ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CSMD1

Gene summary

Gene information	Gene symbol	CSMD1
	Gene ID	64478
	Gene name	CUB and Sushi multiple domains 1
	Synonyms	PPP1R24
	Cytomap	8p23.2
	Type of gene	protein-coding
	Description	CUB and sushi domain-containing protein 1protein phosphatase 1, regulatory subunit 24
	Modification date	20200313
	UniProtAcc	E5RIG2, F5GZ18, F8W9C3, H7BXU2, Q96PZ7,
	Context	- 25845235([Replicative association analysis of genetic markers of cognitive traits with Alzheimer's disease in a Russian population])

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

Gene

GO ID

GO term

PubMed ID

Top

Gene structures and expression levels for CSMD1

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.

ENSG00000183117

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

Landscape of isoform expressions across multiple brain tissues between AD and control.

Top

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CSMD1

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_227445	chr8	3118399:3118587:3142465:3142674:3151397:3151513	3142465:3142674
exon_skip_264041	chr8	2951114:2951275:2954224:2954268:2955589:2955768	2954224:2954268
exon_skip_286315	chr8	3188887:3189011:3189912:3190115:3199714:3199809	3189912:3190115
exon_skip_293601	chr8	3708414:3708491:3753930:3754042:3997903:3998110	3753930:3754042
exon_skip_46393	chr8	2998011:2998184:2999958:3000131:3018477:3018650	2999958:3000131
exon_skip_84906	chr8	3214497:3214691:3219255:3219442:3223729:3223867	3219255:3219442
exon_skip_98657	chr8	2999958:3000131:3018477:3018650:3029319:3029513	3018477:3018650

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

Top

Open reading frame (ORF) annotation in the exon skipping event for CSMD1

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
ENST00000635120	3219255	3219442	Frame-shift
ENST00000635120	3753930	3754042	Frame-shift
ENST00000635120	2954224	2954268	In-frame
ENST00000635120	2999958	3000131	In-frame
ENST00000635120	3018477	3018650	In-frame
ENST00000635120	3142465	3142674	In-frame
ENST00000635120	3189912	3190115	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
ENST00000635120	3753930	3754042	Frame-shift
ENST00000635120	2954224	2954268	In-frame
ENST00000635120	3142465	3142674	In-frame
ENST00000635120	3189912	3190115	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
ENST00000635120	2954224	2954268	In-frame
ENST00000635120	3189912	3190115	In-frame

Top

Infer the effects of exon skipping event on protein functional features for CSMD1

p-ENSG00000183117_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
ENST00000635120	11754	3564	3189912	3190115	5751	5953	1731	1799
ENST00000635120	11754	3564	3142465	3142674	6588	6796	2010	2080
ENST00000635120	11754	3564	3018477	3018650	8412	8584	2618	2676
ENST00000635120	11754	3564	2999958	3000131	8586	8758	2676	2734
ENST00000635120	11754	3564	2954224	2954268	10551	10594	3331	3346

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
ENST00000635120	11754	3564	3189912	3190115	5751	5953	1731	1799
ENST00000635120	11754	3564	3142465	3142674	6588	6796	2010	2080
ENST00000635120	11754	3564	2954224	2954268	10551	10594	3331	3346

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
ENST00000635120	11754	3564	3189912	3190115	5751	5953	1731	1799
ENST00000635120	11754	3564	2954224	2954268	10551	10594	3331	3346

