ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SMARCA2

Gene summary

Gene information	Gene symbol	SMARCA2
	Gene ID	6595
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
	Synonyms	BAF190\|BRM\|NCBRS\|SNF2\|SNF2L2\|SNF2LA\|SWI2\|Sth1p\|hBRM\|hSNF2a
	Cytomap	9p24.3
	Type of gene	protein-coding
	Description	probable global transcription activator SNF2L2ATP-dependent helicase SMARCA2BAF190BBRG1-associated factor 190BSNF2-alphaSNF2/SWI2-like protein 2SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2brahma homologglobal transcr
	Modification date	20180519
	UniProtAcc	P51531
	Context	PubMed: SMARCA2 [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
SMARCA2	GO:0008285	negative regulation of cell proliferation	14660596
SMARCA2	GO:0045892	negative regulation of transcription, DNA-templated	12065415
SMARCA2	GO:0045893	positive regulation of transcription, DNA-templated	17984088
SMARCA2	GO:0045944	positive regulation of transcription by RNA polymerase II	15774904

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Exon skipping events across known transcript of Ensembl for SMARCA2 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 SMARCA2

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 SMARCA2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_494766	9	2015373:2015404:2028986:2029247:2032951:2033081	2028986:2029247	ENSG00000080503.15	ENST00000357248.2,ENST00000450198.1
exon_skip_494770	9	2039465:2039900:2047228:2047484:2054596:2054723	2047228:2047484	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000450198.1,ENST00000382194.1
exon_skip_494771	9	2060815:2060986:2070417:2070471:2073211:2073342	2070417:2070471	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000382194.1
exon_skip_494774	9	2073211:2073342:2073565:2073623:2076228:2076329	2073565:2073623	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000382194.1
exon_skip_494775	9	2076228:2076329:2077628:2077776:2081831:2081995	2077628:2077776	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000382194.1
exon_skip_494777	9	2097384:2097471:2101569:2101616:2104002:2104169	2101569:2101616	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000382194.1
exon_skip_494778	9	2110253:2110417:2115821:2116049:2119457:2119535	2115821:2116049	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000357248.2,ENST00000382194.1
exon_skip_494791	9	2158484:2158587:2159813:2159909:2161000:2161035	2159813:2159909	ENSG00000080503.15	ENST00000324954.5
exon_skip_494792	9	2158484:2158587:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000417599.1
exon_skip_494794	9	2158484:2158587:2161000:2161035:2161685:2161903	2161000:2161035	ENSG00000080503.15	ENST00000382186.1
exon_skip_494798	9	2158512:2158594:2159813:2159909:2161000:2161035	2159813:2159909	ENSG00000080503.15	ENST00000382185.1
exon_skip_494799	9	2158512:2158594:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000423555.1
exon_skip_494803	9	2158455:2158978:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000302401.3
exon_skip_494806	9	2159813:2159909:2161000:2161035:2161685:2161903	2161000:2161035	ENSG00000080503.15	ENST00000324954.5,ENST00000382185.1
exon_skip_494809	9	2161685:2161903:2170418:2170472:2181570:2181676	2170418:2170472	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000382186.1,ENST00000452193.1
exon_skip_494814	9	2186095:2186228:2191265:2191408:2192703:2192752	2191265:2191408	ENSG00000080503.15	ENST00000302401.3,ENST00000349721.2,ENST00000382203.1,ENST00000324954.5,ENST00000382186.1,ENST00000357248.2,ENST00000382183.1,ENST00000382185.1,ENST00000382194.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SMARCA2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_494766	9	2015373:2015404:2028986:2029247:2032951:2033081	2028986:2029247	ENSG00000080503.15	ENST00000357248.2,ENST00000450198.1
exon_skip_494770	9	2039465:2039900:2047228:2047484:2054596:2054723	2047228:2047484	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000450198.1,ENST00000382203.1,ENST00000382194.1
exon_skip_494771	9	2060815:2060986:2070417:2070471:2073211:2073342	2070417:2070471	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1
exon_skip_494774	9	2073211:2073342:2073565:2073623:2076228:2076329	2073565:2073623	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1
exon_skip_494775	9	2076228:2076329:2077628:2077776:2081831:2081995	2077628:2077776	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1
exon_skip_494777	9	2097384:2097471:2101569:2101616:2104002:2104169	2101569:2101616	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1
exon_skip_494778	9	2110253:2110417:2115821:2116049:2119457:2119535	2115821:2116049	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1
exon_skip_494791	9	2158484:2158587:2159813:2159909:2161000:2161035	2159813:2159909	ENSG00000080503.15	ENST00000324954.5
exon_skip_494792	9	2158484:2158587:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000417599.1
exon_skip_494794	9	2158484:2158587:2161000:2161035:2161685:2161903	2161000:2161035	ENSG00000080503.15	ENST00000382186.1
exon_skip_494798	9	2158512:2158594:2159813:2159909:2161000:2161035	2159813:2159909	ENSG00000080503.15	ENST00000382185.1
exon_skip_494799	9	2158512:2158594:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000423555.1
exon_skip_494803	9	2158455:2158978:2159813:2159909:2161685:2161903	2159813:2159909	ENSG00000080503.15	ENST00000302401.3
exon_skip_494806	9	2159813:2159909:2161000:2161035:2161685:2161903	2161000:2161035	ENSG00000080503.15	ENST00000324954.5,ENST00000382185.1
exon_skip_494809	9	2161685:2161903:2170418:2170472:2181570:2181676	2170418:2170472	ENSG00000080503.15	ENST00000349721.2,ENST00000382203.1,ENST00000452193.1,ENST00000382186.1
exon_skip_494814	9	2186095:2186228:2191265:2191408:2192703:2192752	2191265:2191408	ENSG00000080503.15	ENST00000349721.2,ENST00000357248.2,ENST00000382203.1,ENST00000382194.1,ENST00000302401.3,ENST00000324954.5,ENST00000382186.1,ENST00000382185.1,ENST00000382183.1

