ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for ARID1B

Gene summary

Gene information	Gene symbol	ARID1B
	Gene ID	57492
	Gene name	AT-rich interaction domain 1B
	Synonyms	6A3-5\|BAF250B\|BRIGHT\|CSS1\|DAN15\|ELD/OSA1\|MRD12\|OSA2\|P250R
	Cytomap	6q25.3
	Type of gene	protein-coding
	Description	AT-rich interactive domain-containing protein 1BARID domain-containing protein 1BAT rich interactive domain 1B (SWI1-like)BRG1-associated factor 250bBRG1-binding protein ELD/OSA1ELD (eyelid)/OSA protein
	Modification date	20200320
	UniProtAcc	A0A1B0GTE8, A0A1B0GTI6, A0A1B0GTJ8, A0A1B0GU09, A0A1B0GU65, A0A1B0GUC6, A0A1B0GUG2, A0A1B0GV63, A0A1B0GV92, A0A1B0GVH0, A0A1B0GVK1, A0A1B0GWI8, A0A1B0GWJ2, A0A3F2YNW7, H0Y2R3, H0Y3S9, H0Y7H8, L8EAX2, Q8NFD5,
	Context

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for ARID1B

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.

ENSG00000049618

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
HCC	UP	ENST00000636254.1	ARID1B-215:retained_intron:ARID1B	2.809321e+01	1.026041e+00	1.354864e-03	4.124620e-02
CB	UP	ENST00000635849.1	ARID1B-210:protein_coding:ARID1B	9.763868e+01	8.141736e-01	1.603174e-06	2.240447e-05
CB	UP	ENST00000636930.1	ARID1B-220:protein_coding:ARID1B	1.472959e+02	1.225394e+00	2.026572e-03	9.316964e-03
CB	UP	ENST00000637741.1	ARID1B-229:lncRNA:ARID1B	1.714655e+00	3.692868e+00	8.998033e-03	3.189224e-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 ARID1B

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_104757	chr6	157174026:157174117:157174847:157175005:157180969:157180994	157174847:157175005
exon_skip_111525	chr6	157196165:157196315:157198811:157198907:157200705:157201488	157198811:157198907
exon_skip_116276	chr6	157148911:157148951:157150725:157150853:157167040:157167185	157150725:157150853
exon_skip_138199	chr6	157084887:157084905:157133028:157133207:157148624:157148951	157133028:157133207
exon_skip_144452	chr6	157133028:157133207:157148624:157148951:157167040:157167185	157148624:157148951
exon_skip_169385	chr6	157148911:157148951:157150725:157150853:157167040:157167140	157150725:157150853
exon_skip_17212	chr6	157036835:157036876:157084662:157084905:157110472:157110561	157084662:157084905
exon_skip_18188	chr6	157084772:157084905:157110472:157110561:157133028:157133207	157110472:157110561
exon_skip_187938	chr6	157084887:157084905:157110472:157110561:157148624:157148951	157110472:157110561
exon_skip_19419	chr6	157133028:157133207:157148624:157148951:157167040:157167140	157148624:157148951
exon_skip_200258	chr6	157110476:157110561:157133028:157133207:157148624:157148951	157133028:157133207
exon_skip_201270	chr6	157110472:157110561:157133028:157133207:157148624:157148951	157133028:157133207
exon_skip_206743	chr6	156829410:156829421:156871614:156871652:156901376:156901525	156871614:156871652
exon_skip_262856	chr6	157084887:157084905:157110472:157110561:157133028:157133207	157110472:157110561
exon_skip_275246	chr6	157084772:157084905:157133028:157133207:157148624:157148951	157133028:157133207
exon_skip_34259	chr6	157174008:157174117:157174847:157175005:157180969:157180994	157174847:157175005
exon_skip_44669	chr6	156779464:156779471:156829227:156829421:156901376:156901525	156829227:156829421
exon_skip_60631	chr6	157084772:157084905:157110472:157110561:157148624:157148951	157110472:157110561
exon_skip_63559	chr6	157110513:157110561:157133028:157133207:157148624:157148951	157133028:157133207
exon_skip_72494	chr6	157084662:157084905:157110472:157110561:157133028:157133207	157110472:157110561
exon_skip_94041	chr6	156829410:156829421:156901376:156901525:156935466:156935576	156901376:156901525

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 ARID1B

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
ENST00000350026	157148624	157148951	Frame-shift
ENST00000350026	156829227	156829421	In-frame
ENST00000350026	156901376	156901525	In-frame
ENST00000350026	157110472	157110561	In-frame
ENST00000350026	157133028	157133207	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
ENST00000350026	157148624	157148951	Frame-shift
ENST00000350026	157110472	157110561	In-frame
ENST00000350026	157133028	157133207	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
ENST00000350026	157148624	157148951	Frame-shift
ENST00000350026	157198811	157198907	Frame-shift
ENST00000350026	156829227	156829421	In-frame
ENST00000350026	156901376	156901525	In-frame
ENST00000350026	157110472	157110561	In-frame
ENST00000350026	157133028	157133207	In-frame

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Infer the effects of exon skipping event on protein functional features for ARID1B

p-ENSG00000049618_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
ENST00000350026	7979	2236	156829227	156829421	1544	1737	514	579
ENST00000350026	7979	2236	156901376	156901525	1739	1887	579	629
ENST00000350026	7979	2236	157110472	157110561	2244	2332	748	777
ENST00000350026	7979	2236	157133028	157133207	2334	2512	778	837

