ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for BRCA1

Gene summary

Gene information	Gene symbol	BRCA1
	Gene ID	672
	Gene name	BRCA1 DNA repair associated
	Synonyms	BRCAI\|BRCC1\|BROVCA1\|FANCS\|IRIS\|PNCA4\|PPP1R53\|PSCP\|RNF53
	Cytomap	17q21.31
	Type of gene	protein-coding
	Description	breast cancer type 1 susceptibility proteinBRCA1/BRCA2-containing complex, subunit 1Fanconi anemia, complementation group SRING finger protein 53breast and ovarian cancer susceptibility protein 1breast cancer 1, early onsetearly onset breast cancer
	Modification date	20200329
	UniProtAcc	A0A024R1V0, A0A024R1V7, A0A024R1V8, A0A024R1W0, A0A024R1Y0, A0A024R1Y1, A0A024R1Z8, A0A068BC97, A0A068BC99, A0A068BCA1, A0A068BCA4, A0A068BCB2, A0A068BCB6, A0A068BCB8, A0A068BDT2, A0A068BDT6, A0A068BDT9, A0A068BDU7, A0A068BDV0, A0A068BEU9, A0A068BEV3, A0A068BEV6, A0A068BEW5, A0A068BFV4, A0A068BFV9, A0A068BFW2, A0A068BFX7, A0A068BFY0, A0A068BI32, A0A068BI36, A0A068BI38, A0A068BI42, A0A068BI44, A0A068BI53, A0A068BI55, A0A0A0MSN1, A0A0A1ESW9, A0A0F6RAC9, A0A0F6RAD1, A0A0F6RAU2, A0A0F6TMQ0, A0A0F6TMZ3, A0A0F6TN19, A0A0F6TN86, A0A0F6TNH6, A0A0F7G9Q0, A0A0F7G9S0, A0A0F7GA54, A0A0F7GBC5, A0A0G3FC22, A0A0G3FCF2, A0A0K0PU86, A0A0K0PU93, A0A0K0PUK0, A0A0K0QR99, A0A0K0QRF6, A0A0N9E014, A0A0R9RX69, A0A0U1RRA9, A0A0U4JDF9, A0A0U4JQJ0, A0A140HIE5, A0A140HIE9, A0A290YM93, A0A2P1MAS5, A0A2R4U2D7, A0A2R4U2D8, A0A2R4U2F8, A0A2R8Y587, A0A2R8Y6Y9, A0A2R8Y7V5, A0A345G161, A0A345G162, A0A345G163, A0A345G165, A0A345G166, A0A386IN29, A0A386IN33, A0A386IN34, A0A386IN41, A0A386IN42, A0A386IN52, A0A386IN53, A0A386IN60, A0A386INH9, A0A386INJ5, A0A386INN6, A0A386INP3, A0A386INP8, A0A386INQ5, A0A386IPA8, A0A386IPB0, A0A386IPK6, A0A386IPL0, A0A386IPW1, A0A386IPW2, A0A386IPW3, A0A386IPW4, A0A386IPW7, A0A386IPY5, A0A386IPY7, A0A386IPY8, A0A386IQ58, A0A386IQ64, A0A386IQ66, A0A386L1T8, A0A3G1CIL2, A0A3G1CIL4, A0A3G1CIM0, A0A3Q8UCB1, A0A3S8V3K0, A0A482E6X8, A0A482E729, A0A494C182, A0A4P8DKQ8, A0A4P8DL17, A0A4P8DLA0, A0A649U8H0, A0A649UB25, B7ZA85, C4PFY7, C6YB45, C6YB47, C9IZW4, E7ENB7, E7EQW4, E7EUM2, E7EWN5, E9PC22, E9PH68, G1UI37, G3XAC3, G4V4Z7, G4V4Z8, G4V500, G4V502, G4V503, G8I0D8, H0Y850, H0Y881, H0Y8B8, H0Y8D8, H6TXS1, K4JTS0, K4JUB1, K4JUB6, K4JWE8, K4JXS7, K4JXT2, K4K7U9, K4K7V3, K7EJW3, K7EPC7, P38398, Q05BZ9, Q3B890, Q3B891, Q3LRH8, Q3YB49, Q3YB50, Q3YB51, Q3YB52, Q3YB53, Q4EW25, Q5U3B7, Q5XLT4, Q5YLB2, Q64FK1, Q64FK2, Q64FK3, Q6P671, Q7KYU6, Q7Z606, Q8IU58, Q8IZK2, Q8IZK3, Q8IZK4, Q8IZT7, Q92897, Q9NQR3, Q9UE29,
	Context

