ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CACNB4

Gene summary

Gene information	Gene symbol	CACNB4
	Gene ID	785
	Gene name	calcium voltage-gated channel auxiliary subunit beta 4
	Synonyms	CAB4\|CACNLB4\|EA5\|EIG9\|EJM\|EJM4\|EJM6
	Cytomap	2q23.3
	Type of gene	protein-coding
	Description	voltage-dependent L-type calcium channel subunit beta-4calcium channel voltage-dependent subunit beta 4dihydropyridine-sensitive L-type, calcium channel beta-4 subunit
	Modification date	20200326
	UniProtAcc	A0A1B0GTA9, A0A1B0GTF6, A0A1B0GTH0, A0A1B0GTK1, A0A1B0GTL1, A0A1B0GTN2, A0A1B0GTN8, A0A1B0GTP5, A0A1B0GTP6, A0A1B0GTS4, A0A1B0GTX2, A0A1B0GTX6, A0A1B0GTX8, A0A1B0GU05, A0A1B0GU07, A0A1B0GU32, A0A1B0GU42, A0A1B0GU53, A0A1B0GUI5, A0A1B0GUI8, A0A1B0GUJ7, A0A1B0GUK3, A0A1B0GUK4, A0A1B0GUM9, A0A1B0GUU5, A0A1B0GUU8, A0A1B0GUW8, A0A1B0GV16, A0A1B0GVB2, A0A1B0GVF0, A0A1B0GVG1, A0A1B0GVP7, A0A1B0GVT6, A0A1B0GVU5, A0A1B0GW58, A0A1B0GW63, A0A1B0GW81, A0A1B0GWF9, A0A1B0GWG5, A0A1B0GXG0, A0A1C7CYX2, C9J224, E7DBM8, E7EN11, H0Y476, O00305, Q53S65, Q580I4, Q9NZA2,
	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 CACNB4

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.

ENSG00000182389

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
CB	UP	ENST00000637550.1	CACNB4-258:nonsense_mediated_decay:CACNB4	3.409137e+00	3.655715e+00	6.988099e-10	3.244705e-08
CB	UP	ENST00000636390.1	CACNB4-224:nonsense_mediated_decay:CACNB4	2.610650e+00	1.444454e+00	7.361272e-07	1.154164e-05
CB	UP	ENST00000638040.1	CACNB4-270:protein_coding:CACNB4	2.894965e+00	3.406890e+00	2.892187e-06	3.698695e-05
CB	UP	ENST00000434468.2	CACNB4-205:protein_coding:CACNB4	1.595157e+00	2.321969e+00	5.593792e-06	6.437793e-05
CB	UP	ENST00000637007.1	CACNB4-240:nonsense_mediated_decay:CACNB4	8.454554e-01	1.782709e+00	1.729201e-05	1.675940e-04
CB	UP	ENST00000637491.1	CACNB4-253:nonsense_mediated_decay:CACNB4	6.944133e+00	1.300129e+00	2.584029e-05	2.349851e-04
CB	UP	ENST00000636664.1	CACNB4-230:nonsense_mediated_decay:CACNB4	1.454292e+00	2.373589e+00	3.986001e-04	2.379191e-03
CB	UP	ENST00000636350.1	CACNB4-222:protein_coding:CACNB4	1.208431e+02	1.333599e+00	3.016135e-03	1.296552e-02
CB	UP	ENST00000636831.1	CACNB4-236:retained_intron:CACNB4	4.407565e+01	1.656591e+00	5.499525e-03	2.129558e-02
CB	UP	ENST00000470066.2	CACNB4-207:retained_intron:CACNB4	4.218253e+00	1.928154e+00	1.145967e-02	3.887405e-02
CB	UP	ENST00000637535.1	CACNB4-256:nonsense_mediated_decay:CACNB4	3.522598e+00	1.583808e+00	1.152608e-02	3.905964e-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 CACNB4