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
ENST00000350026	7979	2236	157110472	157110561	2244	2332	748	777
ENST00000350026	7979	2236	157133028	157133207	2334	2512	778	837

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
ENST00000350026	7979	2236	156829227	156829421	1544	1737	514	579
ENST00000350026	7979	2236	156901376	156901525	1739	1887	579	629
ENST00000350026	7979	2236	157110472	157110561	2244	2332	748	777
ENST00000350026	7979	2236	157133028	157133207	2334	2512	778	837

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
Q8NFD5	514	579	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	514	579	579	579	Alternative sequence	ID=VSP_015226;Note=In isoform 2. Q->QDSGDATWKETFWL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11988099;Dbxref=PMID:11988099
Q8NFD5	514	579	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	514	579	574	633	Compositional bias	Note=Gln-rich
Q8NFD5	514	579	516	516	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8NFD5	514	579	525	525	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:E9Q4N7
Q8NFD5	514	579	557	557	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24129315;Dbxref=PMID:24129315
Q8NFD5	514	579	531	531	Natural variant	ID=VAR_067675;Note=M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22405089;Dbxref=dbSNP:rs141260832,PMID:22405089
Q8NFD5	579	629	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	579	629	579	579	Alternative sequence	ID=VSP_015226;Note=In isoform 2. Q->QDSGDATWKETFWL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11988099;Dbxref=PMID:11988099
Q8NFD5	579	629	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	579	629	574	633	Compositional bias	Note=Gln-rich
Q8NFD5	748	777	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	748	777	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	748	777	684	771	Compositional bias	Note=Ser-rich
Q8NFD5	748	777	771	771	Natural variant	ID=VAR_077456;Note=Found in a patient with short stature%3B unknown pathological significance. S->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26376624;Dbxref=PMID:26376624
Q8NFD5	778	837	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	778	837	814	814	Natural variant	ID=VAR_036257;Note=In a breast cancer sample%3B somatic mutation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974

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
Q8NFD5	748	777	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	748	777	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	748	777	684	771	Compositional bias	Note=Ser-rich
Q8NFD5	748	777	771	771	Natural variant	ID=VAR_077456;Note=Found in a patient with short stature%3B unknown pathological significance. S->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26376624;Dbxref=PMID:26376624
Q8NFD5	778	837	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	778	837	814	814	Natural variant	ID=VAR_036257;Note=In a breast cancer sample%3B somatic mutation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974

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
Q8NFD5	514	579	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	514	579	579	579	Alternative sequence	ID=VSP_015226;Note=In isoform 2. Q->QDSGDATWKETFWL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11988099;Dbxref=PMID:11988099
Q8NFD5	514	579	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	514	579	574	633	Compositional bias	Note=Gln-rich
Q8NFD5	514	579	516	516	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8NFD5	514	579	525	525	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:E9Q4N7
Q8NFD5	514	579	557	557	Modified residue	Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24129315;Dbxref=PMID:24129315
Q8NFD5	514	579	531	531	Natural variant	ID=VAR_067675;Note=M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22405089;Dbxref=dbSNP:rs141260832,PMID:22405089
Q8NFD5	579	629	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	579	629	579	579	Alternative sequence	ID=VSP_015226;Note=In isoform 2. Q->QDSGDATWKETFWL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11988099;Dbxref=PMID:11988099
Q8NFD5	579	629	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	579	629	574	633	Compositional bias	Note=Gln-rich
Q8NFD5	748	777	1	750	Alternative sequence	ID=VSP_040800;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11734557;Dbxref=PMID:11734557
Q8NFD5	748	777	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	748	777	684	771	Compositional bias	Note=Ser-rich
Q8NFD5	748	777	771	771	Natural variant	ID=VAR_077456;Note=Found in a patient with short stature%3B unknown pathological significance. S->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26376624;Dbxref=PMID:26376624
Q8NFD5	778	837	2	2236	Chain	ID=PRO_0000200576;Note=AT-rich interactive domain-containing protein 1B
Q8NFD5	778	837	814	814	Natural variant	ID=VAR_036257;Note=In a breast cancer sample%3B somatic mutation. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974

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3'-UTR located exon skipping events that lost miRNA binding sites in ARID1B

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 ARID1B

- 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 ARID1B

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 ARID1B

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 ARID1B

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
HCC	SRSF5	exon_skip_104757	-4.072854e-01	4.731989e-12
IFG	NOVA1	exon_skip_201270	-4.029690e-01	3.348788e-02
IFG	EWSR1	exon_skip_116276	-4.711201e-01	1.138905e-02
IFG	SRSF5	exon_skip_116276	-5.128929e-01	5.255993e-03

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RelatedDrugs for ARID1B

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 ARID1B

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 ARID1B

Gene structures and expression levels for ARID1B

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ARID1B

Open reading frame (ORF) annotation in the exon skipping event for ARID1B

Infer the effects of exon skipping event on protein functional features for ARID1B

3'-UTR located exon skipping events that lost miRNA binding sites in ARID1B

SNVs in the skipped exons for ARID1B

AD stage-associated exon skippint events for ARID1B

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARID1B

Correlation with RNA binding proteins (RBPs) for ARID1B

RelatedDrugs for ARID1B

RelatedDiseases for ARID1B