ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CADM1

Gene summary

Gene information	Gene symbol	CADM1
	Gene ID	23705
	Gene name	cell adhesion molecule 1
	Synonyms	BL2\|IGSF4\|IGSF4A\|NECL2\|Necl-2\|RA175\|ST17\|SYNCAM\|TSLC1\|sTSLC-1\|sgIGSF\|synCAM1
	Cytomap	11q23.3
	Type of gene	protein-coding
	Description	cell adhesion molecule 1TSLC-1TSLC1/Nectin-like 2/IGSF4immunoglobulin superfamily member 4immunoglobulin superfamily, member 4D variant 1immunoglobulin superfamily, member 4D variant 2nectin-like 2nectin-like protein 2spermatogenic immunoglobulin
	Modification date	20200313
	UniProtAcc	A0A087X0T8, A0A087X1W8, A0A0A0MTJ8, A0A4Z1, F5H0H5, F5H125, F5H372, F5H8J9, H0YG94, H1ZZW3, H1ZZW4, H1ZZW5, H1ZZW6, Q9BY67, X5D7A8, X5D8W0, X5DNF2, X5DQR8, X5DQS5,
	Context	- 25364765(Cardio-miRNAs and onco-miRNAs: circulating miRNA-based diagnostics for non-cancerous and cancerous diseases)

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

Gene	GO ID	GO term	PubMed ID
CADM1	GO:0001913	T cell mediated cytotoxicity	15811952
CADM1	GO:0008037	cell recognition	15811952
CADM1	GO:0042271	susceptibility to natural killer cell mediated cytotoxicity	15811952
CADM1	GO:0045954	positive regulation of natural killer cell mediated cytotoxicity	15811952
CADM1	GO:0050715	positive regulation of cytokine secretion	15811952
CADM1	GO:0050798	activated T cell proliferation	15811952
CADM1	GO:0051606	detection of stimulus	15811952

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Gene structures and expression levels for CADM1

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.

ENSG00000182985

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
DLPFC	DOWN	ENST00000537140.5	CADM1-207:lncRNA:CADM1	3.000537e+00	-9.862195e-01	1.318208e-03	4.044659e-02
CB	UP	ENST00000541434.5	CADM1-211:retained_intron:CADM1	2.527084e+01	9.326795e-01	4.922125e-08	1.162939e-06
CB	UP	ENST00000543375.5	CADM1-215:lncRNA:CADM1	6.834755e+00	8.295393e-01	5.177111e-07	8.566147e-06
CB	DOWN	ENST00000545960.5	CADM1-219:lncRNA:CADM1	9.927841e+00	-1.539485e+00	5.264165e-06	6.120301e-05
CB	UP	ENST00000542450.5	CADM1-213:protein_coding:CADM1	6.380138e+00	1.065987e+00	6.325383e-06	7.151983e-05
CB	UP	ENST00000537058.5	CADM1-206:protein_coding:CADM1	2.065896e+02	1.273744e+00	3.042094e-04	1.894797e-03

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 CADM1

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_112450	chr11	115178644:115178775:115198406:115198438:115209574:115209591	115198406:115198438
exon_skip_117118	chr11	115178644:115178775:115198406:115198438:115209574:115209623	115198406:115198438
exon_skip_123601	chr11	115178644:115178775:115198406:115198438:115209574:115209657	115198406:115198438
exon_skip_18054	chr11	115178644:115178775:115190888:115190941:115198406:115198438	115190888:115190941
exon_skip_188136	chr11	115240274:115240420:115445761:115445836:115504271:115504415	115445761:115445836
exon_skip_218844	chr11	115198406:115198438:115209574:115209657:115214608:115214694	115209574:115209657
exon_skip_222678	chr11	115198406:115198438:115207302:115207307:115209574:115209591	115207302:115207307
exon_skip_230508	chr11	115240274:115240420:115445761:115445836:115504271:115504389	115445761:115445836
exon_skip_231204	chr11	115198406:115198438:115207302:115207307:115209574:115209657	115207302:115207307
exon_skip_27780	chr11	115178644:115178775:115209574:115209657:115214608:115214694	115209574:115209657
exon_skip_51125	chr11	115176467:115176592:115178644:115178775:115209574:115209657	115178644:115178775

