ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CAMK4

Gene summary

Gene information	Gene symbol	CAMK4
	Gene ID	814
	Gene name	calcium/calmodulin dependent protein kinase IV
	Synonyms	CaMK IV\|CaMK-GR\|CaMKIV\|caMK
	Cytomap	5q22.1
	Type of gene	protein-coding
	Description	calcium/calmodulin-dependent protein kinase type IVCAM kinase IVCAM kinase- GRbrain Ca(2+)-calmodulin-dependent protein kinase type IVbrain Ca++-calmodulin-dependent protein kinase type IVcalcium/calmodulin-dependent protein kinase type IV catalytic
	Modification date	20200322
	UniProtAcc	D6RCD6, D6RE65, D6REY7, Q16566,
	Context	- 29089994(Genistein protects hippocampal neurons against injury by regulating calcium/calmodulin dependent protein kinase IV protein levels in Alzheimer's disease model rats)

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

Gene	GO ID	GO term	PubMed ID
CAMK4	GO:0045893	positive regulation of transcription, DNA-templated	8855261

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Gene structures and expression levels for CAMK4

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.

ENSG00000152495

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	ENST00000509645.1	CAMK4-208:retained_intron:CAMK4	1.488832e+01	-9.274427e-01	2.085004e-07	2.695955e-05
CB	UP	ENST00000504544.5	CAMK4-204:nonsense_mediated_decay:CAMK4	2.110046e+01	1.201872e+00	1.409439e-17	1.952791e-14
CB	UP	ENST00000515231.5	CAMK4-213:nonsense_mediated_decay:CAMK4	8.348831e+00	1.798964e+00	1.362940e-05	1.368475e-04
CB	UP	ENST00000514007.5	CAMK4-212:nonsense_mediated_decay:CAMK4	2.263353e+00	9.946537e-01	7.967978e-05	6.114904e-04

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 CAMK4

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_110207	chr5	111446686:111446776:111449129:111449203:111473311:111473324	111449129:111449203
exon_skip_13231	chr5	111344024:111344102:111394710:111394782:111446686:111446776	111394710:111394782
exon_skip_194821	chr5	111449129:111449203:111473311:111473386:111478381:111478507	111473311:111473386
exon_skip_242146	chr5	111473311:111473386:111478381:111478507:111482785:111482816	111478381:111478507
exon_skip_251371	chr5	111344024:111344102:111374850:111374912:111394710:111394749	111374850:111374912
exon_skip_252044	chr5	111344024:111344102:111374850:111374912:111394710:111394782	111374850:111374912
exon_skip_256305	chr5	111374850:111374912:111376860:111376942:111394710:111394782	111376860:111376942
exon_skip_39736	chr5	111344048:111344102:111374850:111374912:111394710:111394749	111374850:111374912
exon_skip_56277	chr5	111224464:111224644:111344024:111344102:111394710:111394749	111344024:111344102
exon_skip_65569	chr5	111224464:111224644:111344024:111344102:111374850:111374912	111344024:111344102
exon_skip_70093	chr5	111374850:111374912:111376860:111376942:111394710:111394749	111376860:111376942
exon_skip_77291	chr5	111394710:111394782:111446686:111446776:111449129:111449193	111446686:111446776
exon_skip_93421	chr5	111344024:111344102:111374850:111374912:111376860:111376942	111374850:111374912

