ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for VRK3

Gene summary

Gene information	Gene symbol	VRK3
	Gene ID	51231
	Gene name	VRK serine/threonine kinase 3
	Synonyms	-
	Cytomap	19q13.33
	Type of gene	protein-coding
	Description	inactive serine/threonine-protein kinase VRK3serine/threonine-protein kinase VRK3serine/threonine-protein pseudokinase VRK3vaccinia related kinase 3
	Modification date	20200313
	UniProtAcc	A0A024QZI4, M0QX88, M0QXD7, M0QXV1, M0QYA8, M0QYG0, M0QZ79, M0R025, M0R073, M0R164, M0R200, M0R3H2, Q8IV63,
	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 VRK3

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.

ENSG00000105053

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	DOWN	ENST00000593912.5	VRK3-204:protein_coding:VRK3	6.035651e+01	-8.000809e-01	1.379541e-11	1.269454e-09
CB	UP	ENST00000596121.5	VRK3-210:nonsense_mediated_decay:VRK3	1.543316e+01	1.029434e+00	7.346824e-03	2.699755e-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 VRK3

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_101751	chr19	49995205:49995275:49997504:49997570:50000790:50000854	49997504:49997570
exon_skip_14378	chr19	49992860:49992952:49994814:49994919:49995191:49995275	49994814:49994919
exon_skip_16987	chr19	50016024:50016163:50020462:50020647:50025346:50025369	50020462:50020647
exon_skip_175637	chr19	49989696:49989771:49992860:49992952:49994814:49994919	49992860:49992952
exon_skip_180678	chr19	50007778:50007826:50009236:50009385:50015732:50015793	50009236:50009385
exon_skip_199456	chr19	49979083:49979242:49980955:49981013:49988372:49988492	49980955:49981013
exon_skip_208913	chr19	49992860:49992952:49994814:49994919:50000790:50000854	49994814:49994919
exon_skip_244281	chr19	49981700:49982188:49988372:49988492:49989639:49989771	49988372:49988492
exon_skip_256531	chr19	49994863:49994919:49995191:49995275:49997504:49997541	49995191:49995275
exon_skip_267479	chr19	50009236:50009385:50015732:50015793:50016024:50016163	50015732:50015793
exon_skip_42059	chr19	49994863:49994919:49995191:49995275:50000790:50000854	49995191:49995275
exon_skip_46569	chr19	50016024:50016163:50020585:50020647:50025346:50025369	50020585:50020647
exon_skip_53083	chr19	50007778:50007826:50009236:50009385:50016024:50016163	50009236:50009385
exon_skip_73581	chr19	50007778:50007826:50009236:50009289:50016024:50016163	50009236:50009289

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 VRK3

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
ENST00000594948	50020585	50020647	3UTR-3UTR
ENST00000599538	50020585	50020647	3UTR-3UTR
ENST00000316763	49980955	49981013	Frame-shift
ENST00000594948	49980955	49981013	Frame-shift
ENST00000599538	49980955	49981013	Frame-shift
ENST00000316763	49995191	49995275	Frame-shift
ENST00000594948	49995191	49995275	Frame-shift
ENST00000599538	49995191	49995275	Frame-shift
ENST00000316763	49997504	49997570	Frame-shift
ENST00000594948	49997504	49997570	Frame-shift
ENST00000599538	49997504	49997570	Frame-shift
ENST00000316763	49992860	49992952	In-frame
ENST00000594948	49992860	49992952	In-frame
ENST00000599538	49992860	49992952	In-frame
ENST00000316763	50009236	50009385	In-frame
ENST00000594948	50009236	50009385	In-frame
ENST00000599538	50009236	50009385	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
ENST00000316763	49997504	49997570	Frame-shift
ENST00000594948	49997504	49997570	Frame-shift
ENST00000599538	49997504	49997570	Frame-shift
ENST00000316763	50009236	50009385	In-frame
ENST00000594948	50009236	50009385	In-frame
ENST00000599538	50009236	50009385	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
ENST00000594948	50020585	50020647	3UTR-3UTR
ENST00000599538	50020585	50020647	3UTR-3UTR
ENST00000316763	49980955	49981013	Frame-shift
ENST00000594948	49980955	49981013	Frame-shift
ENST00000599538	49980955	49981013	Frame-shift
ENST00000316763	49994814	49994919	Frame-shift
ENST00000594948	49994814	49994919	Frame-shift
ENST00000599538	49994814	49994919	Frame-shift
ENST00000316763	49995191	49995275	Frame-shift
ENST00000594948	49995191	49995275	Frame-shift
ENST00000599538	49995191	49995275	Frame-shift
ENST00000316763	49997504	49997570	Frame-shift
ENST00000594948	49997504	49997570	Frame-shift
ENST00000599538	49997504	49997570	Frame-shift
ENST00000316763	49992860	49992952	In-frame
ENST00000594948	49992860	49992952	In-frame
ENST00000599538	49992860	49992952	In-frame
ENST00000316763	50009236	50009385	In-frame
ENST00000594948	50009236	50009385	In-frame
ENST00000599538	50009236	50009385	In-frame