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_218844	MSBB_STG	6.552632e-01	5.363636e-01	1.188995e-01	7.109780e-03
exon_skip_18054	Mayo_CB	3.345122e-01	4.650000e-01	-1.304878e-01	4.354946e-07

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Open reading frame (ORF) annotation in the exon skipping event for CADM1

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
ENST00000452722	115178644	115178775	In-frame
ENST00000452722	115209574	115209657	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
ENST00000452722	115209574	115209657	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
ENST00000452722	115178644	115178775	In-frame
ENST00000452722	115209574	115209657	In-frame

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Infer the effects of exon skipping event on protein functional features for CADM1

p-ENSG00000182985_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
ENST00000452722	8605	442	115209574	115209657	1016	1098	331	359
ENST00000452722	8605	442	115178644	115178775	1100	1230	359	403

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
ENST00000452722	8605	442	115209574	115209657	1016	1098	331	359

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
ENST00000452722	8605	442	115209574	115209657	1016	1098	331	359
ENST00000452722	8605	442	115178644	115178775	1100	1230	359	403

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
Q9BY67	331	359	332	333	Alternative sequence	ID=VSP_052461;Note=In isoform 2. DP->GT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	333	360	Alternative sequence	ID=VSP_047405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:24722188;Dbxref=PMID:15489334,PMID:24722188
Q9BY67	331	359	334	442	Alternative sequence	ID=VSP_052462;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047406;Note=In isoform 3. T->TDTTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047407;Note=In isoform 4. T->TDTTATTEPAVH;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	45	442	Chain	ID=PRO_0000291968;Note=Cell adhesion molecule 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	331	359	333	359	Sequence conflict	Note=PPTTIPPPTTTTTTTTTTTTTILTIIT->TTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9BY67	331	359	45	374	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	333	360	Alternative sequence	ID=VSP_047405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:24722188;Dbxref=PMID:15489334,PMID:24722188
Q9BY67	359	403	334	442	Alternative sequence	ID=VSP_052462;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	359	403	359	359	Alternative sequence	ID=VSP_047406;Note=In isoform 3. T->TDTTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	359	403	359	359	Alternative sequence	ID=VSP_047407;Note=In isoform 4. T->TDTTATTEPAVH;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	359	403	45	442	Chain	ID=PRO_0000291968;Note=Cell adhesion molecule 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	333	359	Sequence conflict	Note=PPTTIPPPTTTTTTTTTTTTTILTIIT->TTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9BY67	359	403	45	374	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	396	442	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	375	395	Transmembrane	Note=Helical;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
Q9BY67	331	359	332	333	Alternative sequence	ID=VSP_052461;Note=In isoform 2. DP->GT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	333	360	Alternative sequence	ID=VSP_047405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:24722188;Dbxref=PMID:15489334,PMID:24722188
Q9BY67	331	359	334	442	Alternative sequence	ID=VSP_052462;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047406;Note=In isoform 3. T->TDTTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047407;Note=In isoform 4. T->TDTTATTEPAVH;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	45	442	Chain	ID=PRO_0000291968;Note=Cell adhesion molecule 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	331	359	333	359	Sequence conflict	Note=PPTTIPPPTTTTTTTTTTTTTILTIIT->TTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9BY67	331	359	45	374	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
Q9BY67	331	359	332	333	Alternative sequence	ID=VSP_052461;Note=In isoform 2. DP->GT;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	333	360	Alternative sequence	ID=VSP_047405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:24722188;Dbxref=PMID:15489334,PMID:24722188
Q9BY67	331	359	334	442	Alternative sequence	ID=VSP_052462;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047406;Note=In isoform 3. T->TDTTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	359	359	Alternative sequence	ID=VSP_047407;Note=In isoform 4. T->TDTTATTEPAVH;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	331	359	45	442	Chain	ID=PRO_0000291968;Note=Cell adhesion molecule 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	331	359	333	359	Sequence conflict	Note=PPTTIPPPTTTTTTTTTTTTTILTIIT->TTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9BY67	331	359	45	374	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	333	360	Alternative sequence	ID=VSP_047405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:24722188;Dbxref=PMID:15489334,PMID:24722188
Q9BY67	359	403	334	442	Alternative sequence	ID=VSP_052462;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
Q9BY67	359	403	359	359	Alternative sequence	ID=VSP_047406;Note=In isoform 3. T->TDTTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	359	403	359	359	Alternative sequence	ID=VSP_047407;Note=In isoform 4. T->TDTTATTEPAVH;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:22438059;Dbxref=PMID:22438059
Q9BY67	359	403	45	442	Chain	ID=PRO_0000291968;Note=Cell adhesion molecule 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	333	359	Sequence conflict	Note=PPTTIPPPTTTTTTTTTTTTTILTIIT->TTATTEPAVHGLTQLPNSAEELDSEDLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9BY67	359	403	45	374	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	396	442	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BY67	359	403	375	395	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in CADM1

