ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for BCAS1

Gene summary

Gene information	Gene symbol	BCAS1
	Gene ID	8537
	Gene name	breast carcinoma amplified sequence 1
	Synonyms	AIBC1\|NABC1
	Cytomap	20q13.2
	Type of gene	protein-coding
	Description	breast carcinoma-amplified sequence 1amplified and overexpressed in breast cancernovel amplified in breast cancer 1
	Modification date	20180519
	UniProtAcc	O75363
	Context	PubMed: BCAS1 [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

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Exon skipping events across known transcript of Ensembl for BCAS1 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 BCAS1

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 BCAS1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_358154	20	52557996:52558063:52561464:52561535:52569970:52570234	52561464:52561535	ENSG00000064787.8	ENST00000371440.3,ENST00000448484.1
exon_skip_358156	20	52561464:52561535:52569970:52570234:52583444:52583612	52569970:52570234	ENSG00000064787.8	ENST00000371440.3,ENST00000448484.1
exon_skip_358157	20	52561464:52561535:52569970:52570234:52591927:52591969	52569970:52570234	ENSG00000064787.8	ENST00000371435.2
exon_skip_358158	20	52561464:52561535:52569970:52570234:52601825:52601972	52569970:52570234	ENSG00000064787.8	ENST00000434986.2
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENSG00000064787.8	ENST00000395961.3
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENSG00000064787.8	ENST00000422805.1
exon_skip_358181	20	52569970:52570234:52583444:52583612:52601825:52601972	52583444:52583612	ENSG00000064787.8	ENST00000371440.3,ENST00000448484.1
exon_skip_358184	20	52569970:52570234:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000371435.2
exon_skip_358192	20	52573970:52574036:52583444:52583612:52591927:52591969	52583444:52583612	ENSG00000064787.8	ENST00000395961.3
exon_skip_358196	20	52573970:52574036:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000422805.1
exon_skip_358197	20	52583444:52583612:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000395961.3
exon_skip_358200	20	52601825:52602038:52609050:52609185:52611550:52611595	52609050:52609185	ENSG00000064787.8	ENST00000371440.3,ENST00000448484.1,ENST00000434986.2
exon_skip_358204	20	52674623:52674693:52675185:52675262:52686971:52687030	52675185:52675262	ENSG00000064787.8	ENST00000371440.3,ENST00000371435.2,ENST00000395961.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for BCAS1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_358154	20	52557996:52558063:52561464:52561535:52569970:52570234	52561464:52561535	ENSG00000064787.8	ENST00000448484.1,ENST00000371440.3
exon_skip_358156	20	52561464:52561535:52569970:52570234:52583444:52583612	52569970:52570234	ENSG00000064787.8	ENST00000448484.1,ENST00000371440.3
exon_skip_358157	20	52561464:52561535:52569970:52570234:52591927:52591969	52569970:52570234	ENSG00000064787.8	ENST00000371435.2
exon_skip_358158	20	52561464:52561535:52569970:52570234:52601825:52601972	52569970:52570234	ENSG00000064787.8	ENST00000434986.2
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENSG00000064787.8	ENST00000395961.3
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENSG00000064787.8	ENST00000422805.1
exon_skip_358181	20	52569970:52570234:52583444:52583612:52601825:52601972	52583444:52583612	ENSG00000064787.8	ENST00000448484.1,ENST00000371440.3
exon_skip_358184	20	52569970:52570234:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000371435.2
exon_skip_358192	20	52573970:52574036:52583444:52583612:52591927:52591969	52583444:52583612	ENSG00000064787.8	ENST00000395961.3
exon_skip_358196	20	52573970:52574036:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000422805.1
exon_skip_358197	20	52583444:52583612:52591927:52591969:52601825:52601972	52591927:52591969	ENSG00000064787.8	ENST00000395961.3
exon_skip_358200	20	52601825:52602038:52609050:52609185:52611550:52611595	52609050:52609185	ENSG00000064787.8	ENST00000448484.1,ENST00000371440.3,ENST00000434986.2
exon_skip_358204	20	52674623:52674693:52675185:52675262:52686971:52687030	52675185:52675262	ENSG00000064787.8	ENST00000371440.3,ENST00000371435.2,ENST00000395961.3

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 BCAS1

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
ENST00000395961	52675185	52675262	3UTR-3CDS
ENST00000395961	52573970	52574036	In-frame
ENST00000395961	52583444	52583612	In-frame
ENST00000395961	52591927	52591969	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
ENST00000395961	52675185	52675262	3UTR-3CDS
ENST00000395961	52573970	52574036	In-frame
ENST00000395961	52583444	52583612	In-frame
ENST00000395961	52591927	52591969	In-frame

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Infer the effects of exon skipping event on protein functional features for BCAS1

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
ENST00000395961	3320	584	52591927	52591969	1308	1349	380	394
ENST00000395961	3320	584	52583444	52583612	1350	1517	394	450
ENST00000395961	3320	584	52573970	52574036	1518	1583	450	472

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
ENST00000395961	3320	584	52591927	52591969	1308	1349	380	394
ENST00000395961	3320	584	52583444	52583612	1350	1517	394	450
ENST00000395961	3320	584	52573970	52574036	1518	1583	450	472

