ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CDHR2

Gene summary

Gene information	Gene symbol	CDHR2
	Gene ID	54825
	Gene name	cadherin related family member 2
	Synonyms	PCDH24\|PCLKC
	Cytomap	5q35.2
	Type of gene	protein-coding
	Description	cadherin-related family member 2protocadherin-24
	Modification date	20180519
	UniProtAcc	Q9BYE9
	Context	PubMed: CDHR2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
CDHR2	GO:0030855	epithelial cell differentiation	12117771
CDHR2	GO:0044331	cell-cell adhesion mediated by cadherin	12117771
CDHR2	GO:0060243	negative regulation of cell growth involved in contact inhibition	12117771

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Exon skipping events across known transcript of Ensembl for CDHR2 from UCSC genome browser

Skipped exons in TCGA and GTEx 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.

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Gene isoform structures and expression levels for CDHR2

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for CDHR2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_439872	5	175992338:175992405:175992672:175992744:175995678:175995768	175992672:175992744	ENSG00000074276.6	ENST00000261944.5,ENST00000510636.1,ENST00000506348.1
exon_skip_439874	5	175992672:175992744:175993946:175994115:175995678:175995768	175993946:175994115	ENSG00000074276.6	ENST00000510124.1
exon_skip_439875	5	176004637:176004799:176005034:176005096:176005365:176005609	176005034:176005096	ENSG00000074276.6	ENST00000261944.5,ENST00000510636.1,ENST00000506348.1
exon_skip_439876	5	176005365:176005609:176008343:176008583:176011190:176011260	176008343:176008583	ENSG00000074276.6	ENST00000261944.5,ENST00000510636.1,ENST00000506348.1
exon_skip_439879	5	176012954:176013026:176013793:176013843:176016031:176016183	176013793:176013843	ENSG00000074276.6	ENST00000261944.5,ENST00000510636.1,ENST00000506348.1
exon_skip_439880	5	176017425:176017486:176017563:176017688:176018210:176018324	176017563:176017688	ENSG00000074276.6	ENST00000261944.5,ENST00000510636.1,ENST00000506348.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CDHR2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_439872	5	175992338:175992405:175992672:175992744:175995678:175995768	175992672:175992744	ENSG00000074276.6	ENST00000510636.1,ENST00000261944.5,ENST00000506348.1
exon_skip_439874	5	175992672:175992744:175993946:175994115:175995678:175995768	175993946:175994115	ENSG00000074276.6	ENST00000510124.1
exon_skip_439875	5	176004637:176004799:176005034:176005096:176005365:176005609	176005034:176005096	ENSG00000074276.6	ENST00000510636.1,ENST00000261944.5,ENST00000506348.1
exon_skip_439876	5	176005365:176005609:176008343:176008583:176011190:176011260	176008343:176008583	ENSG00000074276.6	ENST00000510636.1,ENST00000261944.5,ENST00000506348.1
exon_skip_439879	5	176012954:176013026:176013793:176013843:176016031:176016183	176013793:176013843	ENSG00000074276.6	ENST00000510636.1,ENST00000261944.5,ENST00000506348.1
exon_skip_439880	5	176017425:176017486:176017563:176017688:176018210:176018324	176017563:176017688	ENSG00000074276.6	ENST00000510636.1,ENST00000261944.5,ENST00000506348.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for CDHR2

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000261944	176005034	176005096	Frame-shift
ENST00000506348	176005034	176005096	Frame-shift
ENST00000510636	176005034	176005096	Frame-shift
ENST00000261944	176013793	176013843	Frame-shift
ENST00000506348	176013793	176013843	Frame-shift
ENST00000510636	176013793	176013843	Frame-shift
ENST00000261944	176017563	176017688	Frame-shift
ENST00000506348	176017563	176017688	Frame-shift
ENST00000510636	176017563	176017688	Frame-shift
ENST00000261944	175992672	175992744	In-frame
ENST00000506348	175992672	175992744	In-frame
ENST00000510636	175992672	175992744	In-frame
ENST00000261944	176008343	176008583	In-frame
ENST00000506348	176008343	176008583	In-frame
ENST00000510636	176008343	176008583	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000261944	176005034	176005096	Frame-shift
ENST00000506348	176005034	176005096	Frame-shift
ENST00000510636	176005034	176005096	Frame-shift
ENST00000261944	176013793	176013843	Frame-shift
ENST00000506348	176013793	176013843	Frame-shift
ENST00000510636	176013793	176013843	Frame-shift
ENST00000261944	176017563	176017688	Frame-shift
ENST00000506348	176017563	176017688	Frame-shift
ENST00000510636	176017563	176017688	Frame-shift
ENST00000261944	175992672	175992744	In-frame
ENST00000506348	175992672	175992744	In-frame
ENST00000510636	175992672	175992744	In-frame
ENST00000261944	176008343	176008583	In-frame
ENST00000506348	176008343	176008583	In-frame
ENST00000510636	176008343	176008583	In-frame

