ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SMARCC1

Gene summary

Gene information	Gene symbol	SMARCC1
	Gene ID	6599
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1
	Synonyms	BAF155\|CRACC1\|Rsc8\|SRG3\|SWI3
	Cytomap	3p21.31
	Type of gene	protein-coding
	Description	SWI/SNF complex subunit SMARCC1BRG1-associated factor 155SWI/SNF complex 155 kDa subunitSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1chromatin remodeling complex BAF155 subunitmammalian chromatin remode
	Modification date	20180523
	UniProtAcc	Q92922
	Context	PubMed: SMARCC1 [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
SMARCC1	GO:0006337	nucleosome disassembly	8895581
SMARCC1	GO:0006338	chromatin remodeling	10078207\|11018012\|11726552
SMARCC1	GO:0045893	positive regulation of transcription, DNA-templated	11018012

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Exon skipping events across known transcript of Ensembl for SMARCC1 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 SMARCC1

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 SMARCC1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_383245	3	47629079:47629796:47632150:47632327:47651555:47651817	47632150:47632327	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383247	3	47651555:47651817:47663696:47663831:47676679:47676831	47663696:47663831	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383250	3	47663696:47663831:47676679:47676834:47677511:47677626	47676679:47676834	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383256	3	47677511:47677626:47680214:47680270:47702783:47702945	47680214:47680270	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383260	3	47680214:47680270:47702783:47702945:47703823:47704082	47702783:47702945	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383263	3	47702783:47702945:47703823:47704082:47712147:47712207	47703823:47704082	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383264	3	47703823:47704082:47712147:47712207:47716964:47717060	47712147:47712207	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383266	3	47712147:47712207:47716964:47717078:47718118:47718272	47716964:47717078	ENSG00000173473.6	ENST00000483847.1,ENST00000425518.1,ENST00000254480.5
exon_skip_383269	3	47716964:47717078:47718118:47718272:47719687:47719801	47718118:47718272	ENSG00000173473.6	ENST00000483847.1,ENST00000425518.1,ENST00000254480.5
exon_skip_383272	3	47719687:47719801:47721926:47721998:47727538:47727660	47721926:47721998	ENSG00000173473.6	ENST00000425518.1,ENST00000462198.1,ENST00000254480.5
exon_skip_383273	3	47727538:47727660:47730876:47730914:47734730:47734790	47730876:47730914	ENSG00000173473.6	ENST00000425518.1,ENST00000462198.1,ENST00000485737.1,ENST00000254480.5
exon_skip_383274	3	47734730:47734790:47742767:47742892:47747898:47748016	47742767:47742892	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383276	3	47747898:47748020:47752172:47752298:47755904:47755980	47752172:47752298	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383280	3	47755904:47755980:47762155:47762225:47770514:47770584	47762155:47762225	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383282	3	47762155:47762225:47770514:47770584:47777523:47777616	47770514:47770584	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383284	3	47770526:47770584:47777523:47777616:47779518:47779600	47777523:47777616	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5,ENST00000485833.1
exon_skip_383285	3	47777523:47777616:47779518:47779600:47787397:47787483	47779518:47779600	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5,ENST00000485833.1
exon_skip_383287	3	47777523:47777616:47787397:47787483:47814306:47814426	47787397:47787483	ENSG00000173473.6	ENST00000454240.1
exon_skip_383288	3	47779518:47779600:47787397:47787483:47814306:47814426	47787397:47787483	ENSG00000173473.6	ENST00000425518.1,ENST00000254480.5
exon_skip_383291	3	47787397:47787483:47814306:47814426:47823092:47823371	47814306:47814426	ENSG00000173473.6	ENST00000454240.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SMARCC1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_383245	3	47629079:47629796:47632150:47632327:47651555:47651817	47632150:47632327	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383247	3	47651555:47651817:47663696:47663831:47676679:47676831	47663696:47663831	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383250	3	47663696:47663831:47676679:47676834:47677511:47677626	47676679:47676834	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383256	3	47677511:47677626:47680214:47680270:47702783:47702945	47680214:47680270	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383260	3	47680214:47680270:47702783:47702945:47703823:47704082	47702783:47702945	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383263	3	47702783:47702945:47703823:47704082:47712147:47712207	47703823:47704082	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383264	3	47703823:47704082:47712147:47712207:47716964:47717060	47712147:47712207	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383266	3	47712147:47712207:47716964:47717078:47718118:47718272	47716964:47717078	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000483847.1
exon_skip_383269	3	47716964:47717078:47718118:47718272:47719687:47719801	47718118:47718272	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000483847.1
exon_skip_383272	3	47719687:47719801:47721926:47721998:47727538:47727660	47721926:47721998	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000462198.1
exon_skip_383273	3	47727538:47727660:47730876:47730914:47734730:47734790	47730876:47730914	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000462198.1,ENST00000485737.1
exon_skip_383274	3	47734730:47734790:47742767:47742892:47747898:47748016	47742767:47742892	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383276	3	47747898:47748020:47752172:47752298:47755904:47755980	47752172:47752298	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383280	3	47755904:47755980:47762155:47762225:47770514:47770584	47762155:47762225	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383282	3	47762155:47762225:47770514:47770584:47777523:47777616	47770514:47770584	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383284	3	47770526:47770584:47777523:47777616:47779518:47779600	47777523:47777616	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000485833.1
exon_skip_383285	3	47777523:47777616:47779518:47779600:47787397:47787483	47779518:47779600	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1,ENST00000485833.1
exon_skip_383287	3	47777523:47777616:47787397:47787483:47814306:47814426	47787397:47787483	ENSG00000173473.6	ENST00000454240.1
exon_skip_383288	3	47779518:47779600:47787397:47787483:47814306:47814426	47787397:47787483	ENSG00000173473.6	ENST00000254480.5,ENST00000425518.1
exon_skip_383291	3	47787397:47787483:47814306:47814426:47823092:47823371	47814306:47814426	ENSG00000173473.6	ENST00000454240.1