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
Q96PZ7	1731	1799	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	1731	1799	1741	1781	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1767	1798	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1625	1733	Domain	Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00059
Q96PZ7	1731	1799	1739	1800	Domain	Note=Sushi 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1792	1792	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	1731	1799	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2010	2080	2012	2012	Alternative sequence	ID=VSP_009032;Note=In isoform 4. A->K;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2010	2080	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2010	2080	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	2010	2080	1974	2082	Domain	Note=CUB 12;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00059
Q96PZ7	2010	2080	2018	2018	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2010	2080	2040	2040	Natural variant	ID=VAR_059634;Note=M->I;Dbxref=dbSNP:rs6995799
Q96PZ7	2010	2080	2061	2061	Sequence conflict	Note=L->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q96PZ7	2010	2080	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2618	2676	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2618	2676	2110	3564	Alternative sequence	ID=VSP_009031;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q96PZ7	2618	2676	2619	2676	Alternative sequence	ID=VSP_009034;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472063;Dbxref=PMID:11472063
Q96PZ7	2618	2676	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	2618	2676	2622	2662	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2618	2676	2648	2675	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2618	2676	2555	2619	Domain	Note=Sushi 16;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2618	2676	2620	2677	Domain	Note=Sushi 17;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2618	2676	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2676	2734	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2676	2734	2110	3564	Alternative sequence	ID=VSP_009031;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q96PZ7	2676	2734	2619	2676	Alternative sequence	ID=VSP_009034;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472063;Dbxref=PMID:11472063
Q96PZ7	2676	2734	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	2676	2734	2680	2720	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2676	2734	2706	2733	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2676	2734	2620	2677	Domain	Note=Sushi 17;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2676	2734	2678	2735	Domain	Note=Sushi 18;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	2676	2734	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	3331	3346	2110	3564	Alternative sequence	ID=VSP_009031;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q96PZ7	3331	3346	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	3331	3346	3273	3332	Domain	Note=Sushi 28;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	3331	3346	3339	3339	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	27	3487	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
Q96PZ7	1731	1799	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	1731	1799	1741	1781	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1767	1798	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1625	1733	Domain	Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00059
Q96PZ7	1731	1799	1739	1800	Domain	Note=Sushi 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1792	1792	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	1731	1799	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2010	2080	2012	2012	Alternative sequence	ID=VSP_009032;Note=In isoform 4. A->K;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2010	2080	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	2010	2080	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	2010	2080	1974	2082	Domain	Note=CUB 12;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00059
Q96PZ7	2010	2080	2018	2018	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	2010	2080	2040	2040	Natural variant	ID=VAR_059634;Note=M->I;Dbxref=dbSNP:rs6995799
Q96PZ7	2010	2080	2061	2061	Sequence conflict	Note=L->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q96PZ7	2010	2080	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	3331	3346	2110	3564	Alternative sequence	ID=VSP_009031;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q96PZ7	3331	3346	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	3331	3346	3273	3332	Domain	Note=Sushi 28;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	3331	3346	3339	3339	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	27	3487	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
Q96PZ7	1731	1799	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	1731	1799	1741	1781	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1767	1798	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1625	1733	Domain	Note=CUB 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00059
Q96PZ7	1731	1799	1739	1800	Domain	Note=Sushi 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	1731	1799	1792	1792	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	1731	1799	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	2013	3564	Alternative sequence	ID=VSP_009033;Note=In isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11572484,ECO:0000303\|PubMed:12975309;Dbxref=PMID:11572484,PMID:12975309
Q96PZ7	3331	3346	2110	3564	Alternative sequence	ID=VSP_009031;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q96PZ7	3331	3346	27	3564	Chain	ID=PRO_0000021025;Note=CUB and sushi domain-containing protein 1
Q96PZ7	3331	3346	3273	3332	Domain	Note=Sushi 28;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00302
Q96PZ7	3331	3346	3339	3339	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96PZ7	3331	3346	27	3487	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

Top

3'-UTR located exon skipping events that lost miRNA binding sites in CSMD1

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

Top

SNVs in the skipped exons for CSMD1

- 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

Top

AD stage-associated exon skippint events for CSMD1

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

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CSMD1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

Top

Correlation with RNA binding proteins (RBPs) for CSMD1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	TARDBP	exon_skip_264041	-4.951733e-01	1.628711e-02
IFG	CNOT4	exon_skip_264041	-4.321455e-01	3.946540e-02
IFG	RBM5	exon_skip_264041	-4.714050e-01	2.316468e-02
IFG	RBM46	exon_skip_264041	-4.279162e-01	4.165588e-02

Top

RelatedDrugs for CSMD1

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

RelatedDiseases for CSMD1

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

Home

Download

Statistics

Landscape

Help

Contact

Gene summary for CSMD1

Gene structures and expression levels for CSMD1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CSMD1

Open reading frame (ORF) annotation in the exon skipping event for CSMD1

Infer the effects of exon skipping event on protein functional features for CSMD1

3'-UTR located exon skipping events that lost miRNA binding sites in CSMD1

SNVs in the skipped exons for CSMD1

AD stage-associated exon skippint events for CSMD1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CSMD1

Correlation with RNA binding proteins (RBPs) for CSMD1

RelatedDrugs for CSMD1

RelatedDiseases for CSMD1