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_10031	chr2	151870531:151870611:151870842:151870902:151872417:151872493	151870842:151870902
exon_skip_108976	chr2	151883251:151883370:151970281:151970426:151971545:151971704	151970281:151970426
exon_skip_109902	chr2	151855224:151855375:151860711:151860820:151870531:151870611	151860711:151860820
exon_skip_131043	chr2	151860711:151860820:151870531:151870611:151870842:151870861	151870531:151870611
exon_skip_131791	chr2	151841903:151842088:151853448:151853543:151855224:151855375	151853448:151853543
exon_skip_132990	chr2	151860711:151860820:151869177:151870611:151870842:151870861	151869177:151870611
exon_skip_155175	chr2	151872417:151872493:151874920:151874970:151876426:151876556	151874920:151874970
exon_skip_170033	chr2	151883251:151883370:151971545:151971700:151973669:151973933	151971545:151971700
exon_skip_180293	chr2	151860711:151860820:151869177:151869193:151870531:151870611	151869177:151869193
exon_skip_197106	chr2	151841903:151842088:151870531:151870611:151870842:151870861	151870531:151870611
exon_skip_207509	chr2	151876426:151876556:151880800:151880922:151883251:151883370	151880800:151880922
exon_skip_211433	chr2	151855224:151855375:151870531:151870611:151872417:151872493	151870531:151870611
exon_skip_212428	chr2	151860711:151860820:151870531:151870611:151872417:151872493	151870531:151870611
exon_skip_217198	chr2	151841903:151842088:151853448:151853564:151855224:151855375	151853448:151853564
exon_skip_217304	chr2	151870531:151870611:151870842:151870861:151872417:151872493	151870842:151870861
exon_skip_235018	chr2	151860711:151860820:151872417:151872493:151876426:151876556	151872417:151872493
exon_skip_256492	chr2	151860711:151860820:151869177:151869235:151870531:151870611	151869177:151869235
exon_skip_260408	chr2	151883251:151883370:151967537:151967610:151971545:151971704	151967537:151967610
exon_skip_26949	chr2	151841903:151842088:151855224:151855375:151870531:151870611	151855224:151855375
exon_skip_287008	chr2	151883251:151883370:151971545:151971704:152098330:152098413	151971545:151971704
exon_skip_296058	chr2	151860711:151860820:151869177:151872493:151876426:151876556	151869177:151872493
exon_skip_41745	chr2	151855224:151855375:151860711:151860820:151872417:151872493	151860711:151860820
exon_skip_44019	chr2	151860711:151860820:151870842:151870861:151872417:151872493	151870842:151870861
exon_skip_52031	chr2	151860711:151860820:151869177:151869735:151870531:151870611	151869177:151869735
exon_skip_79669	chr2	151883251:151883370:151971545:151971704:151973669:151973928	151971545:151971704

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 CACNB4

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
ENST00000539935	151869177	151869235	Frame-shift
ENST00000539935	151870842	151870861	Frame-shift
ENST00000539935	151853448	151853543	In-frame
ENST00000539935	151880800	151880922	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
ENST00000539935	151869177	151869235	Frame-shift
ENST00000539935	151870842	151870861	Frame-shift
ENST00000539935	151853448	151853543	In-frame
ENST00000539935	151880800	151880922	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
ENST00000539935	151869177	151869235	Frame-shift
ENST00000539935	151870842	151870861	Frame-shift
ENST00000539935	151853448	151853543	In-frame
ENST00000539935	151880800	151880922	In-frame

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Infer the effects of exon skipping event on protein functional features for CACNB4

p-ENSG00000182389_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
ENST00000539935	8395	520	151880800	151880922	732	853	89	129
ENST00000539935	8395	520	151853448	151853543	1485	1579	340	371

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
ENST00000539935	8395	520	151880800	151880922	732	853	89	129
ENST00000539935	8395	520	151853448	151853543	1485	1579	340	371

