ExonSkipDB: 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	20180522
	UniProtAcc	Q15796
	Context	PubMed: SMAD2 [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
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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Exon skipping events across known transcript of Ensembl for SMAD2 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 SMAD2

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 SMAD2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_299090	18	45374845:45375058:45377644:45377698:45391429:45391504	45377644:45377698	ENSG00000175387.11	ENST00000356825.4,ENST00000586040.1,ENST00000591214.1,ENST00000402690.2,ENST00000262160.6
exon_skip_299091	18	45377644:45377698:45391429:45391504:45394693:45394828	45391429:45391504	ENSG00000175387.11	ENST00000356825.4,ENST00000586040.1,ENST00000591214.1,ENST00000402690.2,ENST00000262160.6
exon_skip_299096	18	45395722:45395807:45396845:45396935:45422891:45423180	45396845:45396935	ENSG00000175387.11	ENST00000587421.1,ENST00000402690.2,ENST00000586514.1,ENST00000262160.6,ENST00000587269.1
exon_skip_299104	18	45396845:45396935:45422891:45423180:45446442:45446540	45422891:45423180	ENSG00000175387.11	ENST00000585978.1,ENST00000587269.1
exon_skip_299105	18	45396845:45396935:45422891:45423180:45456731:45456817	45422891:45423180	ENSG00000175387.11	ENST00000589877.1,ENST00000586514.1
exon_skip_299106	18	45396845:45396935:45422891:45423180:45457170:45457208	45422891:45423180	ENSG00000175387.11	ENST00000402690.2
exon_skip_299113	18	45422891:45423180:45446442:45446540:45448917:45449026	45446442:45446540	ENSG00000175387.11	ENST00000585978.1
exon_skip_299115	18	45423135:45423180:45446442:45446540:45456731:45456817	45446442:45446540	ENSG00000175387.11	ENST00000587269.1
exon_skip_299119	18	45422891:45423180:45456731:45456817:45457166:45457226	45456731:45456817	ENSG00000175387.11	ENST00000589877.1
exon_skip_299120	18	45423135:45423180:45456731:45456817:45457170:45457208	45456731:45456817	ENSG00000175387.11	ENST00000586514.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SMAD2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_299090	18	45374845:45375058:45377644:45377698:45391429:45391504	45377644:45377698	ENSG00000175387.11	ENST00000262160.6,ENST00000402690.2,ENST00000356825.4,ENST00000586040.1,ENST00000591214.1
exon_skip_299091	18	45377644:45377698:45391429:45391504:45394693:45394828	45391429:45391504	ENSG00000175387.11	ENST00000262160.6,ENST00000402690.2,ENST00000356825.4,ENST00000586040.1,ENST00000591214.1
exon_skip_299096	18	45395722:45395807:45396845:45396935:45422891:45423180	45396845:45396935	ENSG00000175387.11	ENST00000262160.6,ENST00000402690.2,ENST00000587269.1,ENST00000586514.1,ENST00000587421.1
exon_skip_299104	18	45396845:45396935:45422891:45423180:45446442:45446540	45422891:45423180	ENSG00000175387.11	ENST00000587269.1,ENST00000585978.1
exon_skip_299105	18	45396845:45396935:45422891:45423180:45456731:45456817	45422891:45423180	ENSG00000175387.11	ENST00000586514.1,ENST00000589877.1
exon_skip_299106	18	45396845:45396935:45422891:45423180:45457170:45457208	45422891:45423180	ENSG00000175387.11	ENST00000402690.2
exon_skip_299115	18	45423135:45423180:45446442:45446540:45456731:45456817	45446442:45446540	ENSG00000175387.11	ENST00000587269.1
exon_skip_299119	18	45422891:45423180:45456731:45456817:45457166:45457226	45456731:45456817	ENSG00000175387.11	ENST00000589877.1
exon_skip_299120	18	45423135:45423180:45456731:45456817:45457170:45457208	45456731:45456817	ENSG00000175387.11	ENST00000586514.1

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 SMAD2

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
ENST00000402690	45422891	45423180	3UTR-3CDS
ENST00000262160	45377644	45377698	In-frame
ENST00000402690	45377644	45377698	In-frame
ENST00000262160	45391429	45391504	In-frame
ENST00000402690	45391429	45391504	In-frame
ENST00000262160	45396845	45396935	In-frame
ENST00000402690	45396845	45396935	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
ENST00000402690	45422891	45423180	3UTR-3CDS
ENST00000262160	45377644	45377698	In-frame
ENST00000402690	45377644	45377698	In-frame
ENST00000262160	45391429	45391504	In-frame
ENST00000402690	45391429	45391504	In-frame
ENST00000262160	45396845	45396935	In-frame
ENST00000402690	45396845	45396935	In-frame

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

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
ENST00000262160	11949	467	45396845	45396935	489	578	79	108
ENST00000402690	12092	467	45396845	45396935	632	721	79	108
ENST00000262160	11949	467	45391429	45391504	908	982	218	243
ENST00000402690	12092	467	45391429	45391504	1051	1125	218	243
ENST00000262160	11949	467	45377644	45377698	983	1036	243	261
ENST00000402690	12092	467	45377644	45377698	1126	1179	243	261

