ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SMAD2

Gene summary

Gene information	Gene symbol	SMAD2
	Gene ID	4087
	Gene name	SMAD family member 2
	Synonyms	JV18\|JV18-1\|MADH2\|MADR2\|hMAD-2\|hSMAD2
	Cytomap	18q21.1
	Type of gene	protein-coding
	Description	mothers against decapentaplegic homolog 2MAD homolog 2SMAD, mothers against DPP homolog 2Sma- and Mad-related protein 2mother against DPP homolog 2
	Modification date	20200322
	UniProtAcc	B7Z5N5, K7EJX0, K7EL92, K7ERC7, K7ESI8, Q15796, Q53XR6,
	Context

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

Gene	GO ID	GO term	PubMed ID
SMAD2	GO:0007179	transforming growth factor beta receptor signaling pathway	8752209\|9389648\|9732876\|18548003
SMAD2	GO:0007182	common-partner SMAD protein phosphorylation	16806156
SMAD2	GO:0007183	SMAD protein complex assembly	9111321
SMAD2	GO:0045893	positive regulation of transcription, DNA-templated	9311995\|9389648\|9732876
SMAD2	GO:0045944	positive regulation of transcription by RNA polymerase II	9389648
SMAD2	GO:0070723	response to cholesterol	17878231

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Gene structures and expression levels for SMAD2

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.

ENSG00000175387

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	ENST00000587421.5	SMAD2-210:protein_coding:SMAD2	2.508341e+00	2.924587e+00	3.498775e-03	3.555475e-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 SMAD2

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_192006	chr18	47896521:47896809:47920072:47920169:47930361:47930446	47920072:47920169
exon_skip_203873	chr18	47896521:47896809:47930361:47930446:47930800:47930842	47930361:47930446
exon_skip_223535	chr18	47869422:47869436:47870475:47870564:47896521:47896809	47870475:47870564

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

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Open reading frame (ORF) annotation in the exon skipping event for SMAD2

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
ENST00000262160	47870475	47870564	In-frame
ENST00000402690	47870475	47870564	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
ENST00000262160	47870475	47870564	In-frame
ENST00000402690	47870475	47870564	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
ENST00000262160	47870475	47870564	In-frame
ENST00000402690	47870475	47870564	In-frame

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Infer the effects of exon skipping event on protein functional features for SMAD2

p-ENSG00000175387_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
ENST00000262160	34543	467	47870475	47870564	489	577	79	108
ENST00000402690	12092	467	47870475	47870564	632	720	79	108

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
ENST00000262160	34543	467	47870475	47870564	489	577	79	108
ENST00000402690	12092	467	47870475	47870564	632	720	79	108

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
ENST00000262160	34543	467	47870475	47870564	489	577	79	108
ENST00000402690	12092	467	47870475	47870564	632	720	79	108

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
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438

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
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438

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
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	79	108	Alternative sequence	ID=VSP_006178;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438
Q15796	79	108	10	176	Domain	Note=MH1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00438

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3'-UTR located exon skipping events that lost miRNA binding sites in SMAD2

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 SMAD2

- 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 SMAD2

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

ADstage

MSBB

IFG

exon_skip_216020

4.205280e-01

2.586434e-02

chr18

47870475

47870564

47873897

47873955

47896521

47896809

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMAD2

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 SMAD2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TARDBP	exon_skip_223535	-4.091351e-01	1.139340e-07
CB	HNRNPK	exon_skip_223535	-4.614155e-01	1.342008e-09
CB	HNRNPL	exon_skip_223535	-4.439133e-01	6.458387e-09
CB	EWSR1	exon_skip_223535	-4.123602e-01	8.848924e-08
CB	RBM4	exon_skip_203873	5.370875e-01	7.530952e-11
CB	RBM4B	exon_skip_203873	4.172253e-01	1.061743e-06
HCC	ZC3H10	exon_skip_223535	5.358898e-01	1.074147e-21
IFG	IGF2BP2	exon_skip_223535	4.315968e-01	2.183119e-02
IFG	RBM6	exon_skip_203873	4.503956e-01	2.386248e-02
IFG	HNRNPK	exon_skip_203873	4.122526e-01	4.057692e-02
IFG	SRSF1	exon_skip_203873	4.326726e-01	3.075349e-02
IFG	SRSF9	exon_skip_203873	5.453850e-01	4.807833e-03
IFG	SRSF5	exon_skip_203873	4.704303e-01	1.763513e-02
PCC	PABPC1	exon_skip_223535	4.105728e-01	4.549528e-10
PCC	SAMD4A	exon_skip_203873	4.310221e-01	1.367488e-10
PG	IGF2BP2	exon_skip_223535	4.290906e-01	2.556650e-10
PG	HNRNPK	exon_skip_223535	-4.185878e-01	7.623660e-10
PG	PUF60	exon_skip_223535	-4.284222e-01	2.743842e-10
PG	HNRNPL	exon_skip_223535	-4.221532e-01	5.283405e-10
STG	ESRP2	exon_skip_223535	4.401631e-01	1.776576e-05
TC	MBNL1	exon_skip_223535	-4.055062e-01	1.041131e-07
TC	NUP42	exon_skip_223535	-6.503002e-01	1.332252e-20
TC	HNRNPL	exon_skip_223535	-4.150273e-01	4.850469e-08
TC	RBM6	exon_skip_203873	4.168618e-01	4.458214e-07

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RelatedDrugs for SMAD2

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 SMAD2

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 SMAD2

Gene structures and expression levels for SMAD2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SMAD2

Open reading frame (ORF) annotation in the exon skipping event for SMAD2

Infer the effects of exon skipping event on protein functional features for SMAD2

3'-UTR located exon skipping events that lost miRNA binding sites in SMAD2

SNVs in the skipped exons for SMAD2

AD stage-associated exon skippint events for SMAD2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMAD2

Correlation with RNA binding proteins (RBPs) for SMAD2

RelatedDrugs for SMAD2

RelatedDiseases for SMAD2