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 SMARCA2

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
ENST00000349721	2047228	2047484	Frame-shift
ENST00000382203	2047228	2047484	Frame-shift
ENST00000349721	2073565	2073623	Frame-shift
ENST00000382203	2073565	2073623	Frame-shift
ENST00000349721	2077628	2077776	Frame-shift
ENST00000382203	2077628	2077776	Frame-shift
ENST00000349721	2101569	2101616	Frame-shift
ENST00000382203	2101569	2101616	Frame-shift
ENST00000349721	2191265	2191408	Frame-shift
ENST00000382203	2191265	2191408	Frame-shift
ENST00000349721	2070417	2070471	In-frame
ENST00000382203	2070417	2070471	In-frame
ENST00000349721	2115821	2116049	In-frame
ENST00000382203	2115821	2116049	In-frame
ENST00000349721	2170418	2170472	In-frame
ENST00000382203	2170418	2170472	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
ENST00000349721	2047228	2047484	Frame-shift
ENST00000382203	2047228	2047484	Frame-shift
ENST00000349721	2073565	2073623	Frame-shift
ENST00000382203	2073565	2073623	Frame-shift
ENST00000349721	2077628	2077776	Frame-shift
ENST00000382203	2077628	2077776	Frame-shift
ENST00000349721	2101569	2101616	Frame-shift
ENST00000382203	2101569	2101616	Frame-shift
ENST00000349721	2191265	2191408	Frame-shift
ENST00000382203	2191265	2191408	Frame-shift
ENST00000349721	2070417	2070471	In-frame
ENST00000382203	2070417	2070471	In-frame
ENST00000349721	2115821	2116049	In-frame
ENST00000382203	2115821	2116049	In-frame
ENST00000349721	2170418	2170472	In-frame
ENST00000382203	2170418	2170472	In-frame

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Infer the effects of exon skipping event on protein functional features for SMARCA2

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
ENST00000349721	5774	1590	2070417	2070471	1792	1845	564	582
ENST00000382203	5884	1590	2070417	2070471	1902	1955	564	582
ENST00000349721	5774	1590	2115821	2116049	3556	3783	1152	1228
ENST00000382203	5884	1590	2115821	2116049	3666	3893	1152	1228
ENST00000349721	5774	1590	2170418	2170472	4299	4352	1400	1417
ENST00000382203	5884	1590	2170418	2170472	4409	4462	1400	1417