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 SMARCC1

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
ENST00000254480	47676679	47676834	Frame-shift
ENST00000254480	47680214	47680270	Frame-shift
ENST00000254480	47703823	47704082	Frame-shift
ENST00000254480	47718118	47718272	Frame-shift
ENST00000254480	47730876	47730914	Frame-shift
ENST00000254480	47742767	47742892	Frame-shift
ENST00000254480	47762155	47762225	Frame-shift
ENST00000254480	47770514	47770584	Frame-shift
ENST00000254480	47779518	47779600	Frame-shift
ENST00000254480	47787397	47787483	Frame-shift
ENST00000254480	47632150	47632327	In-frame
ENST00000254480	47663696	47663831	In-frame
ENST00000254480	47702783	47702945	In-frame
ENST00000254480	47712147	47712207	In-frame
ENST00000254480	47716964	47717078	In-frame
ENST00000254480	47721926	47721998	In-frame
ENST00000254480	47752172	47752298	In-frame
ENST00000254480	47777523	47777616	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
ENST00000254480	47676679	47676834	Frame-shift
ENST00000254480	47680214	47680270	Frame-shift
ENST00000254480	47703823	47704082	Frame-shift
ENST00000254480	47718118	47718272	Frame-shift
ENST00000254480	47730876	47730914	Frame-shift
ENST00000254480	47742767	47742892	Frame-shift
ENST00000254480	47762155	47762225	Frame-shift
ENST00000254480	47770514	47770584	Frame-shift
ENST00000254480	47779518	47779600	Frame-shift
ENST00000254480	47787397	47787483	Frame-shift
ENST00000254480	47632150	47632327	In-frame
ENST00000254480	47663696	47663831	In-frame
ENST00000254480	47702783	47702945	In-frame
ENST00000254480	47712147	47712207	In-frame
ENST00000254480	47716964	47717078	In-frame
ENST00000254480	47721926	47721998	In-frame
ENST00000254480	47752172	47752298	In-frame
ENST00000254480	47777523	47777616	In-frame

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Infer the effects of exon skipping event on protein functional features for SMARCC1

