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

Gene ID: 51231, updated on 1-Mar-2024

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 MIM:619771; AllianceGenome:HGNC:18996
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
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Genomic context

See VRK3 in Genome Data Viewer
Location:
19q13.33
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49976468..50025372, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52976576..53025796, complement)
105.20220307 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 uncharacterized LOC124904745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50474918-50475418 Neighboring gene sialic acid binding Ig like lectin 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14970 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50490479-50490646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50497521-50498022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50498023-50498522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10949 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50527935-50528436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14973 Neighboring gene zinc finger protein 473 Neighboring gene uncharacterized LOC124904744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50554133-50554813 Neighboring gene ZNF473 cis regulating lncRNA 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein phosphatase binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in negative regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
 
involved_in peptidyl-serine phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in skeletal muscle tissue development IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

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
XP_047294854.1
XP_047294855.1
XP_047294856.1
XP_047294857.1
XP_047294858.1
XP_047294859.1
XP_054177127.1
XP_054177128.1
XP_054177129.1
XP_054177130.1
XP_054177131.1
XP_054177132.1
XP_054177133.1
XP_054177134.1
XP_054177135.1
XP_054177136.1

NCBI Reference Sequences (RefSeq)

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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/TrEMBL
    M0R073
    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/TrEMBL
    M0QYA8
    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
    A6NEG5, A8KA53, Q502Y2, Q8IV63, Q9P2V8
    UniProtKB/TrEMBL
    M0QYA8
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    49976468..50025372 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005258972.5XP_005259029.1  inactive serine/threonine-protein kinase VRK3 isoform X3

    See identical proteins and their annotated locations for XP_005259029.1

    UniProtKB/TrEMBL
    M0R073
    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
    A6NEG5, A8KA53, Q502Y2, Q8IV63, Q9P2V8
    UniProtKB/TrEMBL
    M0QYA8
    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_006723237.4XP_006723300.1  inactive serine/threonine-protein kinase VRK3 isoform X1

    See identical proteins and their annotated locations for XP_006723300.1

    UniProtKB/Swiss-Prot
    A6NEG5, A8KA53, Q502Y2, Q8IV63, Q9P2V8
    UniProtKB/TrEMBL
    M0QYA8
    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_006723238.5XP_006723301.1  inactive serine/threonine-protein kinase VRK3 isoform X3

    See identical proteins and their annotated locations for XP_006723301.1

    UniProtKB/TrEMBL
    M0R073
    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
  5. XM_047438900.1XP_047294856.1  inactive serine/threonine-protein kinase VRK3 isoform X4

    UniProtKB/TrEMBL
    M0R073
  6. XM_047438898.1XP_047294854.1  inactive serine/threonine-protein kinase VRK3 isoform X2

    UniProtKB/TrEMBL
    M0QYA8
  7. XM_047438901.1XP_047294857.1  inactive serine/threonine-protein kinase VRK3 isoform X4

    UniProtKB/TrEMBL
    M0R073
  8. XM_047438899.1XP_047294855.1  inactive serine/threonine-protein kinase VRK3 isoform X2

    UniProtKB/TrEMBL
    M0QYA8
  9. XM_047438902.1XP_047294858.1  inactive serine/threonine-protein kinase VRK3 isoform X5

    UniProtKB/TrEMBL
    B4E0U5
    Related
    ENSP00000469802.1, ENST00000596121.5
  10. XM_047438903.1XP_047294859.1  inactive serine/threonine-protein kinase VRK3 isoform X5

    UniProtKB/TrEMBL
    B4E0U5

RNA

  1. XR_007066860.1 RNA Sequence

  2. XR_007066859.1 RNA Sequence

  3. XR_007066855.1 RNA Sequence

  4. XR_007066857.1 RNA Sequence

  5. XR_007066858.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    52976576..53025796 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321156.1XP_054177131.1  inactive serine/threonine-protein kinase VRK3 isoform X3

    UniProtKB/TrEMBL
    M0R073
  2. XM_054321152.1XP_054177127.1  inactive serine/threonine-protein kinase VRK3 isoform X1

    UniProtKB/Swiss-Prot
    A6NEG5, A8KA53, Q502Y2, Q8IV63, Q9P2V8
    UniProtKB/TrEMBL
    M0QYA8
  3. XM_054321153.1XP_054177128.1  inactive serine/threonine-protein kinase VRK3 isoform X1

    UniProtKB/Swiss-Prot
    A6NEG5, A8KA53, Q502Y2, Q8IV63, Q9P2V8
    UniProtKB/TrEMBL
    M0QYA8
  4. XM_054321157.1XP_054177132.1  inactive serine/threonine-protein kinase VRK3 isoform X3

    UniProtKB/TrEMBL
    M0R073
  5. XM_054321158.1XP_054177133.1  inactive serine/threonine-protein kinase VRK3 isoform X4

    UniProtKB/TrEMBL
    M0R073
  6. XM_054321154.1XP_054177129.1  inactive serine/threonine-protein kinase VRK3 isoform X2

    UniProtKB/TrEMBL
    M0QYA8
  7. XM_054321159.1XP_054177134.1  inactive serine/threonine-protein kinase VRK3 isoform X4

    UniProtKB/TrEMBL
    M0R073
  8. XM_054321155.1XP_054177130.1  inactive serine/threonine-protein kinase VRK3 isoform X2

    UniProtKB/TrEMBL
    M0QYA8
  9. XM_054321160.1XP_054177135.1  inactive serine/threonine-protein kinase VRK3 isoform X5

    UniProtKB/TrEMBL
    B4E0U5
  10. XM_054321161.1XP_054177136.1  inactive serine/threonine-protein kinase VRK3 isoform X5

    UniProtKB/TrEMBL
    B4E0U5

RNA

  1. XR_008485164.1 RNA Sequence

  2. XR_008485163.1 RNA Sequence

  3. XR_008485160.1 RNA Sequence

  4. XR_008485161.1 RNA Sequence

  5. XR_008485162.1 RNA Sequence