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
ENST00000349721	5774	1590	2070417	2070471	1792	1845	564	582
ENST00000382203	5884	1590	2070417	2070471	1902	1955	564	582
ENST00000349721	5774	1590	2115821	2116049	3556	3783	1152	1228
ENST00000382203	5884	1590	2115821	2116049	3666	3893	1152	1228
ENST00000349721	5774	1590	2170418	2170472	4299	4352	1400	1417
ENST00000382203	5884	1590	2170418	2170472	4409	4462	1400	1417

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
P51531	564	582	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	564	582	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1054	1216	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
P51531	1152	1228	1054	1216	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
P51531	1152	1228	1158	1158	Natural variant	ID=VAR_068199;Note=In NCBRS. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875240,PMID:22366787
P51531	1152	1228	1158	1158	Natural variant	ID=VAR_068199;Note=In NCBRS. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875240,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068200;Note=In NCBRS. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875184,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068200;Note=In NCBRS. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875184,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068201;Note=In NCBRS. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068201;Note=In NCBRS. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068202;Note=In NCBRS. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068202;Note=In NCBRS. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1162	1162	Natural variant	ID=VAR_068203;Note=In NCBRS. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875186,PMID:22366787
P51531	1152	1228	1162	1162	Natural variant	ID=VAR_068203;Note=In NCBRS. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875186,PMID:22366787
P51531	1152	1228	1188	1188	Natural variant	ID=VAR_068204;Note=In NCBRS. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875196,PMID:22366787
P51531	1152	1228	1188	1188	Natural variant	ID=VAR_068204;Note=In NCBRS. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875196,PMID:22366787
P51531	1152	1228	1201	1201	Natural variant	ID=VAR_068205;Note=In NCBRS. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875189,PMID:22366787
P51531	1152	1228	1201	1201	Natural variant	ID=VAR_068205;Note=In NCBRS. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875189,PMID:22366787
P51531	1152	1228	1202	1202	Natural variant	ID=VAR_068206;Note=In NCBRS. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875239,PMID:22366787
P51531	1152	1228	1202	1202	Natural variant	ID=VAR_068206;Note=In NCBRS. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875239,PMID:22366787
P51531	1152	1228	1205	1205	Natural variant	ID=VAR_068207;Note=In NCBRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875201,PMID:22366787
P51531	1152	1228	1205	1205	Natural variant	ID=VAR_068207;Note=In NCBRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875201,PMID:22366787
P51531	1152	1228	1213	1213	Natural variant	ID=VAR_068208;Note=In NCBRS. R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875238,PMID:22366787
P51531	1152	1228	1213	1213	Natural variant	ID=VAR_068208;Note=In NCBRS. R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875238,PMID:22366787
P51531	1400	1417	1400	1417	Alternative sequence	ID=VSP_000577;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8208605;Dbxref=PMID:8208605
P51531	1400	1417	1400	1417	Alternative sequence	ID=VSP_000577;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8208605;Dbxref=PMID:8208605
P51531	1400	1417	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1400	1417	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1400	1417	1416	1416	Natural variant	ID=VAR_049501;Note=G->A;Dbxref=dbSNP:rs3793510
P51531	1400	1417	1416	1416	Natural variant	ID=VAR_049501;Note=G->A;Dbxref=dbSNP:rs3793510