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

Gene	GO ID	GO term	PubMed ID
BRCA1	GO:0000724	double-strand break repair via homologous recombination	17349954
BRCA1	GO:0006301	postreplication repair	17349954
BRCA1	GO:0006302	double-strand break repair	22186889
BRCA1	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	14654789
BRCA1	GO:0016567	protein ubiquitination	17349954
BRCA1	GO:0031398	positive regulation of protein ubiquitination	15965487
BRCA1	GO:0035066	positive regulation of histone acetylation	20820192
BRCA1	GO:0043627	response to estrogen	8895509
BRCA1	GO:0045892	negative regulation of transcription, DNA-templated	16288014
BRCA1	GO:0045893	positive regulation of transcription, DNA-templated	20160719
BRCA1	GO:0045944	positive regulation of transcription by RNA polymerase II	16331276
BRCA1	GO:0051571	positive regulation of histone H3-K4 methylation	20820192
BRCA1	GO:0051573	negative regulation of histone H3-K9 methylation	20820192
BRCA1	GO:0051865	protein autoubiquitination	12890688\|20351172
BRCA1	GO:0070512	positive regulation of histone H4-K20 methylation	20820192
BRCA1	GO:0071158	positive regulation of cell cycle arrest	21102443
BRCA1	GO:0071681	cellular response to indole-3-methanol	10868478
BRCA1	GO:0085020	protein K6-linked ubiquitination	12890688\|20351172
BRCA1	GO:2000617	positive regulation of histone H3-K9 acetylation	20820192
BRCA1	GO:2000620	positive regulation of histone H4-K16 acetylation	20820192

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Gene structures and expression levels for BRCA1

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.

ENSG00000012048

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

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 BRCA1

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_116640	chr17	43076488:43076611:43079334:43079399:43082404:43082575	43079334:43079399
exon_skip_11860	chr17	43115726:43115779:43124017:43124115:43125271:43125300	43124017:43124115
exon_skip_137537	chr17	43076537:43076611:43079334:43079399:43082404:43082572	43079334:43079399
exon_skip_156769	chr17	43104868:43104956:43106456:43106533:43115726:43115779	43106456:43106533
exon_skip_165671	chr17	43076537:43076611:43082404:43082575:43090944:43091032	43082404:43082575
exon_skip_174291	chr17	43095846:43095922:43097244:43097289:43099775:43099877	43097244:43097289
exon_skip_183108	chr17	43047643:43047703:43049121:43049194:43051063:43051117	43049121:43049194
exon_skip_197333	chr17	43076488:43076614:43079334:43079399:43082404:43082572	43079334:43079399
exon_skip_209723	chr17	43074331:43074521:43076488:43076611:43082404:43082575	43076488:43076611
exon_skip_219130	chr17	43104868:43104956:43106478:43106533:43115726:43115779	43106478:43106533
exon_skip_222664	chr17	43106478:43106533:43110465:43110580:43115726:43115779	43110465:43110580
exon_skip_241039	chr17	43076488:43076614:43079334:43079399:43082404:43082575	43079334:43079399
exon_skip_272366	chr17	43074331:43074521:43076488:43076614:43082404:43082575	43076488:43076614
exon_skip_283012	chr17	43094744:43094860:43095846:43095922:43097244:43097289	43095846:43095922
exon_skip_39178	chr17	43106456:43106533:43110465:43110580:43115726:43115779	43110465:43110580
exon_skip_55671	chr17	43106456:43106533:43115726:43115779:43124017:43124115	43115726:43115779
exon_skip_63731	chr17	43063874:43063951:43067608:43067695:43070928:43071066	43067608:43067695
exon_skip_86603	chr17	43076488:43076611:43079334:43079399:43082404:43082572	43079334:43079399

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 BRCA1

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
ENST00000357654	43049121	43049194	Frame-shift
ENST00000357654	43067608	43067695	Frame-shift
ENST00000357654	43076488	43076614	Frame-shift
ENST00000357654	43106456	43106533	In-frame
ENST00000357654	43115726	43115779	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
ENST00000357654	43106456	43106533	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
ENST00000357654	43124017	43124115	3UTR-3CDS
ENST00000357654	43049121	43049194	Frame-shift
ENST00000357654	43067608	43067695	Frame-shift
ENST00000357654	43095846	43095922	Frame-shift
ENST00000357654	43097244	43097289	Frame-shift
ENST00000357654	43106456	43106533	In-frame

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Infer the effects of exon skipping event on protein functional features for BRCA1

p-ENSG00000012048_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
ENST00000357654	7224	1863	43115726	43115779	313	365	27	44
ENST00000357654	7224	1863	43106456	43106533	367	443	45	70

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
ENST00000357654	7224	1863	43106456	43106533	367	443	45	70

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
ENST00000357654	7224	1863	43106456	43106533	367	443	45	70