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
ENST00000254480	6392	1105	47777523	47777616	604	696	161	192
ENST00000254480	6392	1105	47752172	47752298	913	1038	264	306
ENST00000254480	6392	1105	47721926	47721998	1506	1577	462	485
ENST00000254480	6392	1105	47716964	47717078	1846	1959	575	613
ENST00000254480	6392	1105	47712147	47712207	1960	2019	613	633
ENST00000254480	6392	1105	47702783	47702945	2279	2440	719	773
ENST00000254480	6392	1105	47663696	47663831	2767	2901	882	927
ENST00000254480	6392	1105	47632150	47632327	3164	3340	1014	1073

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
ENST00000254480	6392	1105	47777523	47777616	604	696	161	192
ENST00000254480	6392	1105	47752172	47752298	913	1038	264	306
ENST00000254480	6392	1105	47721926	47721998	1506	1577	462	485
ENST00000254480	6392	1105	47716964	47717078	1846	1959	575	613
ENST00000254480	6392	1105	47712147	47712207	1960	2019	613	633
ENST00000254480	6392	1105	47702783	47702945	2279	2440	719	773
ENST00000254480	6392	1105	47663696	47663831	2767	2901	882	927
ENST00000254480	6392	1105	47632150	47632327	3164	3340	1014	1073

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
Q92922	161	192	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	161	192	179	179	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q92922	264	306	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	462	485	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	462	485	449	546	Domain	Note=SWIRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00247
Q92922	462	485	465	470	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	462	485	472	474	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	462	485	484	500	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	575	613	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	575	613	592	592	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:25755297,ECO:0000244\|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
Q92922	613	633	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	613	633	618	669	Domain	Note=SANT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00624
Q92922	613	633	625	637	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2YUS
Q92922	613	633	622	622	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92922	719	773	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	719	773	769	863	Compositional bias	Note=Glu-rich
Q92922	719	773	739	739	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q92922	882	927	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	882	927	914	946	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92922	882	927	916	916	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92922	1014	1073	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	1014	1073	977	1105	Compositional bias	Note=Pro-rich
Q92922	1014	1073	1064	1064	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97496

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
Q92922	161	192	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	161	192	179	179	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q92922	264	306	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	462	485	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	462	485	449	546	Domain	Note=SWIRM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00247
Q92922	462	485	465	470	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	462	485	472	474	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	462	485	484	500	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5GJK
Q92922	575	613	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	575	613	592	592	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:25755297,ECO:0000244\|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
Q92922	613	633	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	613	633	618	669	Domain	Note=SANT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00624
Q92922	613	633	625	637	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2YUS
Q92922	613	633	622	622	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92922	719	773	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	719	773	769	863	Compositional bias	Note=Glu-rich
Q92922	719	773	739	739	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q92922	882	927	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	882	927	914	946	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92922	882	927	916	916	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q92922	1014	1073	2	1105	Chain	ID=PRO_0000197115;Note=SWI/SNF complex subunit SMARCC1
Q92922	1014	1073	977	1105	Compositional bias	Note=Pro-rich
Q92922	1014	1073	1064	1064	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97496

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SNVs in the skipped exons for SMARCC1

- 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.

