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Prkdc protein kinase, DNA activated, catalytic polypeptide [ Mus musculus (house mouse) ]

Gene ID: 19090, updated on 11-Apr-2024

Summary

Official Symbol
Prkdcprovided by MGI
Official Full Name
protein kinase, DNA activated, catalytic polypeptideprovided by MGI
Primary source
MGI:MGI:104779
See related
Ensembl:ENSMUSG00000022672 AllianceGenome:MGI:104779
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
p460; scid; slip; DNAPK; DNPK1; HYRC1; XRCC7; dxnph; DOXNPH; DNAPDcs; DNA-PKcs
Summary
Enables DNA-dependent protein kinase activity; double-stranded DNA binding activity; and enzyme binding activity. Involved in several processes, including regulation of cellular protein metabolic process; regulation of hematopoietic stem cell differentiation; and regulation of hemopoiesis. Acts upstream of or within several processes, including DNA metabolic process; ectopic germ cell programmed cell death; and immune system development. Located in nucleus. Is expressed in several structures, including central nervous system; neural retina; and thymus primordium. Used to study severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive. Human ortholog(s) of this gene implicated in immunodeficiency 26. Orthologous to human PRKDC (protein kinase, DNA-activated, catalytic subunit). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 1.5), frontal lobe adult (RPKM 1.2) and 27 other tissues See more
Orthologs
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Genomic context

See Prkdc in Genome Data Viewer
Location:
16 10.09 cM; 16 A2
Exon count:
87
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (15455698..15660103)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (15637444..15842239)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene predicted gene 7748 Neighboring gene minichromosome maintenance complex component 4 Neighboring gene STARR-seq mESC enhancer starr_40212 Neighboring gene predicted gene, 52255 Neighboring gene STARR-seq mESC enhancer starr_40215 Neighboring gene STARR-seq mESC enhancer starr_40216 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:15863142-15863251 Neighboring gene STARR-positive B cell enhancer ABC_E5527 Neighboring gene mitotic spindle organizing protein 2 Neighboring gene predicted gene, 41425 Neighboring gene 60S ribosomal protein L30-like

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-dependent protein kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-dependent protein kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables U3 snoRNA binding ISO
Inferred from Sequence Orthology
more info
 
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables histone H2AXS139 kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables kinase activity IEA
Inferred from Electronic Annotation
more info
 
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
enables protein kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein serine/threonine kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within B cell lineage commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within T cell lineage commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within T cell receptor V(D)J recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within V(D)J recombination IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in activation of innate immune response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within brain development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cellular response to insulin stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within double-strand break repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in double-strand break repair ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in double-strand break repair via nonhomologous end joining NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within ectopic germ cell programmed cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within heart development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within immature B cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
 
involved_in immunoglobulin V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within immunoglobulin V(D)J recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within innate immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in intrinsic apoptotic signaling pathway in response to DNA damage IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lymphocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in maturation of 5.8S rRNA ISO
Inferred from Sequence Orthology
more info
 
involved_in mitotic G1 DNA damage checkpoint signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cGAS/STING signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cellular senescence ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of immunoglobulin production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of response to gamma radiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within peptidyl-serine phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in peptidyl-threonine phosphorylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within phosphorylation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of developmental growth ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of erythrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of fibroblast proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of immune system process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of lymphocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of platelet formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within pro-B cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within protein destabilization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of circadian rhythm IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of epithelial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of hematopoietic stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of smooth muscle cell proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to gamma radiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to ionizing radiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within rhythmic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within ribosome biogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in small-subunit processome assembly ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within somitogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in spleen development ISO
Inferred from Sequence Orthology
more info
 
involved_in telomere capping ISO
Inferred from Sequence Orthology
more info
 
involved_in telomere maintenance IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in thymus development ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of DNA-dependent protein kinase complex ISO
Inferred from Sequence Orthology
more info
 
part_of DNA-dependent protein kinase-DNA ligase 4 complex ISO
Inferred from Sequence Orthology
more info
 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
part_of nonhomologous end joining complex ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of protein-DNA complex ISO
Inferred from Sequence Orthology
more info
 
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
 
part_of small-subunit processome ISO
Inferred from Sequence Orthology
more info
 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
DNA-dependent protein kinase catalytic subunit
Names
DNA-PK catalytic subunit
doxorubicin nephropathy
severe combined immunodeficiency
NP_035289.2
XP_006521924.1
XP_017172381.1

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_011159.2NP_035289.2  DNA-dependent protein kinase catalytic subunit

    See identical proteins and their annotated locations for NP_035289.2

    Status: VALIDATED

    Source sequence(s)
    AB007544, AB011543, AK084827, AK137732, AU019811, CT030649
    Consensus CDS
    CCDS27978.1
    UniProtKB/Swiss-Prot
    E9QN15, O88187, P97313, P97928, Q307W9, Q3V2W8, Q8C2A7, Q9Z341
    Related
    ENSMUSP00000023352.8, ENSMUST00000023352.9
    Conserved Domains (5) summary
    cd05172
    Location:37194014
    PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase
    pfam02259
    Location:30243470
    FAT; FAT domain
    pfam02260
    Location:40974128
    FATC; FATC domain
    pfam08163
    Location:18122198
    NUC194; NUC194 domain
    pfam11728
    Location:17661822
    ArAE_1_C; Putative aromatic acid exporter C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    15455698..15660103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006521861.5XP_006521924.1  DNA-dependent protein kinase catalytic subunit isoform X1

    Conserved Domains (2) summary
    pfam02259
    Location:30893301
    FAT; FAT domain
    pfam08163
    Location:18132198
    NUC194; NUC194 domain
  2. XM_017316892.3XP_017172381.1  DNA-dependent protein kinase catalytic subunit isoform X2

    Conserved Domains (2) summary
    pfam02259
    Location:30893301
    FAT; FAT domain
    pfam08163
    Location:18132198
    NUC194; NUC194 domain