ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CERCAM

Gene summary

Gene information	Gene symbol	CERCAM
	Gene ID	51148
	Gene name	cerebral endothelial cell adhesion molecule
	Synonyms	CEECAM1\|GLT25D3
	Cytomap	9q34.11
	Type of gene	protein-coding
	Description	inactive glycosyltransferase 25 family member 3cerebral cell adhesion moleculecerebral endothelial cell adhesion molecule 1glycosyltransferase 25 domain containing 3glycosyltransferase 25 family member 3probable inactive glycosyltransferase 25 family
	Modification date	20200313
	UniProtAcc	A0A087WUJ5, A0A087WYE2, B7ZBS8, B7ZBS9, B7ZBT0, Q5T4B2, X6RL83,
	Context

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

Gene	GO ID	GO term	PubMed ID
CERCAM	GO:0007155	cell adhesion	10608765

Top

Gene structures and expression levels for CERCAM

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.

ENSG00000167123

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
CB	DOWN	2.660845e+03	-8.704841e-01	1.313307e-09	4.029140e-08
TC	DOWN	1.550811e+04	-9.884082e-01	6.127041e-11	5.820853e-09

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	ENST00000372838.9	CERCAM-201:protein_coding:CERCAM	8.349376e+02	-1.348777e+00	2.368845e-15	1.139733e-12
CB	DOWN	ENST00000483893.5	CERCAM-210:lncRNA:CERCAM	7.275958e+00	-9.020885e-01	5.114465e-06	5.975108e-05
CB	DOWN	ENST00000493788.5	CERCAM-212:lncRNA:CERCAM	1.742404e+01	-1.136064e+00	9.551517e-04	4.970674e-03
TC	DOWN	ENST00000372838.9	CERCAM-201:protein_coding:CERCAM	3.535648e+03	-1.622119e+00	2.714237e-18	5.045399e-15
TC	DOWN	ENST00000483893.5	CERCAM-210:lncRNA:CERCAM	3.702228e+01	-9.134164e-01	4.411757e-09	4.549203e-07
TC	DOWN	ENST00000493788.5	CERCAM-212:lncRNA:CERCAM	1.249158e+02	-9.943475e-01	1.096191e-06	4.323657e-05
TC	DOWN	ENST00000487001.6	CERCAM-211:lncRNA:CERCAM	3.442350e+01	-8.885214e-01	2.946293e-04	3.790500e-03

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

Top

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

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_111994	chr9	128424206:128424272:128424410:128424614:128428302:128428421	128424410:128424614
exon_skip_136855	chr9	128424602:128424614:128427652:128427779:128428302:128428421	128427652:128427779
exon_skip_137837	chr9	128411766:128412072:128419160:128419278:128420187:128422978	128419160:128419278
exon_skip_15778	chr9	128423157:128423263:128424138:128424272:128424410:128424614	128424138:128424272
exon_skip_163107	chr9	128420857:128421074:128421204:128421511:128422868:128422978	128421204:128421511
exon_skip_182766	chr9	128411766:128412072:128419160:128419278:128420187:128422190	128419160:128419278
exon_skip_201595	chr9	128420873:128421074:128421204:128421511:128422868:128422978	128421204:128421511
exon_skip_218728	chr9	128411766:128412072:128419160:128419278:128420187:128420225	128419160:128419278
exon_skip_220431	chr9	128424602:128424614:128427652:128427779:128428302:128428338	128427652:128427779
exon_skip_236314	chr9	128422905:128422978:128423146:128423263:128424138:128424182	128423146:128423263
exon_skip_252705	chr9	128428388:128428421:128428757:128428833:128428930:128429031	128428757:128428833
exon_skip_259925	chr9	128419160:128419278:128422868:128422978:128423146:128423263	128422868:128422978
exon_skip_280120	chr9	128419160:128419278:128420187:128422978:128423146:128423263	128420187:128422978
exon_skip_289311	chr9	128411766:128412072:128419160:128419278:128420187:128422786	128419160:128419278
exon_skip_29820	chr9	128424410:128424614:128427652:128427779:128428302:128428421	128427652:128427779
exon_skip_3480	chr9	128411766:128412072:128419160:128419278:128420187:128422354	128419160:128419278
exon_skip_37921	chr9	128423146:128423263:128424138:128424272:128424410:128424614	128424138:128424272
exon_skip_39630	chr9	128434102:128434229:128434410:128434613:128435653:128435755	128434410:128434613

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_163107	Mayo_TC	4.165432e-01	5.488312e-01	-1.322880e-01	9.343209e-05
exon_skip_21931	Mayo_TC	4.064198e-01	5.196053e-01	-1.131855e-01	2.001080e-04
exon_skip_228642	Mayo_TC	5.103704e-01	6.633766e-01	-1.530063e-01	9.023423e-07