SMARCC1_HNSC_exon_skip_383264_psi_boxplot.png
boxplot

- 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
LUAD	TCGA-44-2659-01	exon_skip_383245	47632151	47632327	47632266	47632266	Frame_Shift_Del	G	-	p.P1035fs
LIHC	TCGA-DD-A3A1-01	exon_skip_383245	47632151	47632327	47632282	47632282	Frame_Shift_Del	G	-	p.P1030fs
LIHC	TCGA-DD-A1EG-01	exon_skip_383247	47663697	47663831	47663795	47663795	Frame_Shift_Del	G	-	p.L895fs
LIHC	TCGA-DD-A3A0-01	exon_skip_383263	47703824	47704082	47703877	47703877	Frame_Shift_Del	A	-	p.L702fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_383263	47703824	47704082	47703877	47703877	Frame_Shift_Del	A	-	p.L702fs
LIHC	TCGA-DD-A1EG-01	exon_skip_383263	47703824	47704082	47703976	47703976	Frame_Shift_Del	G	-	p.P669fs
LIHC	TCGA-DD-A39Y-01	exon_skip_383276	47752173	47752298	47752203	47752203	Frame_Shift_Del	A	-	p.F296fs
COAD	TCGA-D5-6532-01	exon_skip_383276	47752173	47752298	47752267	47752268	Frame_Shift_Del	AT	-	p.275_275del
LIHC	TCGA-DD-A1EG-01	exon_skip_383285	47779519	47779600	47779546	47779546	Frame_Shift_Del	A	-	p.F152fs
LIHC	TCGA-DD-A1EG-01	exon_skip_383285	47779519	47779600	47779551	47779551	Frame_Shift_Del	T	-	p.M151fs
LIHC	TCGA-DD-A39Y-01	exon_skip_383287 exon_skip_383288	47787398	47787483	47787410	47787410	Frame_Shift_Del	T	-	p.N130fs
LIHC	TCGA-DD-A3A0-01	exon_skip_383287 exon_skip_383288	47787398	47787483	47787410	47787410	Frame_Shift_Del	T	-	p.N130fs
LIHC	TCGA-DD-A3A0-01	exon_skip_383291	47814307	47814426	47814343	47814343	Frame_Shift_Del	C	-	p.G93fs
LGG	TCGA-DU-6392-01	exon_skip_383247	47663697	47663831	47663813	47663813	Nonsense_Mutation	C	A	p.E889*
UCEC	TCGA-BS-A0UF-01	exon_skip_383250	47676680	47676834	47676808	47676808	Nonsense_Mutation	C	A	p.E840*
STAD	TCGA-BR-4184-01	exon_skip_383264	47712148	47712207	47712178	47712178	Nonsense_Mutation	C	T	p.W623*
UCEC	TCGA-BS-A0UV-01	exon_skip_383269	47718119	47718272	47718130	47718130	Nonsense_Mutation	G	A	p.R572*
HNSC	TCGA-CR-7371-01	exon_skip_383264	47712148	47712207	47712147	47712147	Splice_Site	C	A	p.E633_splice
STAD	TCGA-CG-4477-01	exon_skip_383273	47730877	47730914	47730865	47730876	Splice_Site	CTGAATTGTTAC	-	.
STAD	TCGA-CG-4477-01	exon_skip_383273	47730877	47730914	47730865	47730876	Splice_Site	CTGAATTGTTAC	-	p.K421_splice
LUSC	TCGA-33-4566-01	exon_skip_383274	47742768	47742892	47742767	47742767	Splice_Site	C	A	p.V389_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-CR-7371-01
	Cancer type: HNSC
	ESID: exon_skip_383264
	Skipped exon start: 47712148
	Skipped exon end: 47712207
	Mutation start: 47712147
	Mutation end: 47712147
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: p.E633_splice
exon_skip_366646_HNSC_TCGA-CR-7371-01.png
exon_skip_383264_HNSC_TCGA-CR-7371-01.png