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
ENST00000539935	8395	520	151880800	151880922	732	853	89	129
ENST00000539935	8395	520	151853448	151853543	1485	1579	340	371

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
O00305	89	129	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4
O00305	89	129	92	161	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O00305	89	129	104	104	Natural variant	ID=VAR_013669;Note=In EA5%3B associated with susceptibility to EIG9. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10762541;Dbxref=dbSNP:rs1805031,PMID:10762541
O00305	340	371	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4

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
O00305	89	129	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4
O00305	89	129	92	161	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O00305	89	129	104	104	Natural variant	ID=VAR_013669;Note=In EA5%3B associated with susceptibility to EIG9. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10762541;Dbxref=dbSNP:rs1805031,PMID:10762541
O00305	340	371	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4

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
O00305	89	129	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4
O00305	89	129	92	161	Domain	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192
O00305	89	129	104	104	Natural variant	ID=VAR_013669;Note=In EA5%3B associated with susceptibility to EIG9. C->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10762541;Dbxref=dbSNP:rs1805031,PMID:10762541
O00305	340	371	1	520	Chain	ID=PRO_0000144060;Note=Voltage-dependent L-type calcium channel subunit beta-4

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3'-UTR located exon skipping events that lost miRNA binding sites in CACNB4

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 CACNB4

- 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 CACNB4

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 CACNB4

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_217304	rs2461835	chr2:151885470	1.636405e-04	1.377584e-02
HCC	exon_skip_217304	rs7558481	chr2:151960679	1.935095e-04	1.576108e-02
HCC	exon_skip_217304	rs12992504	chr2:151967716	2.418668e-04	1.897774e-02
HCC	exon_skip_217304	rs7602165	chr2:151966808	2.440663e-04	1.910597e-02
HCC	exon_skip_217304	rs6729612	chr2:151923653	2.448250e-04	1.915326e-02
HCC	exon_skip_217304	rs3768653	chr2:151860114	5.128138e-04	3.463207e-02

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Correlation with RNA binding proteins (RBPs) for CACNB4

