ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CTNND1

Gene summary

Gene information	Gene symbol	CTNND1
	Gene ID	1500
	Gene name	catenin delta 1
	Synonyms	BCDS2\|CAS\|CTNND\|P120CAS\|P120CTN\|p120\|p120(CAS)\|p120(CTN)
	Cytomap	11q12.1
	Type of gene	protein-coding
	Description	catenin delta-1cadherin-associated Src substratecatenin (cadherin-associated protein), delta 1p120 catenin
	Modification date	20200327
	UniProtAcc	A0A024R4Y7, A0A024R4Z0, C9JZR2, E9PKL1, E9PKY0, E9PRE2, H0YC95, O60716, Q96FS1,
	Context

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

Gene	GO ID	GO term	PubMed ID
CTNND1	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	18602475

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Gene structures and expression levels for CTNND1

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.

ENSG00000198561

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
PG	UP	ENST00000526772.5	CTNND1-214:protein_coding:CTNND1	4.148681e+01	3.816235e+00	3.152576e-03	3.295454e-02
PG	UP	ENST00000531014.5	CTNND1-229:protein_coding:CTNND1	2.070430e+00	4.245239e+00	4.686241e-03	4.368485e-02
CB	UP	ENST00000534647.1	CTNND1-238:protein_coding:CTNND1	4.419202e+01	9.436183e-01	3.209000e-10	1.704472e-08
CB	DOWN	ENST00000531014.5	CTNND1-229:protein_coding:CTNND1	1.721882e+00	-2.749836e+00	5.747829e-04	3.242238e-03
CB	UP	ENST00000526938.5	CTNND1-215:protein_coding:CTNND1	1.753240e+01	1.163904e+00	7.941006e-04	4.254205e-03
CB	DOWN	ENST00000526772.5	CTNND1-214:protein_coding:CTNND1	2.198109e+02	-2.326591e+00	2.347726e-03	1.052331e-02
CB	UP	ENST00000532787.5	CTNND1-233:protein_coding:CTNND1	4.023524e+00	1.073969e+00	8.763236e-03	3.119405e-02
TC	UP	ENST00000530094.5	CTNND1-225:protein_coding:CTNND1	2.580232e+00	1.417104e+00	2.006007e-04	2.801119e-03
TC	UP	ENST00000361332.8	CTNND1-202:protein_coding:CTNND1	2.425801e+00	1.790305e+00	8.564432e-04	8.766196e-03
TC	UP	ENST00000526938.5	CTNND1-215:protein_coding:CTNND1	1.463577e+01	8.149633e-01	6.841822e-03	4.229624e-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 CTNND1

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_131998	chr11	57815394:57815500:57815915:57816001:57816297:57819178	57815915:57816001
exon_skip_215244	chr11	57805882:57806035:57806461:57806478:57806915:57806983	57806461:57806478
exon_skip_222638	chr11	57761797:57762046:57791385:57791673:57794010:57794081	57791385:57791673
exon_skip_235062	chr11	57761797:57762046:57794010:57794081:57795577:57795729	57794010:57794081
exon_skip_265333	chr11	57815394:57815500:57815915:57816001:57816297:57816336	57815915:57816001
exon_skip_276901	chr11	57811399:57811486:57814311:57814373:57815394:57815481	57814311:57814373
exon_skip_279338	chr11	57809274:57809466:57810109:57810223:57811399:57811486	57810109:57810223
exon_skip_295492	chr11	57810145:57810223:57811399:57811486:57815394:57815481	57811399:57811486
exon_skip_30654	chr11	57810145:57810223:57811399:57811486:57814311:57814373	57811399:57811486
exon_skip_45456	chr11	57815394:57815500:57815915:57816001:57816297:57816717	57815915:57816001
exon_skip_51083	chr11	57805889:57806035:57806461:57806478:57806915:57806983	57806461:57806478
exon_skip_80641	chr11	57761797:57762046:57789037:57789155:57791385:57791673	57789037:57789155

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
exon_skip_215244	MSBB_PG	3.137121e-01	5.120370e-01	-1.983249e-01	3.520076e-05
exon_skip_51083	Mayo_TC	2.310976e-01	3.368056e-01	-1.057080e-01	2.276485e-05

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Open reading frame (ORF) annotation in the exon skipping event for CTNND1

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
ENST00000399050	57810109	57810223	Frame-shift
ENST00000399050	57811399	57811486	Frame-shift
ENST00000399050	57806461	57806478	In-frame
ENST00000399050	57814311	57814373	In-frame
ENST00000399050	57815915	57816001	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
ENST00000399050	57811399	57811486	Frame-shift
ENST00000399050	57806461	57806478	In-frame
ENST00000399050	57814311	57814373	In-frame
ENST00000399050	57815915	57816001	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
ENST00000399050	57811399	57811486	Frame-shift
ENST00000399050	57806461	57806478	In-frame
ENST00000399050	57814311	57814373	In-frame
ENST00000399050	57815915	57816001	In-frame

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Infer the effects of exon skipping event on protein functional features for CTNND1

p-ENSG00000198561_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
ENST00000399050	6330	968	57814311	57814373	3176	3237	880	900
ENST00000399050	6330	968	57815915	57816001	3346	3431	936	965