- 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
SKOV3_OVARY	47676680	47676834	47676782	47676785	Frame_Shift_Del	TCTT	-	p.ER847fs
LS411N_LARGE_INTESTINE	47718119	47718272	47718258	47718258	Frame_Shift_Del	A	-	p.L529fs
A101D_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
A375_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
COLO679_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
COLO800_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
LOVO_LARGE_INTESTINE	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
MELJUSO_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
MEWO_SKIN	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
PC3JPC3_LUNG	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
RCM1_LARGE_INTESTINE	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
SW1463_LARGE_INTESTINE	47676680	47676834	47676722	47676723	Frame_Shift_Ins	-	G	p.T868fs
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47779519	47779600	47779529	47779530	Frame_Shift_Ins	-	T	p.T158fs
HUCCT1_BILIARY_TRACT	47632151	47632327	47632178	47632178	Missense_Mutation	C	A	p.V1065L
NCIH1651_LUNG	47632151	47632327	47632276	47632276	Missense_Mutation	C	A	p.R1032L
NCIH1793_LUNG	47632151	47632327	47632289	47632289	Missense_Mutation	G	T	p.H1028N
YH13_CENTRAL_NERVOUS_SYSTEM	47632151	47632327	47632304	47632304	Missense_Mutation	T	C	p.M1023V
HS172T_FIBROBLAST	47632151	47632327	47632307	47632307	Missense_Mutation	A	T	p.S1022T
CL14_LARGE_INTESTINE	47676680	47676834	47676691	47676691	Missense_Mutation	T	C	p.T879A
A549_LUNG	47676680	47676834	47676724	47676724	Missense_Mutation	T	G	p.T868P
IGROV1_OVARY	47702784	47702945	47702797	47702797	Missense_Mutation	C	A	p.E769D
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47702784	47702945	47702883	47702883	Missense_Mutation	C	T	p.V741I
MEWO_SKIN	47703824	47704082	47703944	47703944	Missense_Mutation	G	A	p.P680S
NCIH2171_LUNG	47703824	47704082	47704054	47704054	Missense_Mutation	T	A	p.N643I
RL952_ENDOMETRIUM	47716965	47717078	47717000	47717000	Missense_Mutation	G	A	p.R602C
D423MG_CENTRAL_NERVOUS_SYSTEM	47716965	47717078	47717057	47717058	Missense_Mutation	GC	AT	p.M582I
ES5_BONE	47716965	47717078	47717057	47717058	Missense_Mutation	GC	AT	p.M582I
NCIH2373_PLEURA	47716965	47717078	47717057	47717058	Missense_Mutation	GC	AT	p.M582I
SW780_URINARY_TRACT	47716965	47717078	47717057	47717058	Missense_Mutation	GC	AT	p.M582I
T84_LARGE_INTESTINE	47716965	47717078	47717057	47717058	Missense_Mutation	GC	AT	p.M582I
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47718119	47718272	47718148	47718148	Missense_Mutation	G	T	p.L566I
YD10B_UPPER_AERODIGESTIVE_TRACT	47742768	47742892	47742791	47742791	Missense_Mutation	T	C	p.E381G
JHUEM7_ENDOMETRIUM	47752173	47752298	47752196	47752196	Missense_Mutation	G	A	p.R299W
HEC1_ENDOMETRIUM	47762156	47762225	47762210	47762210	Missense_Mutation	G	A	p.P221L
RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47762156	47762225	47762210	47762210	Missense_Mutation	G	A	p.P221L
D283MED_CENTRAL_NERVOUS_SYSTEM	47777524	47777616	47777540	47777540	Missense_Mutation	A	G	p.I187T
SNU1040_LARGE_INTESTINE	47779519	47779600	47779523	47779523	Missense_Mutation	A	G	p.V160A
DV90_LUNG	47779519	47779600	47779562	47779562	Missense_Mutation	C	T	p.R147H
DM3_FIBROBLAST	47779519	47779600	47779578	47779578	Missense_Mutation	G	C	p.P142A
BICR18_UPPER_AERODIGESTIVE_TRACT	47787398	47787483	47787450	47787450	Missense_Mutation	C	T	p.A117T
LNCAPCLONEFGC_PROSTATE	47787398	47787483	47787458	47787458	Missense_Mutation	G	A	p.A114V
CW2_LARGE_INTESTINE	47814307	47814426	47814417	47814417	Missense_Mutation	C	T	p.A69T
SNU81_LARGE_INTESTINE	47676680	47676834	47676808	47676808	Nonsense_Mutation	C	A	p.E840*
LNCAPCLONEFGC_PROSTATE	47680215	47680270	47680226	47680226	Nonsense_Mutation	G	A	p.Q789*
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	47730877	47730914	47730878	47730878	Splice_Site	T	C	p.K421R
MHHNB11_AUTONOMIC_GANGLIA	47770515	47770584	47770516	47770516	Splice_Site	A	G	p.D215D
HN_UPPER_AERODIGESTIVE_TRACT	47770515	47770584	47770583	47770583	Splice_Site	C	T	p.G193E

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCC1

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 SMARCC1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCC1

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RelatedDrugs for SMARCC1

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 SMARCC1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SMARCC1	C0001418	Adenocarcinoma	1	CTD_human
SMARCC1	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
SMARCC1	C0024121	Lung Neoplasms	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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