ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SMARCA4

Gene summary

Gene information	Gene symbol	SMARCA4
	Gene ID	6597
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
	Synonyms	BAF190\|BAF190A\|BRG1\|CSS4\|MRD16\|RTPS2\|SNF2\|SNF2-beta\|SNF2L4\|SNF2LB\|SWI2\|hSNF2b
	Cytomap	19p13.2
	Type of gene	protein-coding
	Description	transcription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription a
	Modification date	20200315
	UniProtAcc	A0A0A0MT49, A0A2R8Y440, A0A2R8Y4C5, A0A2R8Y4P4, A0A2R8Y4R6, A0A2R8Y523, A0A2R8Y526, A0A2R8Y583, A0A2R8Y5K3, A0A2R8Y6N0, A0A2R8Y6V2, A0A2R8Y7F3, A0A2R8Y7R0, A0A2R8Y7S2, A0A2R8Y7Y7, A0A2R8Y866, A0A2R8YCY3, A0A2R8YDA1, A0A2R8YF38, A0A2R8YF58, A0A2R8YF80, A0A2R8YFK5, A0A2R8YFV8, A0A2R8YG32, A0A2R8YGG3, A0A2R8YGP5, A5D6X0, A7E2E1, B9EGQ8, K7EP28, K7EQF0, P51532, Q9HBD4,
	Context

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

Gene	GO ID	GO term	PubMed ID
SMARCA4	GO:0006337	nucleosome disassembly	8895581
SMARCA4	GO:0006338	chromatin remodeling	10943845\|11726552
SMARCA4	GO:0045892	negative regulation of transcription, DNA-templated	12065415
SMARCA4	GO:0045944	positive regulation of transcription by RNA polymerase II	15774904\|17938176
SMARCA4	GO:0051091	positive regulation of DNA-binding transcription factor activity	11950834\|17938176
SMARCA4	GO:1902661	positive regulation of glucose mediated signaling pathway	22368283

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Gene structures and expression levels for SMARCA4

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.

ENSG00000127616

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	ENST00000586921.1	SMARCA4-211:lncRNA:SMARCA4	5.657336e+00	1.499454e+00	1.126575e-03	1.592425e-02
CB	DOWN	ENST00000586921.1	SMARCA4-211:lncRNA:SMARCA4	1.266978e+02	-1.537269e+00	1.640772e-08	4.593329e-07
CB	DOWN	ENST00000643929.1	SMARCA4-229:retained_intron:SMARCA4	2.985247e+02	-1.023677e+00	4.682154e-07	7.871336e-06
CB	DOWN	ENST00000646889.1	SMARCA4-251:retained_intron:SMARCA4	1.192033e+02	-8.285074e-01	3.064901e-04	1.906173e-03
TC	DOWN	ENST00000646889.1	SMARCA4-251:retained_intron:SMARCA4	9.252239e+01	-9.166290e-01	5.154673e-03	3.430841e-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 SMARCA4

