST00000428935.5	WAC-209:protein_coding:WAC	2.191758e+01	2.005868e+00	1.433197e-04	1.372672e-02
CB	UP	ENST00000526722.1	WAC-217:protein_coding:WAC	2.056323e+01	1.000341e+00	9.375220e-10	4.155998e-08
CB	UP	ENST00000532233.5	WAC-220:lncRNA:WAC	2.481411e+01	1.169743e+00	3.491708e-09	1.243770e-07
CB	UP	ENST00000476046.1	WAC-214:retained_intron:WAC	3.554954e+01	9.644624e-01	5.804297e-09	1.904473e-07
CB	UP	ENST00000628285.2	WAC-221:protein_coding:WAC	1.239945e+03	1.028900e+00	6.585776e-09	2.119687e-07
CB	UP	ENST00000375646.5	WAC-204:protein_coding:WAC	1.066434e+02	1.617709e+00	7.363769e-08	1.638843e-06
CB	UP	ENST00000428935.5	WAC-209:protein_coding:WAC	4.164512e+01	2.159235e+00	2.713063e-06	3.502619e-05
CB	UP	ENST00000347934.8	WAC-202:protein_coding:WAC	3.497682e+03	9.542511e-01	5.441313e-06	6.297345e-05
CB	UP	ENST00000439676.5	WAC-210:nonsense_mediated_decay:WAC	1.509555e+01	2.083243e+00	7.844978e-06	8.606446e-05
CB	UP	ENST00000414108.5	WAC-206:protein_coding:WAC	2.151891e+02	1.252775e+00	2.757006e-05	2.484232e-04
CB	UP	ENST00000420266.5	WAC-207:protein_coding:WAC	1.030522e+01	1.178125e+00	1.165234e-03	5.875940e-03
CB	UP	ENST00000528491.5	WAC-218:lncRNA:WAC	1.331640e+00	2.027245e+00	4.749211e-03	1.886582e-02
TC	UP	ENST00000532233.5	WAC-220:lncRNA:WAC	9.964304e+00	8.550620e-01	4.758711e-08	3.339741e-06
TC	UP	ENST00000414108.5	WAC-206:protein_coding:WAC	7.448571e+01	8.784072e-01	3.944398e-05	7.686634e-04
TC	UP	ENST00000428935.5	WAC-209:protein_coding:WAC	2.424618e+01	1.523447e+00	6.835540e-03	4.226311e-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 WAC

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_101919	chr10	28532784:28533007:28533998:28534182:28535562:28535726	28533998:28534182
exon_skip_136633	chr10	28532784:28533007:28533998:28534034:28535562:28535726	28533998:28534034
exon_skip_151862	chr10	28533998:28534034:28534234:28534346:28535562:28535757	28534234:28534346
exon_skip_156509	chr10	28590720:28590832:28608186:28608431:28610699:28610710	28608186:28608431
exon_skip_160269	chr10	28614567:28614685:28616176:28616362:28617657:28617784	28616176:28616362
exon_skip_163571	chr10	28614572:28614685:28616173:28616362:28617657:28617784	28616173:28616362
exon_skip_171924	chr10	28533998:28534034:28534234:28534346:28535562:28535726	28534234:28534346
exon_skip_189024	chr10	28590727:28590832:28595733:28596041:28608186:28608431	28595733:28596041
exon_skip_19647	chr10	28590720:28590832:28595733:28596041:28608186:28608431	28595733:28596041
exon_skip_199349	chr10	28610711:28610821:28611255:28611481:28611774:28611922	28611255:28611481
exon_skip_225599	chr10	28614572:28614685:28616176:28616362:28617657:28617784	28616176:28616362
exon_skip_22780	chr10	28610801:28610821:28611255:28611481:28611774:28611922	28611255:28611481
exon_skip_231871	chr10	28614567:28614685:28616173:28616362:28617657:28617784	28616173:28616362
exon_skip_236271	chr10	28610711:28610821:28611255:28611481:28611774:28611859	28611255:28611481
exon_skip_45022	chr10	28533597:28533620:28533998:28534034:28535562:28535726	28533998:28534034
exon_skip_9438	chr10	28590722:28590832:28595733:28596041:28608186:28608431	28595733:28596041

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 WAC

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
ENST00000354911	28616173	28616362	Frame-shift
ENST00000354911	28595733	28596041	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
ENST00000354911	28595733	28596041	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
ENST00000354911	28533998	28534034	Frame-shift
ENST00000354911	28616173	28616362	Frame-shift
ENST00000354911	28595733	28596041	In-frame

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

p-ENSG00000095787_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
ENST00000354911	3059	647	28595733	28596041	773	1080	204	306