Top

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

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
ENST00000372838	128423146	128423263	Frame-shift
ENST00000372838	128424410	128424614	Frame-shift
ENST00000372838	128428757	128428833	Frame-shift
ENST00000372838	128424138	128424272	In-frame
ENST00000372838	128434410	128434613	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
ENST00000372838	128428757	128428833	Frame-shift
ENST00000372838	128424138	128424272	In-frame
ENST00000372838	128434410	128434613	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
ENST00000372838	128423146	128423263	Frame-shift
ENST00000372838	128424410	128424614	Frame-shift
ENST00000372838	128428757	128428833	Frame-shift
ENST00000372838	128424138	128424272	In-frame
ENST00000372838	128434410	128434613	In-frame

Top

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

p-ENSG00000167123_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
ENST00000372838	2702	595	128424138	128424272	826	959	142	187
ENST00000372838	2702	595	128434410	128434613	1731	1933	444	511

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
ENST00000372838	2702	595	128424138	128424272	826	959	142	187
ENST00000372838	2702	595	128434410	128434613	1731	1933	444	511

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
ENST00000372838	2702	595	128424138	128424272	826	959	142	187
ENST00000372838	2702	595	128434410	128434613	1731	1933	444	511

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
Q5T4B2	142	187	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	142	187	153	153	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q5T4B2	444	511	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	444	511	450	450	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B M-451%3B Q-452 and V-453 in a chimeric construct with COLGALT1. Q->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	451	451	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B Q-452 and V-453 in a chimeric construct with COLGALT1. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	452	452	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and V-453 in a chimeric construct with COLGALT1. N->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	453	453	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and Q-452 in a chimeric construct with COLGALT1. P->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269

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
Q5T4B2	142	187	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	142	187	153	153	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q5T4B2	444	511	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	444	511	450	450	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B M-451%3B Q-452 and V-453 in a chimeric construct with COLGALT1. Q->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	451	451	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B Q-452 and V-453 in a chimeric construct with COLGALT1. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	452	452	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and V-453 in a chimeric construct with COLGALT1. N->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	453	453	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and Q-452 in a chimeric construct with COLGALT1. P->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269

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
Q5T4B2	142	187	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	142	187	153	153	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q5T4B2	444	511	23	595	Chain	ID=PRO_0000309544;Note=Inactive glycosyltransferase 25 family member 3
Q5T4B2	444	511	450	450	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B M-451%3B Q-452 and V-453 in a chimeric construct with COLGALT1. Q->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	451	451	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B Q-452 and V-453 in a chimeric construct with COLGALT1. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	452	452	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and V-453 in a chimeric construct with COLGALT1. N->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269
Q5T4B2	444	511	453	453	Mutagenesis	Note=Exhibits some galactosyltransferase activity%3B when associated with D-440%3B R-450%3B M-451 and Q-452 in a chimeric construct with COLGALT1. P->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22216269;Dbxref=PMID:22216269

Top

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

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 CERCAM

- 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 CERCAM

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 CERCAM

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
CB	exon_skip_39630	rs2072400	chr9:128423682	4.547578e-11	4.969593e-08
CB	exon_skip_39630	rs2270202	chr9:128429124	4.547578e-11	4.969593e-08
CB	exon_skip_39630	rs4837264	chr9:128439616	2.896246e-07	1.246703e-04
CB	exon_skip_39630	rs10988015	chr9:128525677	1.742019e-05	4.172172e-03
CB	exon_skip_39630	rs869455	chr9:128527321	1.742019e-05	4.172172e-03
CB	exon_skip_39630	rs7849186	chr9:128450093	4.843383e-05	9.595535e-03

Top

Correlation with RNA binding proteins (RBPs) for CERCAM

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
TC	SAMD4A	exon_skip_204076	-4.823257e-01	5.428145e-09
TC	RBM3	exon_skip_204076	5.264777e-01	1.055982e-10
TC	FUS	exon_skip_204076	4.188357e-01	6.401180e-07
TC	RBM4	exon_skip_204076	-4.844356e-01	4.553065e-09
TC	RBM4B	exon_skip_204076	-4.114959e-01	1.046242e-06
TC	RBMS2	exon_skip_269449	-4.145241e-01	1.337729e-07
TC	SAMD4A	exon_skip_269449	-4.608509e-01	2.948896e-09
TC	RBM3	exon_skip_269449	4.686901e-01	1.458894e-09
TC	RBM4	exon_skip_269449	-4.712019e-01	1.159980e-09
TC	SAMD4A	exon_skip_163107	-4.175438e-01	4.810504e-08
TC	RBM3	exon_skip_163107	4.702669e-01	4.534156e-10
TC	PCBP4	exon_skip_163107	5.515631e-01	5.884812e-14
TC	SAMD4A	exon_skip_21931	-4.150805e-01	6.471700e-08
TC	PCBP4	exon_skip_21931	5.023212e-01	2.041358e-11
TC	RBMS2	exon_skip_228642	-4.623238e-01	9.642016e-10
TC	MSI1	exon_skip_228642	-4.742522e-01	3.082495e-10
TC	SAMD4A	exon_skip_228642	-4.318450e-01	1.466863e-08
TC	PCBP4	exon_skip_228642	4.804675e-01	1.671854e-10

Top

RelatedDrugs for CERCAM

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 CERCAM

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