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_100269	chr19	10987666:10987924:10989317:10989443:10991150:10991323	10989317:10989443
exon_skip_106324	chr19	11041307:11041560:11056217:11056382:11058255:11058363	11056217:11056382
exon_skip_11950	chr19	11041439:11041560:11047595:11047795:11058255:11058363	11047595:11047795
exon_skip_127513	chr19	11035022:11035132:11039458:11039553:11041307:11041560	11039458:11039553
exon_skip_128819	chr19	11007905:11008023:11010381:11010531:11012949:11013112	11010381:11010531
exon_skip_12982	chr19	11035091:11035132:11039458:11039553:11041298:11041560	11039458:11039553
exon_skip_130067	chr19	11041439:11041560:11056217:11056382:11058255:11058363	11056217:11056382
exon_skip_154030	chr19	11033480:11033517:11033767:11033865:11034123:11034200	11033767:11033865
exon_skip_155465	chr19	11058261:11058363:11058788:11058889:11059753:11059845	11058788:11058889
exon_skip_15718	chr19	11007902:11008023:11010381:11010531:11012949:11013112	11010381:11010531
exon_skip_162654	chr19	10961110:10961174:10983480:10983711:10984124:10984373	10983480:10983711
exon_skip_166319	chr19	11058258:11058363:11058788:11058889:11059753:11059830	11058788:11058889
exon_skip_16940	chr19	10961110:10961174:10980777:10980852:10984124:10984194	10980777:10980852
exon_skip_169935	chr19	11058258:11058363:11058788:11058889:11059753:11059831	11058788:11058889
exon_skip_174087	chr19	11003340:11003397:11007902:11008023:11010381:11010531	11007902:11008023
exon_skip_189601	chr19	11025422:11025508:11026300:11026346:11027784:11027861	11026300:11026346
exon_skip_19	chr19	11035091:11035132:11039458:11039553:11041307:11041560	11039458:11039553
exon_skip_214617	chr19	10961110:10961174:10980777:10980852:10984124:10984373	10980777:10980852
exon_skip_220791	chr19	11033290:11033517:11033772:11033865:11034123:11034200	11033772:11033865
exon_skip_236509	chr19	11033455:11033517:11033772:11033865:11034123:11034200	11033772:11033865
exon_skip_237699	chr19	10961110:10961174:10977653:10977815:10984124:10984373	10977653:10977815
exon_skip_248666	chr19	11033455:11033517:11033767:11033865:11034123:11034200	11033767:11033865
exon_skip_264349	chr19	11035022:11035132:11039458:11039553:11041298:11041457	11039458:11039553
exon_skip_267553	chr19	10961081:10961174:10977653:10977815:10984124:10984373	10977653:10977815
exon_skip_275521	chr19	11033480:11033517:11033772:11033865:11034123:11034200	11033772:11033865
exon_skip_277607	chr19	10961010:10961174:10980777:10980852:10984124:10984373	10980777:10980852
exon_skip_279859	chr19	11041482:11041560:11047595:11047795:11058255:11058363	11047595:11047795
exon_skip_285642	chr19	11058258:11058363:11058788:11058889:11059753:11059845	11058788:11058889
exon_skip_289696	chr19	11035022:11035132:11041307:11041560:11058255:11058363	11041307:11041560
exon_skip_293769	chr19	10961010:10961174:10980777:10980852:10984121:10984373	10980777:10980852
exon_skip_29665	chr19	11035022:11035132:11039458:11039553:11041307:11041457	11039458:11039553
exon_skip_39372	chr19	10961110:10961174:10965307:10965309:10984124:10984373	10965307:10965309
exon_skip_60246	chr19	10961105:10961174:10983480:10983711:10984124:10984373	10983480:10983711
exon_skip_72000	chr19	11003340:11003397:11007902:11008023:11012949:11013112	11007902:11008023
exon_skip_72012	chr19	10987725:10987924:10989317:10989443:10991150:10991323	10989317:10989443
exon_skip_86079	chr19	11035022:11035132:11039458:11039553:11041298:11041560	11039458:11039553
exon_skip_88663	chr19	11007962:11008023:11010381:11010531:11012949:11013112	11010381:11010531
exon_skip_90659	chr19	10961110:10961174:10980777:10980852:10984121:10984373	10980777:10980852
exon_skip_9110	chr19	11033290:11033517:11033767:11033865:11034123:11034200	11033767:11033865
exon_skip_96782	chr19	11035022:11035132:11041298:11041560:11058255:11058363	11041298:11041560