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 CAMK4

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
ENST00000282356	111344024	111344102	Frame-shift
ENST00000512453	111344024	111344102	Frame-shift
ENST00000282356	111376860	111376942	Frame-shift
ENST00000512453	111376860	111376942	Frame-shift
ENST00000282356	111446686	111446776	Frame-shift
ENST00000512453	111446686	111446776	Frame-shift
ENST00000282356	111473311	111473386	Frame-shift
ENST00000512453	111473311	111473386	Frame-shift
ENST00000282356	111478381	111478507	Frame-shift
ENST00000512453	111478381	111478507	Frame-shift
ENST00000282356	111374850	111374912	In-frame
ENST00000512453	111374850	111374912	In-frame
ENST00000282356	111449129	111449203	In-frame
ENST00000512453	111449129	111449203	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
ENST00000282356	111344024	111344102	Frame-shift
ENST00000512453	111344024	111344102	Frame-shift
ENST00000282356	111376860	111376942	Frame-shift
ENST00000512453	111376860	111376942	Frame-shift
ENST00000282356	111449129	111449203	In-frame
ENST00000512453	111449129	111449203	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
ENST00000282356	111344024	111344102	Frame-shift
ENST00000512453	111344024	111344102	Frame-shift
ENST00000282356	111376860	111376942	Frame-shift
ENST00000512453	111376860	111376942	Frame-shift
ENST00000282356	111446686	111446776	Frame-shift
ENST00000512453	111446686	111446776	Frame-shift
ENST00000282356	111473311	111473386	Frame-shift
ENST00000512453	111473311	111473386	Frame-shift
ENST00000282356	111478381	111478507	Frame-shift
ENST00000512453	111478381	111478507	Frame-shift
ENST00000282356	111374850	111374912	In-frame
ENST00000512453	111374850	111374912	In-frame
ENST00000282356	111449129	111449203	In-frame
ENST00000512453	111449129	111449203	In-frame

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Infer the effects of exon skipping event on protein functional features for CAMK4

p-ENSG00000152495_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
ENST00000282356	12257	473	111374850	111374912	640	701	80	101
ENST00000512453	1657	473	111374850	111374912	341	402	80	101
ENST00000282356	12257	473	111449129	111449203	950	1023	184	208
ENST00000512453	1657	473	111449129	111449203	651	724	184	208

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
ENST00000282356	12257	473	111449129	111449203	950	1023	184	208
ENST00000512453	1657	473	111449129	111449203	651	724	184	208

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
ENST00000282356	12257	473	111374850	111374912	640	701	80	101
ENST00000512453	1657	473	111374850	111374912	341	402	80	101
ENST00000282356	12257	473	111449129	111449203	950	1023	184	208
ENST00000512453	1657	473	111449129	111449203	651	724	184	208

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
Q16566	80	101	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	80	101	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	80	101	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	80	101	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	80	101	91	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	80	101	91	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261

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
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261

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
Q16566	80	101	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	80	101	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	80	101	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	80	101	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	80	101	91	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	80	101	91	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	1	473	Chain	ID=PRO_0000086106;Note=Calcium/calmodulin-dependent protein kinase type IV
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	46	300	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Glycosylation	Note=O-linked (GlcNAc) serine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	205	207	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2W4O
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	200	200	Modified residue	Note=Phosphothreonine%3B by CaMKK1 and CaMKK2;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15143065,ECO:0000269\|PubMed:19506079,ECO:0000269\|PubMed:8702940;Dbxref=PMID:15143065,PMID:19506079,PMID:8702940
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	189	189	Mutagenesis	Note=Increases phosphorylation of CREB1 2-fold. Decreases total O-linked glycosylation 2-fold. Increases ATP-binding affinity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19506079;Dbxref=PMID:19506079
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261
Q16566	184	208	200	200	Mutagenesis	Note=Loss of activation by CaMKK1 or CaMKK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8855261;Dbxref=PMID:8855261

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3'-UTR located exon skipping events that lost miRNA binding sites in CAMK4

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 CAMK4

- 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 CAMK4

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 CAMK4

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 CAMK4

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	CNOT4	exon_skip_56277	-6.200547e-01	1.898692e-16
CB	FXR2	exon_skip_56277	-4.722852e-01	2.959413e-09
CB	TRA2A	exon_skip_56277	-4.453017e-01	2.811403e-08
CB	RBM4B	exon_skip_56277	-5.191037e-01	3.627712e-11
CB	HNRNPL	exon_skip_13231	-4.738559e-01	3.817536e-09

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RelatedDrugs for CAMK4

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 CAMK4

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 CAMK4

Gene structures and expression levels for CAMK4

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CAMK4

Open reading frame (ORF) annotation in the exon skipping event for CAMK4

Infer the effects of exon skipping event on protein functional features for CAMK4

3'-UTR located exon skipping events that lost miRNA binding sites in CAMK4

SNVs in the skipped exons for CAMK4

AD stage-associated exon skippint events for CAMK4

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CAMK4

Correlation with RNA binding proteins (RBPs) for CAMK4

RelatedDrugs for CAMK4

RelatedDiseases for CAMK4