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Aliases for VRK3 Gene

Aliases for VRK3 Gene

  • Vaccinia Related Kinase 3 2 3 5
  • Serine/Threonine-Protein Pseudokinase VRK3 4
  • Vaccinia-Related Kinase 3 4

External Ids for VRK3 Gene

Previous GeneCards Identifiers for VRK3 Gene

  • GC19M055155
  • GC19M055171
  • GC19M050479
  • GC19M046855

Summaries for VRK3 Gene

Entrez Gene Summary for VRK3 Gene

  • This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. In both human and mouse, this gene has substitutions at several residues within the ATP binding motifs that in other kinases have been shown to be required for catalysis. In vitro assays indicate the protein lacks phosphorylation activity. The protein, however, likely retains its substrate binding capability. This gene is widely expressed in human tissues and its protein localizes to the nucleus. Alternative splicing results in multiple transcripts encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for VRK3 Gene

VRK3 (Vaccinia Related Kinase 3) is a Protein Coding gene. Diseases associated with VRK3 include Vaccinia. Among its related pathways are Innate Immune System and RET signaling. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein serine/threonine kinase activity. An important paralog of this gene is VRK1.

UniProtKB/Swiss-Prot for VRK3 Gene

  • Inactive kinase that suppresses ERK activity by promoting phosphatase activity of DUSP3 which specifically dephosphorylates and inactivates ERK in the nucleus.

Additional gene information for VRK3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VRK3 Gene

Genomics for VRK3 Gene

GeneHancer (GH) Regulatory Elements for VRK3 Gene

Promoters and enhancers for VRK3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I050022 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 572.3 +1.2 1196 4.5 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 ZNF473 VRK3 POLD1 PTOV1-AS2 SNORD35A NUP62 SNORD35B ALDH16A1 PNKP IRF3
GH19I049589 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.8 +434.0 433974 5.8 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 PRR12 NOSIP PIR34329 NUP62 POLD1 IRF3 ENSG00000268047 ALDH16A1 SNORD35A SNORD35B
GH19I049987 Enhancer 1.1 ENCODE 32.3 +38.7 38718 0.2 MLX ZFP64 DMAP1 IRF4 SLC30A9 ZNF213 E2F8 ZNF143 NFYC MEF2D NUP62 PRR12 PTOV1-AS2 POLD1 SNORD35A IRF3 PIH1D1 SNORD35B ALDH16A1 SNRNP70
GH19I050003 Enhancer 1.1 Ensembl ENCODE 32.2 +21.7 21662 1.9 HDAC1 HDGF ATF1 INSM2 BATF IRF4 ZNF766 ZNF366 FOS IKZF2 VRK3 DKKL1 ZNF473 PTOV1 SCAF1 IL4I1 NUP62 ATF5 SIGLEC16 SIGLEC11
GH19I049486 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 12.2 +535.8 535777 7.5 ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 SNORD35A RPL13A GC19P049514 GC19P049531 GC19P049554 GC19P049556 GC19P049559 GC19P049561 PIR54526 PIR58998
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VRK3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VRK3 gene promoter:

Genomic Locations for VRK3 Gene

Genomic Locations for VRK3 Gene
chr19:49,976,467-50,026,017
(GRCh38/hg38)
Size:
49,551 bases
Orientation:
Minus strand
chr19:50,479,724-50,529,203
(GRCh37/hg19)

Genomic View for VRK3 Gene

Genes around VRK3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VRK3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VRK3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VRK3 Gene

Proteins for VRK3 Gene

  • Protein details for VRK3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IV63-VRK3_HUMAN
    Recommended name:
    Inactive serine/threonine-protein kinase VRK3
    Protein Accession:
    Q8IV63
    Secondary Accessions:
    • A6NEG5
    • A8KA53
    • Q502Y2
    • Q9P2V8

    Protein attributes for VRK3 Gene

    Size:
    474 amino acids
    Molecular mass:
    52881 Da
    Quaternary structure:
    • Interacts with DUSP3 (By similarity). Interacts with RAN.

    Three dimensional structures from OCA and Proteopedia for VRK3 Gene

    Alternative splice isoforms for VRK3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VRK3 Gene

Post-translational modifications for VRK3 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for VRK3 (VRK3)
  • Santa Cruz Biotechnology (SCBT) Antibodies for VRK3

No data available for DME Specific Peptides for VRK3 Gene

Domains & Families for VRK3 Gene

Gene Families for VRK3 Gene

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for VRK3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IV63

UniProtKB/Swiss-Prot:

VRK3_HUMAN :
  • Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily.
Family:
  • Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily.
genes like me logo Genes that share domains with VRK3: view

Function for VRK3 Gene

Molecular function for VRK3 Gene

UniProtKB/Swiss-Prot Function:
Inactive kinase that suppresses ERK activity by promoting phosphatase activity of DUSP3 which specifically dephosphorylates and inactivates ERK in the nucleus.