P51531	1400	1417	1400	1400	Sequence conflict	Note=R->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51531	1400	1417	1400	1400	Sequence conflict	Note=R->S;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
P51531	564	582	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	564	582	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1152	1228	1054	1216	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
P51531	1152	1228	1054	1216	Domain	Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00542
P51531	1152	1228	1158	1158	Natural variant	ID=VAR_068199;Note=In NCBRS. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875240,PMID:22366787
P51531	1152	1228	1158	1158	Natural variant	ID=VAR_068199;Note=In NCBRS. D->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875240,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068200;Note=In NCBRS. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875184,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068200;Note=In NCBRS. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875184,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068201;Note=In NCBRS. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068201;Note=In NCBRS. R->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068202;Note=In NCBRS. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1159	1159	Natural variant	ID=VAR_068202;Note=In NCBRS. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875187,PMID:22366787
P51531	1152	1228	1162	1162	Natural variant	ID=VAR_068203;Note=In NCBRS. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875186,PMID:22366787
P51531	1152	1228	1162	1162	Natural variant	ID=VAR_068203;Note=In NCBRS. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875186,PMID:22366787
P51531	1152	1228	1188	1188	Natural variant	ID=VAR_068204;Note=In NCBRS. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875196,PMID:22366787
P51531	1152	1228	1188	1188	Natural variant	ID=VAR_068204;Note=In NCBRS. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875196,PMID:22366787
P51531	1152	1228	1201	1201	Natural variant	ID=VAR_068205;Note=In NCBRS. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875189,PMID:22366787
P51531	1152	1228	1201	1201	Natural variant	ID=VAR_068205;Note=In NCBRS. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875189,PMID:22366787
P51531	1152	1228	1202	1202	Natural variant	ID=VAR_068206;Note=In NCBRS. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875239,PMID:22366787
P51531	1152	1228	1202	1202	Natural variant	ID=VAR_068206;Note=In NCBRS. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875239,PMID:22366787
P51531	1152	1228	1205	1205	Natural variant	ID=VAR_068207;Note=In NCBRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875201,PMID:22366787
P51531	1152	1228	1205	1205	Natural variant	ID=VAR_068207;Note=In NCBRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875201,PMID:22366787
P51531	1152	1228	1213	1213	Natural variant	ID=VAR_068208;Note=In NCBRS. R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875238,PMID:22366787
P51531	1152	1228	1213	1213	Natural variant	ID=VAR_068208;Note=In NCBRS. R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22366787;Dbxref=dbSNP:rs281875238,PMID:22366787
P51531	1400	1417	1400	1417	Alternative sequence	ID=VSP_000577;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8208605;Dbxref=PMID:8208605
P51531	1400	1417	1400	1417	Alternative sequence	ID=VSP_000577;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8208605;Dbxref=PMID:8208605
P51531	1400	1417	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1400	1417	1	1590	Chain	ID=PRO_0000074352;Note=Probable global transcription activator SNF2L2
P51531	1400	1417	1416	1416	Natural variant	ID=VAR_049501;Note=G->A;Dbxref=dbSNP:rs3793510
P51531	1400	1417	1416	1416	Natural variant	ID=VAR_049501;Note=G->A;Dbxref=dbSNP:rs3793510
P51531	1400	1417	1400	1400	Sequence conflict	Note=R->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P51531	1400	1417	1400	1400	Sequence conflict	Note=R->S;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for SMARCA2

