ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PCDH15

Gene summary

Gene information	Gene symbol	PCDH15
	Gene ID	65217
	Gene name	protocadherin related 15
	Synonyms	CDHR15\|DFNB23\|USH1F
	Cytomap	10q21.1
	Type of gene	protein-coding
	Description	protocadherin-15cadherin-related family member 15
	Modification date	20200313
	UniProtAcc	A0A087WTR6, A0A087WUA8, A0A087WUC7, A0A087WX70, A0A087WXQ6, A0A087WZ37, A0A087WZN4, A0A087WZN9, A0A087WZW3, A0A087X1T6, A0A087X250, A0A2R8Y6C0, A0A2R8YEV2, A2A3D8, A2A3D9, A2A3E1, A2A3E3, A2A3E4, A2A3E5, A2A3E6, A2A3E7, A2A3E8, A9Z1W1, B7ZBT8, C9J4F3, E7EM53, E7EM97, E7EMG0, E7EMG8, Q96QU1,
	Context	- 20182759(Fine mapping of the chromosome 10q11-q21 linkage region in Alzheimer's disease cases and controls)

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 PCDH15

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.

ENSG00000150275

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
CB	DOWN	ENST00000495484.5	PCDH15-223:protein_coding:PCDH15	1.313637e+01	-1.331806e+00	6.369850e-06	7.194506e-05

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 PCDH15

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_130038	chr10	53827393:53827548:53828565:53828573:53831315:53831533	53828565:53828573
exon_skip_203506	chr10	53817995:53818013:53820165:53820230:53827393:53827548	53820165:53820230
exon_skip_207898	chr10	54195683:54195889:54213936:54214048:54236823:54236931	54213936:54214048
exon_skip_2155	chr10	53857175:53857263:53866642:53866857:53903243:53903370	53866642:53866857
exon_skip_218266	chr10	53821110:53823358:53825136:53825141:53827393:53827548	53825136:53825141
exon_skip_233649	chr10	54378782:54378942:54527812:54527877:54664172:54664290	54527812:54527877
exon_skip_269333	chr10	54527812:54527877:54528388:54528402:54664172:54664290	54528388:54528402
exon_skip_279799	chr10	53810556:53810664:53811549:53811619:53816239:53816277	53811549:53811619
exon_skip_293012	chr10	53810556:53810664:53825136:53825141:53827393:53827548	53825136:53825141
exon_skip_90631	chr10	53866642:53866857:53903243:53903370:53938815:53938955	53903243:53903370

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 PCDH15

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
ENST00000320301	53903243	53903370	Frame-shift
ENST00000320301	53828565	53828573	In-frame
ENST00000320301	53866642	53866857	In-frame
ENST00000320301	54527812	54527877	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
ENST00000320301	53903243	53903370	Frame-shift
ENST00000320301	54213936	54214048	Frame-shift
ENST00000320301	54527812	54527877	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
ENST00000320301	53828565	53828573	In-frame
ENST00000320301	53866642	53866857	In-frame
ENST00000320301	54527812	54527877	In-frame

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Infer the effects of exon skipping event on protein functional features for PCDH15

p-ENSG00000150275_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
ENST00000320301	6862	1955	54527812	54527877	487	551	30	52
ENST00000320301	6862	1955	53866642	53866857	3897	4111	1167	1238

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
ENST00000320301	6862	1955	54527812	54527877	487	551	30	52

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
ENST00000320301	6862	1955	54527812	54527877	487	551	30	52
ENST00000320301	6862	1955	53866642	53866857	3897	4111	1167	1238

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
Q96QU1	30	52	1	1118	Alternative sequence	ID=VSP_028257;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14570705;Dbxref=PMID:14570705
Q96QU1	30	52	27	1955	Chain	ID=PRO_0000003998;Note=Protocadherin-15
Q96QU1	30	52	32	120	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q96QU1	30	52	40	147	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q96QU1	30	52	52	52	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	30	52	27	1376	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	1167	1238	962	1955	Alternative sequence	ID=VSP_028260;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:17974005;Dbxref=PMID:17974005
Q96QU1	1167	1238	27	1955	Chain	ID=PRO_0000003998;Note=Protocadherin-15
Q96QU1	1167	1238	1145	1259	Domain	Note=Cadherin 11;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q96QU1	1167	1238	1175	1175	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	1167	1238	27	1376	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
Q96QU1	30	52	1	1118	Alternative sequence	ID=VSP_028257;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14570705;Dbxref=PMID:14570705
Q96QU1	30	52	27	1955	Chain	ID=PRO_0000003998;Note=Protocadherin-15
Q96QU1	30	52	32	120	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q96QU1	30	52	40	147	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q96QU1	30	52	52	52	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	30	52	27	1376	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
Q96QU1	30	52	1	1118	Alternative sequence	ID=VSP_028257;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14570705;Dbxref=PMID:14570705
Q96QU1	30	52	27	1955	Chain	ID=PRO_0000003998;Note=Protocadherin-15
Q96QU1	30	52	32	120	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
Q96QU1	30	52	40	147	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q96QU1	30	52	52	52	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	30	52	27	1376	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	1167	1238	962	1955	Alternative sequence	ID=VSP_028260;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:17974005;Dbxref=PMID:17974005
Q96QU1	1167	1238	27	1955	Chain	ID=PRO_0000003998;Note=Protocadherin-15
Q96QU1	1167	1238	1145	1259	Domain	Note=Cadherin 11;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q96QU1	1167	1238	1175	1175	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96QU1	1167	1238	27	1376	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 PCDH15

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 PCDH15

- 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 PCDH15

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 PCDH15

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 PCDH15

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for PCDH15

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 PCDH15

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 PCDH15

Gene structures and expression levels for PCDH15

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PCDH15

Open reading frame (ORF) annotation in the exon skipping event for PCDH15

Infer the effects of exon skipping event on protein functional features for PCDH15

3'-UTR located exon skipping events that lost miRNA binding sites in PCDH15

SNVs in the skipped exons for PCDH15

AD stage-associated exon skippint events for PCDH15

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PCDH15

Correlation with RNA binding proteins (RBPs) for PCDH15

RelatedDrugs for PCDH15

RelatedDiseases for PCDH15