ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PRKCB

Gene summary

Gene information	Gene symbol	PRKCB
	Gene ID	5579
	Gene name	protein kinase C beta
	Synonyms	PKC-beta\|PKCB\|PKCI(2)\|PKCbeta\|PRKCB1\|PRKCB2
	Cytomap	16p12.2-p12.1
	Type of gene	protein-coding
	Description	protein kinase C beta typePKC-Bprotein kinase C, beta 1 polypeptide
	Modification date	20200313
	UniProtAcc	H3BV73, I3L148, I3L1Z0, P05771,
	Context	- 26510741(Altered Blood Gene Expression of Tumor-Related Genes (PRKCB, BECN1, and CDKN2A) in Alzheimer's Disease)

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

Gene	GO ID	GO term	PubMed ID
PRKCB	GO:0010827	regulation of glucose transmembrane transport	25982116
PRKCB	GO:0035408	histone H3-T6 phosphorylation	20228790

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Gene structures and expression levels for PRKCB

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.

ENSG00000166501

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	DOWN	ENST00000321728.12	PRKCB-201:protein_coding:PRKCB	2.000337e+02	-1.053799e+00	5.793895e-04	9.804457e-03
CB	UP	ENST00000647422.1	PRKCB-212:lncRNA:PRKCB	8.452538e-01	1.118848e+00	4.923503e-03	1.942629e-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 PRKCB

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_13564	chr16	24172270:24172361:24174518:24174580:24180790:24180845	24174518:24174580
exon_skip_158746	chr16	24174518:24174580:24180790:24180928:24185111:24185191	24180790:24180928
exon_skip_268745	chr16	24032136:24032247:24035419:24035547:24092791:24092839	24035419:24035547
exon_skip_292817	chr16	24123835:24123981:24154684:24154857:24172270:24172361	24154684:24154857
exon_skip_292975	chr16	24035535:24035547:24092791:24092947:24094163:24094297	24092791:24092947
exon_skip_7091	chr16	24112973:24113069:24123835:24123981:24154684:24154857	24123835:24123981
exon_skip_82834	chr16	24154684:24154857:24172270:24172361:24174518:24174580	24172270:24172361

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 PRKCB

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
ENST00000321728	24092791	24092947	Frame-shift
ENST00000321728	24172270	24172361	Frame-shift
ENST00000321728	24180790	24180928	Frame-shift
ENST00000321728	24035419	24035547	In-frame
ENST00000321728	24123835	24123981	In-frame
ENST00000321728	24154684	24154857	In-frame
ENST00000321728	24174518	24174580	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
ENST00000321728	24092791	24092947	Frame-shift
ENST00000321728	24172270	24172361	Frame-shift
ENST00000321728	24035419	24035547	In-frame
ENST00000321728	24123835	24123981	In-frame
ENST00000321728	24174518	24174580	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
ENST00000321728	24092791	24092947	Frame-shift
ENST00000321728	24172270	24172361	Frame-shift
ENST00000321728	24180790	24180928	Frame-shift
ENST00000321728	24035419	24035547	In-frame
ENST00000321728	24123835	24123981	In-frame
ENST00000321728	24154684	24154857	In-frame
ENST00000321728	24174518	24174580	In-frame

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

p-ENSG00000166501_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
ENST00000321728	2724	671	24035419	24035547	595	722	134	176
ENST00000321728	2724	671	24123835	24123981	1113	1258	306	355
ENST00000321728	2724	671	24154684	24154857	1260	1432	355	413
ENST00000321728	2724	671	24174518	24174580	1526	1587	444	464

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
ENST00000321728	2724	671	24035419	24035547	595	722	134	176
ENST00000321728	2724	671	24123835	24123981	1113	1258	306	355
ENST00000321728	2724	671	24174518	24174580	1526	1587	444	464

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
ENST00000321728	2724	671	24035419	24035547	595	722	134	176
ENST00000321728	2724	671	24123835	24123981	1113	1258	306	355
ENST00000321728	2724	671	24154684	24154857	1260	1432	355	413
ENST00000321728	2724	671	24174518	24174580	1526	1587	444	464

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
P05771	134	176	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	134	176	173	260	Domain	Note=C2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
P05771	134	176	144	144	Natural variant	ID=VAR_042304;Note=In a colorectal adenocarcinoma sample%3B somatic mutation. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs764534677,PMID:17344846
P05771	134	176	101	151	Zinc finger	Note=Phorbol-ester/DAG-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00226
P05771	306	355	342	351	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	354	361	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	306	355	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	306	355	311	311	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	314	314	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	324	324	Modified residue	Note=Phosphothreonine%3B by autocatalysis;Ontology_term=ECO:0000250,ECO:0000255;evidence=ECO:0000250\|UniProtKB:P68403,ECO:0000255
P05771	306	355	348	356	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	354	361	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	364	374	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	406	411	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	413	421	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	371	371	Binding site	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	355	413	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	375	380	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	384	394	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	348	356	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	444	464	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	440	459	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E

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
P05771	134	176	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	134	176	173	260	Domain	Note=C2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
P05771	134	176	144	144	Natural variant	ID=VAR_042304;Note=In a colorectal adenocarcinoma sample%3B somatic mutation. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs764534677,PMID:17344846
P05771	134	176	101	151	Zinc finger	Note=Phorbol-ester/DAG-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00226
P05771	306	355	342	351	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	354	361	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	306	355	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	306	355	311	311	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	314	314	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	324	324	Modified residue	Note=Phosphothreonine%3B by autocatalysis;Ontology_term=ECO:0000250,ECO:0000255;evidence=ECO:0000250\|UniProtKB:P68403,ECO:0000255
P05771	306	355	348	356	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	444	464	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	440	459	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E

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
P05771	134	176	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	134	176	173	260	Domain	Note=C2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
P05771	134	176	144	144	Natural variant	ID=VAR_042304;Note=In a colorectal adenocarcinoma sample%3B somatic mutation. V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs764534677,PMID:17344846
P05771	134	176	101	151	Zinc finger	Note=Phorbol-ester/DAG-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00226
P05771	306	355	342	351	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	354	361	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	306	355	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	306	355	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	306	355	311	311	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	314	314	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
P05771	306	355	324	324	Modified residue	Note=Phosphothreonine%3B by autocatalysis;Ontology_term=ECO:0000250,ECO:0000255;evidence=ECO:0000250\|UniProtKB:P68403,ECO:0000255
P05771	306	355	348	356	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	354	361	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	364	374	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	406	411	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	413	421	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	371	371	Binding site	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	355	413	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	355	413	375	380	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	384	394	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E
P05771	355	413	348	356	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	2	671	Chain	ID=PRO_0000055684;Note=Protein kinase C beta type
P05771	444	464	342	600	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P05771	444	464	440	459	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I0E

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

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 PRKCB

- 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 PRKCB

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 PRKCB

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 PRKCB

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for PRKCB

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P05771	approved\|investigational	DB08862	Cholecystokinin	small molecule	P05771

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RelatedDiseases for PRKCB

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 PRKCB

Gene structures and expression levels for PRKCB

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

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

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

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

SNVs in the skipped exons for PRKCB

AD stage-associated exon skippint events for PRKCB

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

Correlation with RNA binding proteins (RBPs) for PRKCB

RelatedDrugs for PRKCB

RelatedDiseases for PRKCB