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
O75363	380	394	381	394	Alternative sequence	ID=VSP_018521;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	380	394	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	380	394	381	381	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q80YN3
O75363	394	450	381	394	Alternative sequence	ID=VSP_018521;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	394	450	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	394	450	399	399	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q80YN3
O75363	450	472	451	472	Alternative sequence	ID=VSP_018522;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	450	472	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	450	472	472	472	Natural variant	ID=VAR_050691;Note=Q->H;Dbxref=dbSNP:rs35575210

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
O75363	380	394	381	394	Alternative sequence	ID=VSP_018521;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	380	394	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	380	394	381	381	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q80YN3
O75363	394	450	381	394	Alternative sequence	ID=VSP_018521;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	394	450	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	394	450	399	399	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q80YN3
O75363	450	472	451	472	Alternative sequence	ID=VSP_018522;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10857754,ECO:0000303\|PubMed:17974005;Dbxref=PMID:10857754,PMID:17974005
O75363	450	472	1	584	Chain	ID=PRO_0000064859;Note=Breast carcinoma-amplified sequence 1
O75363	450	472	472	472	Natural variant	ID=VAR_050691;Note=Q->H;Dbxref=dbSNP:rs35575210

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SNVs in the skipped exons for BCAS1

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
KIRP	TCGA-GL-A9DC-01	exon_skip_358157 exon_skip_358156 exon_skip_358158	52569971	52570234	52569985	52569991	Frame_Shift_Del	AGCCCCC	-	p.554_556del
LIHC	TCGA-G3-A3CJ-01	exon_skip_358200	52609051	52609185	52609170	52609170	Frame_Shift_Del	T	-	p.S315fs
COAD	TCGA-AZ-4615-01	exon_skip_358204	52675186	52675262	52675232	52675233	Frame_Shift_Ins	-	G	p.Q9fs
BRCA	TCGA-E2-A150-01	exon_skip_358157 exon_skip_358156 exon_skip_358158	52569971	52570234	52570137	52570137	Nonsense_Mutation	G	T	p.S505*
UCEC	TCGA-BS-A0UV-01	exon_skip_358157 exon_skip_358156 exon_skip_358158	52569971	52570234	52570152	52570152	Nonsense_Mutation	G	A	p.R163*
STAD	TCGA-HF-7132-01	exon_skip_358154	52561465	52561535	52561536	52561536	Splice_Site	C	T	.

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

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LXF289_LUNG	52569971	52570234	52570007	52570007	Missense_Mutation	C	A	p.K548N
SNU1040_LARGE_INTESTINE	52569971	52570234	52570036	52570036	Missense_Mutation	C	A	p.G539W
SNU175_LARGE_INTESTINE	52569971	52570234	52570087	52570087	Missense_Mutation	G	A	p.P522S
T47D_BREAST	52569971	52570234	52570112	52570112	Missense_Mutation	C	G	p.K513N
HEC251_ENDOMETRIUM	52569971	52570234	52570152	52570152	Missense_Mutation	G	A	p.S500L
DMS153_LUNG	52569971	52570234	52570155	52570155	Missense_Mutation	G	A	p.S499F
OVK18_OVARY	52569971	52570234	52570219	52570219	Missense_Mutation	C	T	p.E478K
HT3_CERVIX	52569971	52570234	52570219	52570219	Missense_Mutation	C	T	p.E478K
DU145_PROSTATE	52583445	52583612	52583506	52583506	Missense_Mutation	G	T	p.A430E
CL34_LARGE_INTESTINE	52583445	52583612	52583572	52583572	Missense_Mutation	T	C	p.E408G
OVTOKO_OVARY	52591928	52591969	52591931	52591931	Missense_Mutation	C	G	p.E393D
NCIH2452_PLEURA	52591928	52591969	52591942	52591942	Missense_Mutation	C	G	p.G390R
RT4_URINARY_TRACT	52675186	52675262	52675218	52675218	Missense_Mutation	G	T	p.Q14K
NCIH1869_LUNG	52569971	52570234	52570069	52570069	Nonsense_Mutation	G	A	p.Q528*
BXPC3_PANCREAS	52583445	52583612	52583445	52583445	Splice_Site	C	T	p.M450I

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BCAS1

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_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	LGG	rs35575210	chr20:52573971	T/G	3.09e-11
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	LGG	rs35575210	chr20:52573971	T/G	9.21e-11
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	LGG	rs35575210	chr20:52573971	T/G	3.36e-09
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	LGG	rs35575210	chr20:52573971	T/G	4.34e-04
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	PRAD	rs35575210	chr20:52573971	T/G	8.96e-05
exon_skip_358177	20	52569970:52570234:52573970:52574036:52583444:52583612	52573970:52574036	ENST00000395961.3	PRAD	rs35575210	chr20:52573971	T/G	3.94e-04
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	LGG	rs35575210	chr20:52573971	T/G	3.09e-11
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	LGG	rs35575210	chr20:52573971	T/G	9.21e-11
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	LGG	rs35575210	chr20:52573971	T/G	3.36e-09
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	LGG	rs35575210	chr20:52573971	T/G	4.34e-04
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	PRAD	rs35575210	chr20:52573971	T/G	8.96e-05
exon_skip_358178	20	52569970:52570234:52573970:52574036:52591927:52591969	52573970:52574036	ENST00000422805.1	PRAD	rs35575210	chr20:52573971	T/G	3.94e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BCAS1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BCAS1

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RelatedDrugs for BCAS1

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 BCAS1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
BCAS1	C0033578	Prostatic 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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