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 CADM1

- 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 CADM1

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

CDR

MSBB

IFG

exon_skip_18054

-4.472671e-01

1.701474e-02

chr11

115178644

115178775

115190888

115190941

115198406

115198438

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CADM1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
DLPFC	exon_skip_18054	rs11215464	chr11:115285516	2.791133e-04	2.025366e-02
DLPFC	exon_skip_18054	rs12295738	chr11:115276317	6.595780e-04	4.026970e-02

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Correlation with RNA binding proteins (RBPs) for CADM1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TRA2A	exon_skip_18054	-6.422543e-01	2.778404e-19
CB	HNRNPK	exon_skip_218844	-5.510918e-01	1.567658e-13
CB	PCBP2	exon_skip_218844	-5.197395e-01	5.803116e-12
CB	PTBP3	exon_skip_218844	-4.580197e-01	2.634073e-09
CB	NOVA1	exon_skip_218844	-4.401513e-01	1.247870e-08
HCC	CNOT4	exon_skip_19268	4.518226e-01	1.097890e-14
HCC	RBM45	exon_skip_19268	5.169501e-01	1.926260e-19
HCC	SRSF4	exon_skip_19268	4.713313e-01	5.255207e-16
HCC	RBM6	exon_skip_27780	5.776992e-01	5.446195e-25
HCC	CNOT4	exon_skip_27780	4.157939e-01	1.679188e-12
HCC	PCBP4	exon_skip_27780	5.585397e-01	3.860117e-23
HCC	PCBP2	exon_skip_27780	4.022909e-01	9.920378e-12
HCC	SRSF5	exon_skip_27780	4.730174e-01	3.521328e-16
IFG	TRA2A	exon_skip_18054	-4.967808e-01	7.162528e-03
IFG	CNOT4	exon_skip_19268	5.280627e-01	4.638213e-03
IFG	RBM45	exon_skip_19268	4.804958e-01	1.118594e-02
IFG	RBM6	exon_skip_218844	4.159539e-01	3.093113e-02
IFG	IGF2BP3	exon_skip_218844	4.048676e-01	3.618339e-02
PCC	RBM6	exon_skip_27780	4.041476e-01	5.586298e-09
PCC	PCBP4	exon_skip_27780	4.363840e-01	2.239420e-10
PG	HNRNPK	exon_skip_218844	-5.034956e-01	9.918735e-12
PG	HNRNPL	exon_skip_218844	-4.834158e-01	8.277855e-11
PG	RBM23	exon_skip_218844	-4.282896e-01	1.448551e-08
PG	NOVA1	exon_skip_218844	-5.175421e-01	2.066506e-12
STG	SRSF9	exon_skip_18054	4.224655e-01	1.167239e-04
STG	NOVA1	exon_skip_218844	-4.463683e-01	3.736599e-05
TC	ENOX1	exon_skip_19268	-4.441264e-01	2.461929e-08
TC	HNRNPL	exon_skip_19268	-4.033087e-01	5.384565e-07
TC	CNOT4	exon_skip_27780	-4.156833e-01	1.109936e-07
TC	ENOX1	exon_skip_27780	-4.157826e-01	1.101468e-07
TC	PTBP3	exon_skip_27780	-4.577333e-01	3.440606e-09
TC	NOVA1	exon_skip_27780	-5.012032e-01	5.577858e-11
TC	CNOT4	exon_skip_218844	-4.139860e-01	5.279200e-08
TC	PCBP1	exon_skip_218844	-4.503351e-01	2.301669e-09
TC	ENOX1	exon_skip_218844	-4.576300e-01	1.172723e-09
TC	HNRNPL	exon_skip_218844	-4.374047e-01	7.319309e-09
TC	NOVA1	exon_skip_218844	-4.299922e-01	1.390471e-08

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RelatedDrugs for CADM1

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 CADM1

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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