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    VRK3 VRK serine/threonine kinase 3 [ Homo sapiens (human) ]

    Gene ID: 51231, updated on 2-Mar-2021

    Summary

    Official Symbol
    VRK3provided by HGNC
    Official Full Name
    VRK serine/threonine kinase 3provided by HGNC
    Primary source
    HGNC:HGNC:18996
    See related
    Ensembl:ENSG00000105053
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 36.5), small intestine (RPKM 9.1) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See VRK3 in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    109.20210226 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (49976468..50025535, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50479725..50528629, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene sialic acid binding Ig like lectin 11 Neighboring gene sialic acid binding Ig like lectin 16 Neighboring gene zinc finger protein 473 Neighboring gene uncharacterized LOC400710 Neighboring gene zinc finger protein 420-like

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein phosphatase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein serine/threonine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    negative regulation of ERK1 and ERK2 cascade IEA
    Inferred from Electronic Annotation
    more info
     
    peptidyl-serine phosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of phosphoprotein phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus HDA PubMed 
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    inactive serine/threonine-protein kinase VRK3
    Names
    serine/threonine-protein kinase VRK3
    serine/threonine-protein pseudokinase VRK3
    vaccinia related kinase 3
    NP_001020949.1
    NP_001295349.1
    NP_057524.3
    XP_005259028.1
    XP_005259029.1
    XP_006723300.1
    XP_006723301.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001025778.2NP_001020949.1  inactive serine/threonine-protein kinase VRK3 isoform 2

      See identical proteins and their annotated locations for NP_001020949.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a protein (isoform 2) that is shorter than isoform 1.
      Source sequence(s)
      AC011452, AV706241
      Consensus CDS
      CCDS33076.1
      UniProtKB/Swiss-Prot
      Q8IV63
      Related
      ENSP00000366210.1, ENST00000377011.6
      Conserved Domains (4) summary
      COG0515
      Location:161417
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      cl21453
      Location:105407
      PKc_like; Protein Kinases, catalytic domain
    2. NM_001308420.3NP_001295349.1  inactive serine/threonine-protein kinase VRK3 isoform 3

      See identical proteins and their annotated locations for NP_001295349.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several exons and uses an alternate 3' terminal exon that results in a different 3' UTR and novel 3' coding region compared to variant 1. It encodes isoform 3, which is shorter than and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC023556, BP335032
      Consensus CDS
      CCDS77334.1
      UniProtKB/Swiss-Prot
      Q8IV63
      Related
      ENSP00000472541.1, ENST00000594092.5
      Conserved Domains (5) summary
      COG0515
      Location:211412
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      pfam15087
      Location:82150
      DUF4551; Protein of unknown function (DUF4551)
      cl21453
      Location:155406
      PKc_like; Protein Kinases, catalytic domain
    3. NM_016440.4NP_057524.3  inactive serine/threonine-protein kinase VRK3 isoform 1

      See identical proteins and their annotated locations for NP_057524.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011452, AF514788, AV706241
      Consensus CDS
      CCDS12791.1
      UniProtKB/Swiss-Prot
      Q8IV63
      UniProtKB/TrEMBL
      A0A024QZI4
      Related
      ENSP00000324636.2, ENST00000316763.8
      Conserved Domains (5) summary
      COG0515
      Location:211467
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      pfam15087
      Location:82150
      DUF4551; Protein of unknown function (DUF4551)
      cl21453
      Location:155457
      PKc_like; Protein Kinases, catalytic domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      49976468..50025535 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005258972.4XP_005259029.1  inactive serine/threonine-protein kinase VRK3 isoform X2

      See identical proteins and their annotated locations for XP_005259029.1

      UniProtKB/Swiss-Prot
      Q8IV63
      Related
      ENSP00000470156.1, ENST00000601341.5
      Conserved Domains (4) summary
      COG0515
      Location:161417
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      cl21453
      Location:105407
      PKc_like; Protein Kinases, catalytic domain
    2. XM_005258971.4XP_005259028.1  inactive serine/threonine-protein kinase VRK3 isoform X1

      See identical proteins and their annotated locations for XP_005259028.1

      UniProtKB/Swiss-Prot
      Q8IV63
      UniProtKB/TrEMBL
      A0A024QZI4
      Related
      ENSP00000469880.1, ENST00000599538.5
      Conserved Domains (5) summary
      COG0515
      Location:211467
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      pfam15087
      Location:82150
      DUF4551; Protein of unknown function (DUF4551)
      cl21453
      Location:155457
      PKc_like; Protein Kinases, catalytic domain
    3. XM_006723237.3XP_006723300.1  inactive serine/threonine-protein kinase VRK3 isoform X1

      See identical proteins and their annotated locations for XP_006723300.1

      UniProtKB/Swiss-Prot
      Q8IV63
      UniProtKB/TrEMBL
      A0A024QZI4
      Conserved Domains (5) summary
      COG0515
      Location:211467
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      pfam15087
      Location:82150
      DUF4551; Protein of unknown function (DUF4551)
      cl21453
      Location:155457
      PKc_like; Protein Kinases, catalytic domain
    4. XM_006723238.4XP_006723301.1  inactive serine/threonine-protein kinase VRK3 isoform X2

      See identical proteins and their annotated locations for XP_006723301.1

      UniProtKB/Swiss-Prot
      Q8IV63
      Conserved Domains (4) summary
      COG0515
      Location:161417
      SPS1; Serine/threonine protein kinase [Signal transduction mechanisms]
      pfam12773
      Location:531
      DZR; Double zinc ribbon
      pfam13240
      Location:426
      zinc_ribbon_2; zinc-ribbon domain
      cl21453
      Location:105407
      PKc_like; Protein Kinases, catalytic domain

    RNA

    1. XR_001753697.2 RNA Sequence

    2. XR_001753696.1 RNA Sequence

    3. XR_001753698.2 RNA Sequence

    4. XR_001753695.2 RNA Sequence

    5. XR_002958320.1 RNA Sequence

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