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
ENST00000262160	11949	467	45396845	45396935	489	578	79	108
ENST00000402690	12092	467	45396845	45396935	632	721	79	108
ENST00000262160	11949	467	45391429	45391504	908	982	218	243
ENST00000402690	12092	467	45391429	45391504	1051	1125	218	243
ENST00000262160	11949	467	45377644	45377698	983	1036	243	261
ENST00000402690	12092	467	45377644	45377698	1126	1179	243	261

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
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
Q15796	218	243	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	218	243	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	218	243	220	220	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	218	243	220	220	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	218	243	240	240	Modified residue	Note=Phosphoserine%3B by CAMK2;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00439,ECO:0000269\|PubMed:11879191;Dbxref=PMID:11879191
Q15796	218	243	240	240	Modified residue	Note=Phosphoserine%3B by CAMK2;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00439,ECO:0000269\|PubMed:11879191;Dbxref=PMID:11879191
Q15796	218	243	221	225	Motif	Note=PY-motif
Q15796	218	243	221	225	Motif	Note=PY-motif
Q15796	218	243	221	225	Mutagenesis	Note=Loss of binding to SMURF2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11389444;Dbxref=PMID:11389444
Q15796	218	243	221	225	Mutagenesis	Note=Loss of binding to SMURF2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11389444;Dbxref=PMID:11389444
Q15796	243	261	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	243	261	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	243	261	245	245	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	245	245	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	250	250	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	250	250	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	255	255	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	255	255	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595

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
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
Q15796	218	243	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	218	243	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	218	243	220	220	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	218	243	220	220	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	218	243	240	240	Modified residue	Note=Phosphoserine%3B by CAMK2;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00439,ECO:0000269\|PubMed:11879191;Dbxref=PMID:11879191
Q15796	218	243	240	240	Modified residue	Note=Phosphoserine%3B by CAMK2;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255\|PROSITE-ProRule:PRU00439,ECO:0000269\|PubMed:11879191;Dbxref=PMID:11879191
Q15796	218	243	221	225	Motif	Note=PY-motif
Q15796	218	243	221	225	Motif	Note=PY-motif
Q15796	218	243	221	225	Mutagenesis	Note=Loss of binding to SMURF2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11389444;Dbxref=PMID:11389444
Q15796	218	243	221	225	Mutagenesis	Note=Loss of binding to SMURF2. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11389444;Dbxref=PMID:11389444
Q15796	243	261	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	243	261	2	467	Chain	ID=PRO_0000090852;Note=Mothers against decapentaplegic homolog 2
Q15796	243	261	245	245	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	245	245	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	250	250	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	250	250	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	255	255	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595
Q15796	243	261	255	255	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:12193595;Dbxref=PMID:12193595

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SNVs in the skipped exons for SMAD2

- 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
UCEC	TCGA-AP-A0LP-01	exon_skip_299091	45391430	45391504	45391500	45391501	Frame_Shift_Ins	-	G	p.P221fs
UCEC	TCGA-AP-A0LP-01	exon_skip_299091	45391430	45391504	45391500	45391501	Frame_Shift_Ins	-	G	p.T220fs
READ	TCGA-AG-A011-01	exon_skip_299091	45391430	45391504	45391478	45391478	Nonsense_Mutation	C	A	p.E198X

- 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
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45391430	45391504	45391463	45391463	Missense_Mutation	T	C	p.S233G
SNU175_LARGE_INTESTINE	45391430	45391504	45391501	45391501	Missense_Mutation	G	A	p.T220M
BICR18_UPPER_AERODIGESTIVE_TRACT	45396846	45396935	45396895	45396895	Missense_Mutation	T	C	p.I93V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45396846	45396935	45396895	45396895	Missense_Mutation	T	C	p.I93V
BICR18_UPPER_AERODIGESTIVE_TRACT	45396846	45396935	45396904	45396904	Missense_Mutation	G	C	p.P90A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45396846	45396935	45396904	45396904	Missense_Mutation	G	C	p.P90A
OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45396846	45396935	45396912	45396912	Missense_Mutation	A	C	p.L87R
OPM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45396846	45396935	45396912	45396912	Missense_Mutation	A	C	p.L87R
GP5D_LARGE_INTESTINE	45422892	45423180	45422904	45422904	Missense_Mutation	A	G	p.V75A
IGROV1_OVARY	45422892	45423180	45422929	45422929	Missense_Mutation	T	C	p.T67A
A704_KIDNEY	45422892	45423180	45423040	45423040	Missense_Mutation	C	T	p.G30R
SNU175_LARGE_INTESTINE	45422892	45423180	45423124	45423124	Missense_Mutation	A	G	p.S2P

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

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 SMAD2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMAD2

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RelatedDrugs for SMAD2

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 SMAD2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SMAD2	C0376634	Craniofacial Abnormalities	2	CTD_human
SMAD2	C0019189	Hepatitis, Chronic	1	CTD_human
SMAD2	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
SMAD2	C0265287	Acromicric Dysplasia	1	CTD_human
SMAD2	C0600519	Ventricular Remodeling	1	CTD_human
SMAD2	C1876165	Copper-Overload Cirrhosis	1	CTD_human

	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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