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
P38398	27	44	1	47	Alternative sequence	ID=VSP_057569;Note=In isoform 8. Missing
P38398	27	44	25	27	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	27	44	1	1863	Chain	ID=PRO_0000055830;Note=Breast cancer type 1 susceptibility protein
P38398	27	44	30	30	Natural variant	ID=VAR_035947;Note=In a breast cancer sample%3B somatic mutation. L->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974
P38398	27	44	24	65	Zinc finger	Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00175
P38398	45	70	1	47	Alternative sequence	ID=VSP_057569;Note=In isoform 8. Missing
P38398	45	70	64	1863	Alternative sequence	ID=VSP_047891;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
P38398	45	70	54	58	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	1	1863	Chain	ID=PRO_0000055830;Note=Breast cancer type 1 susceptibility protein
P38398	45	70	46	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	45	45	Natural variant	ID=VAR_070459;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. K->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs769650474,PMID:23867111
P38398	45	70	61	61	Natural variant	ID=VAR_007757;Note=In BC and ovarian cancer%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12938098,ECO:0000269\|PubMed:14746861,ECO:0000269\|Pu
P38398	45	70	64	64	Natural variant	ID=VAR_007758;Note=In BC%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:23867111,ECO:0000269\|PubMed:7894491,ECO:0000269\|PubMed:9482581,ECO:0000269\|PubMed:9528852;Dbxref=dbSNP:rs8
P38398	45	70	64	64	Natural variant	ID=VAR_007759;Note=C->Y;Dbxref=dbSNP:rs55851803
P38398	45	70	67	67	Natural variant	ID=VAR_070460;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs80357102,PMID:23867111
P38398	45	70	62	64	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	70	72	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	24	65	Zinc finger	Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00175

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
P38398	45	70	1	47	Alternative sequence	ID=VSP_057569;Note=In isoform 8. Missing
P38398	45	70	64	1863	Alternative sequence	ID=VSP_047891;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
P38398	45	70	54	58	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	1	1863	Chain	ID=PRO_0000055830;Note=Breast cancer type 1 susceptibility protein
P38398	45	70	46	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	45	45	Natural variant	ID=VAR_070459;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. K->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs769650474,PMID:23867111
P38398	45	70	61	61	Natural variant	ID=VAR_007757;Note=In BC and ovarian cancer%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12938098,ECO:0000269\|PubMed:14746861,ECO:0000269\|Pu
P38398	45	70	64	64	Natural variant	ID=VAR_007758;Note=In BC%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:23867111,ECO:0000269\|PubMed:7894491,ECO:0000269\|PubMed:9482581,ECO:0000269\|PubMed:9528852;Dbxref=dbSNP:rs8
P38398	45	70	64	64	Natural variant	ID=VAR_007759;Note=C->Y;Dbxref=dbSNP:rs55851803
P38398	45	70	67	67	Natural variant	ID=VAR_070460;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs80357102,PMID:23867111
P38398	45	70	62	64	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	70	72	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	24	65	Zinc finger	Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00175

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
P38398	45	70	1	47	Alternative sequence	ID=VSP_057569;Note=In isoform 8. Missing
P38398	45	70	64	1863	Alternative sequence	ID=VSP_047891;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.4
P38398	45	70	54	58	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	1	1863	Chain	ID=PRO_0000055830;Note=Breast cancer type 1 susceptibility protein
P38398	45	70	46	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	45	45	Natural variant	ID=VAR_070459;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. K->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs769650474,PMID:23867111
P38398	45	70	61	61	Natural variant	ID=VAR_007757;Note=In BC and ovarian cancer%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12938098,ECO:0000269\|PubMed:14746861,ECO:0000269\|Pu
P38398	45	70	64	64	Natural variant	ID=VAR_007758;Note=In BC%3B no interaction with BAP1. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:23867111,ECO:0000269\|PubMed:7894491,ECO:0000269\|PubMed:9482581,ECO:0000269\|PubMed:9528852;Dbxref=dbSNP:rs8
P38398	45	70	64	64	Natural variant	ID=VAR_007759;Note=C->Y;Dbxref=dbSNP:rs55851803
P38398	45	70	67	67	Natural variant	ID=VAR_070460;Note=In BC%3B unknown pathological significance%3B functionally neutral in vitro. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23867111;Dbxref=dbSNP:rs80357102,PMID:23867111
P38398	45	70	62	64	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	70	72	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JM7
P38398	45	70	24	65	Zinc finger	Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00175

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3'-UTR located exon skipping events that lost miRNA binding sites in BRCA1

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 BRCA1

- 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 BRCA1

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 BRCA1

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 BRCA1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for BRCA1

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 BRCA1

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 BRCA1

Gene structures and expression levels for BRCA1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for BRCA1

Open reading frame (ORF) annotation in the exon skipping event for BRCA1

Infer the effects of exon skipping event on protein functional features for BRCA1

3'-UTR located exon skipping events that lost miRNA binding sites in BRCA1

SNVs in the skipped exons for BRCA1

AD stage-associated exon skippint events for BRCA1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BRCA1

Correlation with RNA binding proteins (RBPs) for BRCA1

RelatedDrugs for BRCA1

RelatedDiseases for BRCA1