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Infer the effects of exon skipping event on protein functional features for CDHR2

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000261944	4085	1310	175992672	175992744	92	163	17	41
ENST00000506348	4022	1310	175992672	175992744	100	171	17	41
ENST00000510636	4526	1310	175992672	175992744	327	398	17	41
ENST00000261944	4085	1310	176008343	176008583	1858	2097	606	686
ENST00000506348	4022	1310	176008343	176008583	1866	2105	606	686
ENST00000510636	4526	1310	176008343	176008583	2093	2332	606	686

Loci of skipped exons in GTEx 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
ENST00000261944	4085	1310	175992672	175992744	92	163	17	41
ENST00000506348	4022	1310	175992672	175992744	100	171	17	41
ENST00000510636	4526	1310	175992672	175992744	327	398	17	41
ENST00000261944	4085	1310	176008343	176008583	1858	2097	606	686
ENST00000506348	4022	1310	176008343	176008583	1866	2105	606	686
ENST00000510636	4526	1310	176008343	176008583	2093	2332	606	686

Lost protein functional features of individual exon skipping events in TCGA.

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
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

Lost protein functional features of individual exon skipping events in GTEx.

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
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	32	36	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	27	124	Domain	Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	29	29	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	28	31	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5CZR
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	1	20	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	17	41	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	21	1310	Chain	ID=PRO_0000004011;Note=Cadherin-related family member 2
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	586	695	Domain	Note=Cadherin 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00043
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	616	616	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	632	632	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	680	680	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BYE9	606	686	21	1154	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for CDHR2

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-G3-A3CJ-01	exon_skip_439875	176005035	176005096	176005060	176005060	Frame_Shift_Del	G	-	p.W513fs
LIHC	TCGA-DD-A1EG-01	exon_skip_439879	176013794	176013843	176013817	176013817	Frame_Shift_Del	C	-	p.P944fs
STAD	TCGA-BR-4370-01	exon_skip_439880	176017564	176017688	176017671	176017672	Frame_Shift_Ins	-	GT	p.F1174fs
STAD	TCGA-BR-4370-01	exon_skip_439880	176017564	176017688	176017672	176017673	Frame_Shift_Ins	-	GT	p.F1174fs
STAD	TCGA-BR-4280-01	exon_skip_439880	176017564	176017688	176017621	176017621	Nonsense_Mutation	G	T	p.G1158*
PAAD	TCGA-IB-7651-01	exon_skip_439875	176005035	176005096	176005098	176005098	Splice_Site	T	C	.

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
NCIH1339_LUNG	176005035	176005096	176005089	176005089	Frame_Shift_Del	G	-	p.G523fs
CAMA1_BREAST	175992673	175992744	175992679	175992679	Missense_Mutation	C	G	p.A20G
KP2_PANCREAS	175992673	175992744	175992684	175992684	Missense_Mutation	G	A	p.V22M
SNU245_BILIARY_TRACT	175992673	175992744	175992724	175992724	Missense_Mutation	T	A	p.L35Q
RKO_LARGE_INTESTINE	176005035	176005096	176005056	176005056	Missense_Mutation	G	A	p.A512T
JHH5_LIVER	176008344	176008583	176008349	176008349	Missense_Mutation	C	G	p.H608Q
SNU1040_LARGE_INTESTINE	176008344	176008583	176008350	176008350	Missense_Mutation	G	A	p.D609N
HSC4_UPPER_AERODIGESTIVE_TRACT	176008344	176008583	176008494	176008494	Missense_Mutation	C	A	p.L657M
TTC466_BONE	176008344	176008583	176008533	176008533	Missense_Mutation	T	A	p.C670S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CDHR2

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDHR2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDHR2

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RelatedDrugs for CDHR2

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for CDHR2

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 TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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