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
ENST00000399050	6330	968	57814311	57814373	3176	3237	880	900
ENST00000399050	6330	968	57815915	57816001	3346	3431	936	965

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
ENST00000399050	6330	968	57814311	57814373	3176	3237	880	900
ENST00000399050	6330	968	57815915	57816001	3346	3431	936	965

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
O60716	880	900	880	900	Alternative sequence	ID=VSP_006744;Note=In isoform 1BC%2C isoform 1B%2C isoform 1C%2C isoform 1%2C isoform 2BC%2C isoform 2B%2C isoform 2C%2C isoform 2%2C isoform 3BC%2C isoform 3B%2C isoform 3C%2C isoform 3%2C isoform 4BC%2C isoform 4B%2C isoform 4C and isoform 4. Missing;On
O60716	880	900	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	880	900	882	882	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
O60716	880	900	899	899	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P30999
O60716	880	900	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	880	900	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	937	965	Alternative sequence	ID=VSP_006745;Note=In isoform 1AC%2C isoform 1A%2C isoform 1C%2C isoform 1%2C isoform 2AC%2C isoform 2A%2C isoform 2C%2C isoform 2%2C isoform 3AC%2C isoform 3A%2C isoform 3C%2C isoform 3%2C isoform 4AC%2C isoform 4A%2C isoform 4C and isoform 4. Missing;On
O60716	936	965	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	936	965	943	943	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
O60716	936	965	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459

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
O60716	880	900	880	900	Alternative sequence	ID=VSP_006744;Note=In isoform 1BC%2C isoform 1B%2C isoform 1C%2C isoform 1%2C isoform 2BC%2C isoform 2B%2C isoform 2C%2C isoform 2%2C isoform 3BC%2C isoform 3B%2C isoform 3C%2C isoform 3%2C isoform 4BC%2C isoform 4B%2C isoform 4C and isoform 4. Missing;On
O60716	880	900	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	880	900	882	882	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
O60716	880	900	899	899	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P30999
O60716	880	900	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	880	900	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	937	965	Alternative sequence	ID=VSP_006745;Note=In isoform 1AC%2C isoform 1A%2C isoform 1C%2C isoform 1%2C isoform 2AC%2C isoform 2A%2C isoform 2C%2C isoform 2%2C isoform 3AC%2C isoform 3A%2C isoform 3C%2C isoform 3%2C isoform 4AC%2C isoform 4A%2C isoform 4C and isoform 4. Missing;On
O60716	936	965	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	936	965	943	943	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
O60716	936	965	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459

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
O60716	880	900	880	900	Alternative sequence	ID=VSP_006744;Note=In isoform 1BC%2C isoform 1B%2C isoform 1C%2C isoform 1%2C isoform 2BC%2C isoform 2B%2C isoform 2C%2C isoform 2%2C isoform 3BC%2C isoform 3B%2C isoform 3C%2C isoform 3%2C isoform 4BC%2C isoform 4B%2C isoform 4C and isoform 4. Missing;On
O60716	880	900	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	880	900	882	882	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
O60716	880	900	899	899	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P30999
O60716	880	900	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	880	900	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	937	965	Alternative sequence	ID=VSP_006745;Note=In isoform 1AC%2C isoform 1A%2C isoform 1C%2C isoform 1%2C isoform 2AC%2C isoform 2A%2C isoform 2C%2C isoform 2%2C isoform 3AC%2C isoform 3A%2C isoform 3C%2C isoform 3%2C isoform 4AC%2C isoform 4A%2C isoform 4C and isoform 4. Missing;On
O60716	936	965	1	968	Chain	ID=PRO_0000064296;Note=Catenin delta-1
O60716	936	965	943	943	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
O60716	936	965	365	968	Natural variant	ID=VAR_079395;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459
O60716	936	965	700	968	Natural variant	ID=VAR_079396;Note=In BCDS2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28301459;Dbxref=PMID:28301459

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3'-UTR located exon skipping events that lost miRNA binding sites in CTNND1

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 CTNND1

- 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 CTNND1

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 CTNND1

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 CTNND1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TRA2A	exon_skip_276901	-4.881996e-01	1.014032e-10
FL	SRSF9	exon_skip_215244	5.557632e-01	8.567896e-17
HCC	RBM5	exon_skip_215244	-4.201323e-01	4.667763e-13
HCC	RBM3	exon_skip_276901	4.568518e-01	1.973676e-15
PCC	PTBP1	exon_skip_80641	-4.192500e-01	3.225914e-10
STG	RALYL	exon_skip_80641	4.081633e-01	1.161563e-04

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RelatedDrugs for CTNND1

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 CTNND1

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 CTNND1

Gene structures and expression levels for CTNND1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CTNND1

Open reading frame (ORF) annotation in the exon skipping event for CTNND1

Infer the effects of exon skipping event on protein functional features for CTNND1

3'-UTR located exon skipping events that lost miRNA binding sites in CTNND1

SNVs in the skipped exons for CTNND1

AD stage-associated exon skippint events for CTNND1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CTNND1

Correlation with RNA binding proteins (RBPs) for CTNND1

RelatedDrugs for CTNND1

RelatedDiseases for CTNND1