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 SMARCA4

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
ENST00000429416	10980777	10980852	5UTR-5UTR
ENST00000344626	10989317	10989443	Frame-shift
ENST00000429416	10989317	10989443	Frame-shift
ENST00000344626	11007902	11008023	Frame-shift
ENST00000429416	11007902	11008023	Frame-shift
ENST00000344626	11010381	11010531	Frame-shift
ENST00000429416	11010381	11010531	Frame-shift
ENST00000344626	11033767	11033865	In-frame
ENST00000429416	11033767	11033865	In-frame
ENST00000344626	11058788	11058889	In-frame
ENST00000429416	11058788	11058889	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
ENST00000429416	10980777	10980852	5UTR-5UTR
ENST00000344626	10989317	10989443	Frame-shift
ENST00000429416	10989317	10989443	Frame-shift
ENST00000344626	11010381	11010531	Frame-shift
ENST00000429416	11010381	11010531	Frame-shift
ENST00000344626	11033767	11033865	In-frame
ENST00000429416	11033767	11033865	In-frame
ENST00000344626	11058788	11058889	In-frame
ENST00000429416	11058788	11058889	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
ENST00000429416	10980777	10980852	5UTR-5UTR
ENST00000344626	10989317	10989443	Frame-shift
ENST00000429416	10989317	10989443	Frame-shift
ENST00000344626	11007902	11008023	Frame-shift
ENST00000429416	11007902	11008023	Frame-shift
ENST00000344626	11010381	11010531	Frame-shift
ENST00000429416	11010381	11010531	Frame-shift
ENST00000344626	11026300	11026346	Frame-shift
ENST00000429416	11026300	11026346	Frame-shift
ENST00000344626	11041307	11041560	Frame-shift
ENST00000429416	11041307	11041560	Frame-shift
ENST00000344626	11033767	11033865	In-frame
ENST00000429416	11033767	11033865	In-frame
ENST00000344626	11058788	11058889	In-frame
ENST00000429416	11058788	11058889	In-frame

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Infer the effects of exon skipping event on protein functional features for SMARCA4

p-ENSG00000127616_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
ENST00000344626	5808	1647	11033767	11033865	4157	4254	1258	1291
ENST00000429416	5682	1647	11033767	11033865	4057	4154	1258	1291
ENST00000344626	5808	1647	11058788	11058889	4916	5016	1511	1545
ENST00000429416	5682	1647	11058788	11058889	4816	4916	1511	1545

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
ENST00000344626	5808	1647	11033767	11033865	4157	4254	1258	1291
ENST00000429416	5682	1647	11033767	11033865	4057	4154	1258	1291
ENST00000344626	5808	1647	11058788	11058889	4916	5016	1511	1545
ENST00000429416	5682	1647	11058788	11058889	4816	4916	1511	1545

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
ENST00000344626	5808	1647	11033767	11033865	4157	4254	1258	1291
ENST00000429416	5682	1647	11033767	11033865	4057	4154	1258	1291
ENST00000344626	5808	1647	11058788	11058889	4916	5016	1511	1545
ENST00000429416	5682	1647	11058788	11058889	4816	4916	1511	1545

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
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3

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
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3

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
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1259	1291	Alternative sequence	ID=VSP_043137;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:18386774;Dbxref=PMID:18386774
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1258	1291	1247	1446	Region	Note=Sufficient for interaction with DLX1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3TKT4
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1542	1544	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H60
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1	1647	Chain	ID=PRO_0000074353;Note=Transcription activator BRG1
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1477	1547	Domain	Note=Bromo;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1507	1515	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1522	1539	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1545	1567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2GRC
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1539	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1540	1540	Mutagenesis	Note=Abolishes binding to 'Lys-15'-acetylated histone H3. N->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17274598;Dbxref=PMID:17274598
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3
P51532	1511	1545	1539	1540	Site	Note=Required for binding to 'Lys-15'-acetylated histone 3

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3'-UTR located exon skipping events that lost miRNA binding sites in SMARCA4

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 SMARCA4

- 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 SMARCA4

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

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCA4

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 SMARCA4

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
DLPFC	KHDRBS2	exon_skip_9110	4.356508e-01	2.550373e-17
IFG	ELAVL4	exon_skip_86079	4.571054e-01	2.831688e-02
STG	SRSF5	exon_skip_9110	4.115715e-01	6.783921e-05

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RelatedDrugs for SMARCA4

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 SMARCA4

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 SMARCA4

Gene structures and expression levels for SMARCA4

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SMARCA4

Open reading frame (ORF) annotation in the exon skipping event for SMARCA4

Infer the effects of exon skipping event on protein functional features for SMARCA4

3'-UTR located exon skipping events that lost miRNA binding sites in SMARCA4

SNVs in the skipped exons for SMARCA4

AD stage-associated exon skippint events for SMARCA4

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMARCA4

Correlation with RNA binding proteins (RBPs) for SMARCA4

RelatedDrugs for SMARCA4

RelatedDiseases for SMARCA4