- 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.

SMARCA2_ESCA_exon_skip_494778_psi_boxplot.png
boxplot

SMARCA2_KIRC_exon_skip_494778_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
LIHC	TCGA-DD-A39Y-01	exon_skip_494777	2101570	2101616	2101603	2101603	Frame_Shift_Del	G	-	p.G1038fs
ESCA	TCGA-ZR-A9CJ-01	exon_skip_494778	2115822	2116049	2115910	2115910	Frame_Shift_Del	A	-	p.K1183fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_494814	2191266	2191408	2191354	2191354	Frame_Shift_Del	A	-	p.G1561fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_494814	2191266	2191408	2191378	2191378	Frame_Shift_Del	T	-	p.D1569fs
UCS	TCGA-ND-A4WC-01	exon_skip_494814	2191266	2191408	2191349	2191349	Nonsense_Mutation	C	T	p.R1560*
HNSC	TCGA-DQ-7588-01	exon_skip_494777	2101570	2101616	2101568	2101568	Splice_Site	A	G	p.E1027_splice
LIHC	TCGA-DD-AACT-01	exon_skip_494778	2115822	2116049	2115820	2115820	Splice_Site	A	T	.
KIRC	TCGA-B0-5107-01	exon_skip_494778	2115822	2116049	2116050	2116050	Splice_Site	G	A	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-B0-5107-01
	Cancer type: KIRC
	ESID: exon_skip_494778
	Skipped exon start: 2115822
	Skipped exon end: 2116049
	Mutation start: 2116050
	Mutation end: 2116050
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: A
	AAchange: .
exon_skip_489575_KIRC_TCGA-B0-5107-01.png
exon_skip_494778_KIRC_TCGA-B0-5107-01.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
OCIMY5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2028987	2029247	2029052	2029052	Missense_Mutation	G	A	p.M10I
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2028987	2029247	2029195	2029195	Missense_Mutation	C	T	p.P58L
NCIH2228_LUNG	2028987	2029247	2029197	2029197	Missense_Mutation	A	T	p.T59S
EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2047229	2047484	2047282	2047282	Missense_Mutation	G	A	p.A282T
NCIH650_LUNG	2047229	2047484	2047373	2047373	Missense_Mutation	C	T	p.P312L
OMC1_CERVIX	2073566	2073623	2073588	2073588	Missense_Mutation	G	A	p.D634N
TC71_BONE	2073566	2073623	2073612	2073612	Missense_Mutation	T	C	p.Y642H
LS411N_LARGE_INTESTINE	2077629	2077776	2077633	2077633	Missense_Mutation	G	A	p.A681T
SNUC5_LARGE_INTESTINE	2077629	2077776	2077657	2077657	Missense_Mutation	T	C	p.Y689H
HCC1569_BREAST	2077629	2077776	2077678	2077678	Missense_Mutation	A	G	p.R696G
SNU1272_KIDNEY	2101570	2101616	2101574	2101574	Missense_Mutation	C	A	p.S1028Y
OVTOKO_OVARY	2115822	2116049	2115849	2115849	Missense_Mutation	C	T	p.R1162C
SNUC2A_LARGE_INTESTINE	2115822	2116049	2115850	2115850	Missense_Mutation	G	A	p.R1162H
SNUC2B_LARGE_INTESTINE	2115822	2116049	2115850	2115850	Missense_Mutation	G	A	p.R1162H
RCCJF_KIDNEY	2115822	2116049	2115855	2115855	Missense_Mutation	G	T	p.G1164W
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2115822	2116049	2115937	2115937	Missense_Mutation	A	G	p.K1191R
EN_ENDOMETRIUM	2115822	2116049	2115945	2115945	Missense_Mutation	G	A	p.V1194M
RERFLCKJ_LUNG	2115822	2116049	2115969	2115969	Missense_Mutation	G	T	p.G1202C
639V_URINARY_TRACT	2115822	2116049	2116002	2116002	Missense_Mutation	C	T	p.R1213W
SNU1040_LARGE_INTESTINE	2115822	2116049	2116002	2116002	Missense_Mutation	C	T	p.R1213W
HCC2450_LUNG	2115822	2116049	2116035	2116035	Missense_Mutation	G	C	p.E1224Q
BICR18_UPPER_AERODIGESTIVE_TRACT	2170419	2170472	2170441	2170441	Missense_Mutation	A	T	p.S1408C
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2170419	2170472	2170441	2170441	Missense_Mutation	A	T	p.S1408C
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2170419	2170472	2170441	2170441	Missense_Mutation	A	T	p.S1408C
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	2170419	2170472	2170441	2170441	Missense_Mutation	A	T	p.S1408C
RCCFG2_KIDNEY	2191266	2191408	2191269	2191269	Missense_Mutation	A	T	p.K1533I
NCIBL2087_MATCHED_NORMAL_TISSUE	2191266	2191408	2191316	2191316	Missense_Mutation	C	T	p.R1549W
HCT15_LARGE_INTESTINE	2191266	2191408	2191404	2191404	Missense_Mutation	A	G	p.E1578G
SNU719_STOMACH	2191266	2191408	2191406	2191406	Missense_Mutation	C	T	p.R1579C
CORL279_LUNG	2115822	2116049	2115999	2115999	Nonsense_Mutation	G	T	p.E1212*
MKN7_STOMACH	2191266	2191408	2191407	2191407	Splice_Site	G	A	p.R1579H
AM38_CENTRAL_NERVOUS_SYSTEM	2191266	2191408	2191407	2191407	Splice_Site	G	A	p.R1579H

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCA2

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
exon_skip_494766	9	2015373:2015404:2028986:2029247:2032951:2033081	2028986:2029247	ENST00000357248.2,ENST00000450198.1	THCA	rs10964468	chr9:2029018	A/G	1.21e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCA2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMARCA2

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RelatedDrugs for SMARCA2

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 SMARCA2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SMARCA2	C0036341	Schizophrenia	4	PSYGENET
SMARCA2	C1303073	Nicolaides Baraitser syndrome	2	CTD_human;ORPHANET;UNIPROT
SMARCA2	C0010606	Adenoid Cystic Carcinoma	1	CTD_human
SMARCA2	C0265338	Coffin-Siris syndrome	1	CTD_human
SMARCA2	C0345967	Malignant mesothelioma	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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