Phenotypes From GWAS Catalog for VRK3 Gene

Gene Ontology (GO) - Molecular Function for VRK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IEA --
GO:0004674 protein serine/threonine kinase activity IBA --
GO:0005515 protein binding IPI 25609649
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
genes like me logo Genes that share ontologies with VRK3: view
genes like me logo Genes that share phenotypes with VRK3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for VRK3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VRK3 Gene

Localization for VRK3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VRK3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VRK3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VRK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IBA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with VRK3: view

Pathways & Interactions for VRK3 Gene

genes like me logo Genes that share pathways with VRK3: view

Pathways by source for VRK3 Gene

2 Cell Signaling Technology pathways for VRK3 Gene
1 GeneGo (Thomson Reuters) pathway for VRK3 Gene

Gene Ontology (GO) - Biological Process for VRK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA --
GO:0008360 regulation of cell shape IBA --
GO:0016310 phosphorylation IEA --
GO:0018105 peptidyl-serine phosphorylation IBA --
GO:0032516 positive regulation of phosphoprotein phosphatase activity IEA --
genes like me logo Genes that share ontologies with VRK3: view

No data available for SIGNOR curated interactions for VRK3 Gene

Drugs & Compounds for VRK3 Gene

(1) Drugs for VRK3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for VRK3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with VRK3: view

Transcripts for VRK3 Gene

Unigene Clusters for VRK3 Gene

Vaccinia related kinase 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for VRK3

Alternative Splicing Database (ASD) splice patterns (SP) for VRK3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^
SP1: - - - - -
SP2: - - -
SP3: - - -
SP4: - - -
SP5: - -
SP6: - - - -
SP7: - - - - -
SP8: - - - -
SP9: - - - - -
SP10: - -
SP11: -
SP12: - -
SP13: - - - - - - -
SP14:
SP15:

ExUns: 18 ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for VRK3 Gene

GeneLoc Exon Structure for
VRK3
ECgene alternative splicing isoforms for
VRK3

Expression for VRK3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VRK3 Gene

mRNA differential expression in normal tissues according to GTEx for VRK3 Gene

This gene is overexpressed in Testis (x5.5).

Protein differential expression in normal tissues from HIPED for VRK3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.1), Testis (17.1), and CD8 Tcells (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VRK3 Gene



Protein tissue co-expression partners for VRK3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VRK3 Gene:

VRK3

SOURCE GeneReport for Unigene cluster for VRK3 Gene:

Hs.443330

Evidence on tissue expression from TISSUES for VRK3 Gene

  • Nervous system(4.9)
  • Liver(4.2)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with VRK3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VRK3 Gene

Orthologs for VRK3 Gene

This gene was present in the common ancestor of animals.

Orthologs for VRK3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VRK3 33 34
  • 98.87 (n)
dog
(Canis familiaris)
Mammalia VRK3 33 34
  • 83.81 (n)
cow
(Bos Taurus)
Mammalia VRK3 33 34
  • 83.56 (n)
mouse
(Mus musculus)
Mammalia Vrk3 33 16 34
  • 81.53 (n)
rat
(Rattus norvegicus)
Mammalia Vrk3 33
  • 81.09 (n)
oppossum
(Monodelphis domestica)
Mammalia VRK3 34
  • 46 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 19 (a)
ManyToMany
-- 34
  • 11 (a)
ManyToMany
chicken
(Gallus gallus)
Aves VRK3 34
  • 45 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VRK3 34
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vrk3 33
  • 51.92 (n)
Str.7094 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.25500 33
zebrafish
(Danio rerio)
Actinopterygii vrk3 33 34
  • 50.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta ball 34
  • 16 (a)
ManyToMany
CG8878 34
  • 11 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea vrk-1 34
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6830 34
  • 32 (a)
OneToMany
Species where no ortholog for VRK3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VRK3 Gene

ENSEMBL:
Gene Tree for VRK3 (if available)
TreeFam:
Gene Tree for VRK3 (if available)

Paralogs for VRK3 Gene

Variants for VRK3 Gene

Sequence variations from dbSNP and Humsavar for VRK3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000032734 -- 50,010,128(-) C/T intron_variant
rs1000053675 -- 50,014,214(-) C/T intron_variant
rs1000141066 -- 49,978,776(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000165731 -- 50,023,278(-) C/T intron_variant
rs1000245914 -- 50,005,713(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VRK3 Gene

Variant ID Type Subtype PubMed ID
nsv1065753 CNV gain 25217958
nsv1067191 CNV gain 25217958
nsv1140251 OTHER inversion 24896259
nsv458722 CNV gain 19166990
nsv473187 CNV novel sequence insertion 20440878
nsv579912 CNV gain 21841781
nsv579913 CNV gain 21841781
nsv819518 CNV gain 19587683
nsv9739 CNV gain+loss 18304495
nsv1065648 CNV gain 25217958
esv3644635 CNV gain 21293372
esv3644630 CNV gain 21293372
esv29129 CNV loss 19812545
esv2751796 CNV gain 17911159
dgv54n68 CNV loss 17160897
dgv3622n100 CNV gain 25217958

Variation tolerance for VRK3 Gene

Residual Variation Intolerance Score: 79.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.13; 87.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VRK3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VRK3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VRK3 Gene

Disorders for VRK3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VRK3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
vaccinia
- elite association - COSMIC cancer census association via MalaCards
Search VRK3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VRK3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VRK3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VRK3 Gene

Publications for VRK3 Gene

  1. Characterization of three paralogous members of the Mammalian vaccinia related kinase family. (PMID: 14645249) Nichols RJ … Traktman P (The Journal of biological chemistry 2004) 3 4 22 58
  2. Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities. (PMID: 18617507) Sanz-García M … Lazo PA (Molecular & cellular proteomics : MCP 2008) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Vaccinia-related kinase 3 (VRK3) sets the circadian period and amplitude by affecting the subcellular localization of clock proteins in mammalian cells. (PMID: 28412365) Park N … Kim EY (Biochemical and biophysical research communications 2017) 3 58

Products for VRK3 Gene

  • Addgene plasmids for VRK3

Sources for VRK3 Gene

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