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Infer the effects of exon skipping event on protein functional features for VRK3

p-ENSG00000105053_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
ENST00000316763	1955	474	50009236	50009385	324	472	46	96
ENST00000594948	1864	474	50009236	50009385	228	376	46	96
ENST00000599538	2143	474	50009236	50009385	805	953	46	96
ENST00000316763	1955	474	49992860	49992952	1055	1146	290	320
ENST00000594948	1864	474	49992860	49992952	959	1050	290	320
ENST00000599538	2143	474	49992860	49992952	1536	1627	290	320

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
ENST00000316763	1955	474	50009236	50009385	324	472	46	96
ENST00000594948	1864	474	50009236	50009385	228	376	46	96
ENST00000599538	2143	474	50009236	50009385	805	953	46	96

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
ENST00000316763	1955	474	50009236	50009385	324	472	46	96
ENST00000594948	1864	474	50009236	50009385	228	376	46	96
ENST00000599538	2143	474	50009236	50009385	805	953	46	96
ENST00000316763	1955	474	49992860	49992952	1055	1146	290	320
ENST00000594948	1864	474	49992860	49992952	959	1050	290	320
ENST00000599538	2143	474	49992860	49992952	1536	1627	290	320

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
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919

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
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846

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
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	47	96	Alternative sequence	ID=VSP_043409;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	54	54	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	55	55	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	59	59	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	82	82	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	83	83	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:23186163;Dbxref=PMID:19690332,PMID:20068231,PMID:21406692,PMID
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	90	90	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	49	64	Motif	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14645249;Dbxref=PMID:14645249
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	46	96	59	59	Natural variant	ID=VAR_041295;Note=S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=dbSNP:rs2033262,PMID:17344846
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	311	315	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	318	324	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	1	474	Chain	ID=PRO_0000086808;Note=Inactive serine/threonine-protein kinase VRK3
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	166	457	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	280	299	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JII
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919
Q8IV63	290	320	304	304	Natural variant	ID=VAR_051684;Note=H->L;Dbxref=dbSNP:rs35261919

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3'-UTR located exon skipping events that lost miRNA binding sites in VRK3

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 VRK3

- 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 VRK3

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 VRK3

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 VRK3

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	RBM3	exon_skip_53083	-4.366580e-01	2.907981e-02
TC	RBM6	exon_skip_42059	4.357399e-01	6.551230e-07
TC	RBM3	exon_skip_53083	-4.387987e-01	6.476056e-09

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RelatedDrugs for VRK3

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 VRK3

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 VRK3

Gene structures and expression levels for VRK3

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for VRK3

Open reading frame (ORF) annotation in the exon skipping event for VRK3

Infer the effects of exon skipping event on protein functional features for VRK3

3'-UTR located exon skipping events that lost miRNA binding sites in VRK3

SNVs in the skipped exons for VRK3

AD stage-associated exon skippint events for VRK3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VRK3

Correlation with RNA binding proteins (RBPs) for VRK3

RelatedDrugs for VRK3

RelatedDiseases for VRK3