ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for EYA1

Gene summary

Gene information	Gene symbol	EYA1
	Gene ID	2138
	Gene name	EYA transcriptional coactivator and phosphatase 1
	Synonyms	BOP\|BOR\|BOS1\|OFC1
	Cytomap	8q13.3
	Type of gene	protein-coding
	Description	eyes absent homolog 1
	Modification date	20200313
	UniProtAcc	A0A024R813, A0A2R8Y6K4, A0A2R8YET7, A0A2R8YF73, A0A2R8YFS6, A0A2R8YGM9, A6NCB9, E5RHZ7, E5RIQ7, E7EQM5, F8WB53, Q0P517, Q4A4D0, Q99502,
	Context

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

Gene	GO ID	GO term	PubMed ID
EYA1	GO:0010212	response to ionizing radiation	19234442
EYA1	GO:0016576	histone dephosphorylation	19234442

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Gene structures and expression levels for EYA1

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.

ENSG00000104313

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
HCC	UP	ENST00000644424.1	EYA1-220:lncRNA:EYA1	3.347605e+01	1.254072e+00	1.079080e-03	3.558881e-02
TC	UP	ENST00000644229.1	EYA1-219:protein_coding:EYA1	3.849178e+00	2.517511e+00	9.039891e-04	9.144663e-03
TC	UP	ENST00000388741.7	EYA1-204:protein_coding:EYA1	2.398936e+00	2.045094e+00	4.470989e-03	3.080293e-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 EYA1

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_111445	chr8	71322199:71322268:71323956:71323986:71334097:71334174	71323956:71323986
exon_skip_119434	chr8	71334097:71334174:71354782:71354909:71356462:71356511	71354782:71354909
exon_skip_218423	chr8	71216965:71217023:71244603:71244692:71269740:71269823	71244603:71244692
exon_skip_269948	chr8	71299638:71299720:71317552:71317689:71321734:71321812	71317552:71317689
exon_skip_276526	chr8	71299638:71299720:71317552:71317674:71321734:71321812	71317552:71317674
exon_skip_49311	chr8	71356462:71356511:71470858:71470931:71535744:71535848	71470858:71470931
exon_skip_73138	chr8	71216965:71217023:71244603:71244692:71269740:71269821	71244603:71244692
exon_skip_92465	chr8	71216965:71217023:71225152:71225305:71244603:71244692	71225152:71225305

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 EYA1

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
ENST00000340726	71354782	71354909	3UTR-3CDS
ENST00000645793	71354782	71354909	3UTR-3CDS
ENST00000647540	71354782	71354909	3UTR-3CDS
ENST00000647540	71470858	71470931	3UTR-3UTR
ENST00000340726	71244603	71244692	In-frame
ENST00000388742	71244603	71244692	In-frame
ENST00000645793	71244603	71244692	In-frame
ENST00000647540	71244603	71244692	In-frame
ENST00000340726	71317552	71317689	In-frame
ENST00000388742	71317552	71317689	In-frame
ENST00000645793	71317552	71317689	In-frame
ENST00000647540	71317552	71317689	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
ENST00000340726	71354782	71354909	3UTR-3CDS
ENST00000645793	71354782	71354909	3UTR-3CDS
ENST00000647540	71354782	71354909	3UTR-3CDS
ENST00000647540	71470858	71470931	3UTR-3UTR
ENST00000340726	71244603	71244692	In-frame
ENST00000388742	71244603	71244692	In-frame
ENST00000645793	71244603	71244692	In-frame
ENST00000647540	71244603	71244692	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
ENST00000340726	71354782	71354909	3UTR-3CDS
ENST00000645793	71354782	71354909	3UTR-3CDS
ENST00000647540	71354782	71354909	3UTR-3CDS
ENST00000647540	71470858	71470931	3UTR-3UTR
ENST00000340726	71244603	71244692	In-frame
ENST00000388742	71244603	71244692	In-frame
ENST00000645793	71244603	71244692	In-frame
ENST00000647540	71244603	71244692	In-frame

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Infer the effects of exon skipping event on protein functional features for EYA1

p-ENSG00000104313_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
ENST00000340726	4343	592	71317552	71317689	1059	1195	139	185
ENST00000388742	3924	592	71317552	71317689	640	776	139	185
ENST00000645793	4271	592	71317552	71317689	1065	1201	139	185
ENST00000647540	3960	592	71317552	71317689	764	900	139	185
ENST00000340726	4343	592	71244603	71244692	1691	1779	350	379
ENST00000388742	3924	592	71244603	71244692	1272	1360	350	379
ENST00000645793	4271	592	71244603	71244692	1697	1785	350	379
ENST00000647540	3960	592	71244603	71244692	1396	1484	350	379

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
ENST00000340726	4343	592	71244603	71244692	1691	1779	350	379
ENST00000388742	3924	592	71244603	71244692	1272	1360	350	379
ENST00000645793	4271	592	71244603	71244692	1697	1785	350	379
ENST00000647540	3960	592	71244603	71244692	1396	1484	350	379

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
ENST00000340726	4343	592	71244603	71244692	1691	1779	350	379
ENST00000388742	3924	592	71244603	71244692	1272	1360	350	379
ENST00000645793	4271	592	71244603	71244692	1697	1785	350	379
ENST00000647540	3960	592	71244603	71244692	1396	1484	350	379

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
Q99502	139	185	140	144	Alternative sequence	ID=VSP_045793;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	139	185	140	144	Alternative sequence	ID=VSP_045793;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	139	185	140	144	Alternative sequence	ID=VSP_045793;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	139	185	140	144	Alternative sequence	ID=VSP_045793;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	139	185	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	139	185	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	139	185	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	139	185	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	139	185	140	140	Natural variant	ID=VAR_064943;Note=In BOR1. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	139	185	140	140	Natural variant	ID=VAR_064943;Note=In BOR1. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	139	185	140	140	Natural variant	ID=VAR_064943;Note=In BOR1. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	139	185	140	140	Natural variant	ID=VAR_064943;Note=In BOR1. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147

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
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147

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
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	351	380	Alternative sequence	ID=VSP_045794;Note=In isoform EYA1D. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	1	592	Chain	ID=PRO_0000218643;Note=Eyes absent homolog 1
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_016864;Note=In ASA. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10655545;Dbxref=dbSNP:rs121909198,PMID:10655545
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147
Q99502	350	379	363	363	Natural variant	ID=VAR_064944;Note=In BOR1. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21280147;Dbxref=PMID:21280147

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3'-UTR located exon skipping events that lost miRNA binding sites in EYA1

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 EYA1

- 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 EYA1

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 EYA1

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 EYA1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for EYA1

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 EYA1

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 EYA1

Gene structures and expression levels for EYA1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for EYA1

Open reading frame (ORF) annotation in the exon skipping event for EYA1

Infer the effects of exon skipping event on protein functional features for EYA1

3'-UTR located exon skipping events that lost miRNA binding sites in EYA1

SNVs in the skipped exons for EYA1

AD stage-associated exon skippint events for EYA1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for EYA1

Correlation with RNA binding proteins (RBPs) for EYA1

RelatedDrugs for EYA1

RelatedDiseases for EYA1