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_256492	-4.550945e-01	1.233918e-07
CB	TRA2A	exon_skip_256492	-6.603583e-01	9.647138e-17
CB	HNRNPA2B1	exon_skip_256492	-5.142982e-01	1.167532e-09
CB	NUP42	exon_skip_256492	5.515032e-01	3.822434e-11
CB	TARDBP	exon_skip_132990	-5.341316e-01	1.186485e-10
CB	SAMD4A	exon_skip_132990	-5.483682e-01	2.995330e-11
CB	U2AF2	exon_skip_132990	-4.014610e-01	3.177315e-06
CB	CNOT4	exon_skip_132990	-5.555915e-01	1.452845e-11
CB	PCBP4	exon_skip_132990	4.778508e-01	1.529177e-08
CB	TRA2A	exon_skip_132990	-4.769056e-01	1.647165e-08
CB	RC3H1	exon_skip_132990	-4.723879e-01	2.342449e-08
CB	FUBP1	exon_skip_132990	-5.293765e-01	1.852666e-10
CB	HNRNPA2B1	exon_skip_132990	-5.516760e-01	2.155182e-11
CB	HNRNPC	exon_skip_132990	-5.111298e-01	9.622136e-10
CB	NUP42	exon_skip_132990	4.288982e-01	5.422097e-07
CB	EIF4G2	exon_skip_132990	-4.382753e-01	2.856316e-07
CB	PTBP1	exon_skip_132990	-4.072784e-01	2.212469e-06
CB	SRSF1	exon_skip_132990	-4.351846e-01	3.535725e-07
CB	SRSF4	exon_skip_132990	-5.380544e-01	8.171737e-11
CB	HNRNPF	exon_skip_132990	-4.394926e-01	2.624524e-07
CB	RBM4	exon_skip_132990	-4.951973e-01	3.753103e-09
CB	CNOT4	exon_skip_207509	-4.456806e-01	8.547109e-08
CB	RBM45	exon_skip_207509	5.770544e-01	4.416561e-13
CB	NUP42	exon_skip_207509	4.699279e-01	1.309740e-08
CB	PTBP1	exon_skip_207509	-4.328427e-01	2.178543e-07
HCC	RBMS2	exon_skip_7166	-4.073889e-01	2.473129e-11
HCC	RBFOX2	exon_skip_7166	4.370548e-01	5.431487e-13
HCC	SAMD4A	exon_skip_7166	-4.044948e-01	3.519523e-11
HCC	KHDRBS2	exon_skip_7166	5.436528e-01	1.784703e-20
HCC	RBM24	exon_skip_7166	4.567953e-01	3.454916e-14
HCC	HNRNPA0	exon_skip_7166	4.099379e-01	1.807390e-11
HCC	PUM1	exon_skip_7166	4.001230e-01	5.959130e-11
HCC	HNRNPD	exon_skip_7166	4.013377e-01	5.151955e-11
HCC	RALYL	exon_skip_7166	5.507844e-01	4.475958e-21
HCC	PTBP1	exon_skip_7166	-4.120407e-01	1.392622e-11
HCC	EIF4B	exon_skip_7166	5.045409e-01	2.017452e-17
HCC	RBM5	exon_skip_217304	-4.400298e-01	2.913072e-13
HCC	RBM6	exon_skip_79669	4.402936e-01	6.758167e-13
HCC	PTBP1	exon_skip_79669	4.924340e-01	3.468307e-16
IFG	RBM5	exon_skip_217304	-4.411762e-01	1.877043e-02
IFG	NUP42	exon_skip_79669	-4.211613e-01	3.213719e-02
IFG	EWSR1	exon_skip_79669	-4.773161e-01	1.367121e-02
PCC	RBFOX2	exon_skip_7166	4.829909e-01	2.912134e-12
PCC	MSI1	exon_skip_7166	-4.194795e-01	2.529285e-09
PCC	ELAVL4	exon_skip_7166	5.360635e-01	3.147318e-15
PCC	FXR2	exon_skip_7166	4.157120e-01	3.622259e-09
PCC	RBM47	exon_skip_7166	-4.202149e-01	2.356821e-09
PCC	HNRNPA0	exon_skip_7166	4.248739e-01	1.500681e-09
PCC	PUM1	exon_skip_7166	4.570063e-01	5.497337e-11
PCC	RALYL	exon_skip_7166	5.221691e-01	2.113133e-14
PCC	PTBP1	exon_skip_7166	-4.283390e-01	1.067932e-09
PCC	SRSF9	exon_skip_7166	4.060260e-01	8.938394e-09
PCC	ESRP2	exon_skip_7166	-4.807731e-01	3.778811e-12
PCC	NOVA1	exon_skip_7166	4.260000e-01	1.344176e-09
PCC	RBM3	exon_skip_79669	-4.394363e-01	6.767299e-10
STG	RBM24	exon_skip_79669	-4.493443e-01	9.537596e-05

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RelatedDrugs for CACNB4

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
O00305	approved\|investigational	DB00393	Nimodipine	small molecule	O00305
O00305	approved	DB00661	Verapamil	small molecule	O00305
O00305	approved	DB04855	Dronedarone	small molecule	O00305

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RelatedDiseases for CACNB4

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 CACNB4

Gene structures and expression levels for CACNB4

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CACNB4

Open reading frame (ORF) annotation in the exon skipping event for CACNB4

Infer the effects of exon skipping event on protein functional features for CACNB4

3'-UTR located exon skipping events that lost miRNA binding sites in CACNB4

SNVs in the skipped exons for CACNB4

AD stage-associated exon skippint events for CACNB4

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CACNB4

Correlation with RNA binding proteins (RBPs) for CACNB4

RelatedDrugs for CACNB4

RelatedDiseases for CACNB4