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
ENST00000354911	3059	647	28595733	28596041	773	1080	204	306

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
ENST00000354911	3059	647	28595733	28596041	773	1080	204	306

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
Q9BTA9	204	306	204	307	Alternative sequence	ID=VSP_021231;Note=In isoform 4. MEDKHSSDASSLLPQNILSQTSRHNDRDYRLPRAETHSSSTPVQHPIKPVVHPTATPSTVPSSPFTLQSDHQPKKSFDANGASTLSKLPTPTSSVPAQKTERKE->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BTA9	204	306	1	647	Chain	ID=PRO_0000254558;Note=WW domain-containing adapter protein with coiled-coil
Q9BTA9	204	306	225	225	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q9BTA9	204	306	293	293	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:23186163,PMID:24275569
Q9BTA9	204	306	302	302	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q9BTA9	204	306	47	647	Natural variant	ID=VAR_078694;Note=Probable disease-associated mutation found in a patient severe intellectual disability. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23033978;Dbxref=PMID:23033978
Q9BTA9	204	306	242	242	Natural variant	ID=VAR_028838;Note=S->R;Dbxref=dbSNP:rs11595926

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
Q9BTA9	204	306	204	307	Alternative sequence	ID=VSP_021231;Note=In isoform 4. MEDKHSSDASSLLPQNILSQTSRHNDRDYRLPRAETHSSSTPVQHPIKPVVHPTATPSTVPSSPFTLQSDHQPKKSFDANGASTLSKLPTPTSSVPAQKTERKE->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BTA9	204	306	1	647	Chain	ID=PRO_0000254558;Note=WW domain-containing adapter protein with coiled-coil
Q9BTA9	204	306	225	225	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q9BTA9	204	306	293	293	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:23186163,PMID:24275569
Q9BTA9	204	306	302	302	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q9BTA9	204	306	47	647	Natural variant	ID=VAR_078694;Note=Probable disease-associated mutation found in a patient severe intellectual disability. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23033978;Dbxref=PMID:23033978
Q9BTA9	204	306	242	242	Natural variant	ID=VAR_028838;Note=S->R;Dbxref=dbSNP:rs11595926

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
Q9BTA9	204	306	204	307	Alternative sequence	ID=VSP_021231;Note=In isoform 4. MEDKHSSDASSLLPQNILSQTSRHNDRDYRLPRAETHSSSTPVQHPIKPVVHPTATPSTVPSSPFTLQSDHQPKKSFDANGASTLSKLPTPTSSVPAQKTERKE->K;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9BTA9	204	306	1	647	Chain	ID=PRO_0000254558;Note=WW domain-containing adapter protein with coiled-coil
Q9BTA9	204	306	225	225	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q9BTA9	204	306	293	293	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:23186163,PMID:24275569
Q9BTA9	204	306	302	302	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q9BTA9	204	306	47	647	Natural variant	ID=VAR_078694;Note=Probable disease-associated mutation found in a patient severe intellectual disability. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23033978;Dbxref=PMID:23033978
Q9BTA9	204	306	242	242	Natural variant	ID=VAR_028838;Note=S->R;Dbxref=dbSNP:rs11595926

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

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 WAC

- 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 WAC

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 WAC

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
DLPFC	exon_skip_9438	rs12571273	chr10:28659450	3.076001e-04	2.199305e-02
DLPFC	exon_skip_9438	rs11007183	chr10:28650923	5.182467e-04	3.316839e-02

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Correlation with RNA binding proteins (RBPs) for WAC

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
DLPFC	PCBP2	exon_skip_9438	4.100598e-01	3.129875e-11
DLPFC	ENOX1	exon_skip_9438	4.078567e-01	4.078816e-11
IFG	IGF2BP2	exon_skip_9438	-4.525886e-01	1.559389e-02
PCC	RBMS2	exon_skip_9438	-4.215123e-01	1.137108e-10
STG	TRA2A	exon_skip_9438	-4.044795e-01	6.994478e-05
TC	HNRNPA0	exon_skip_9438	5.145987e-01	3.378332e-12
TC	HNRNPD	exon_skip_9438	4.068041e-01	9.394885e-08
TC	RALYL	exon_skip_9438	4.380018e-01	6.945936e-09
TC	SRSF9	exon_skip_9438	4.158742e-01	4.526654e-08

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RelatedDrugs for WAC

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 WAC

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 WAC

Gene structures and expression levels for WAC

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

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

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

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

SNVs in the skipped exons for WAC

AD stage-associated exon skippint events for WAC

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

Correlation with RNA binding proteins (RBPs) for WAC

RelatedDrugs for WAC

RelatedDiseases for WAC