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

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: human all
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Genomic context

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_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DNA-dependent protein kinase regulates cytosolic double-stranded DNA secretion from irradiated macrophages to increase radiosensitivity of tumors.
Title: DNA-dependent protein kinase regulates cytosolic double-stranded DNA secretion from irradiated macrophages to increase radiosensitivity of tumors.
The DNA-dependent protein kinase catalytic subunit exacerbates endotoxemia-induced myocardial microvascular injury by disrupting the MOTS-c/JNK pathway and inducing profilin-mediated lamellipodia degradation.
Title: The DNA-dependent protein kinase catalytic subunit exacerbates endotoxemia-induced myocardial microvascular injury by disrupting the MOTS-c/JNK pathway and inducing profilin-mediated lamellipodia degradation.
Characterization of novel, severely immunodeficient Prkdc[Deltaex57/Deltaex57] mice.
Title: Characterization of novel, severely immunodeficient Prkdc(Δex57/Δex57) mice.
Chemical inhibition of DNA-PKcs impairs the activation and cytotoxicity of CD4[+] helper and CD8[+] effector T cells.
Title: Chemical inhibition of DNA-PKcs impairs the activation and cytotoxicity of CD4(+) helper and CD8(+) effector T cells.
Susceptibility to adriamycin-induced hepatotoxicity in mice depends on PRKDC polymorphism.
Title: Susceptibility to adriamycin-induced hepatotoxicity in mice depends on PRKDC polymorphism.
Phosphorylation of DNA-PKcs at the S2056 cluster ensures efficient and productive lymphocyte development in XLF-deficient mice.
Title: Phosphorylation of DNA-PKcs at the S2056 cluster ensures efficient and productive lymphocyte development in XLF-deficient mice.
Regulation of DNA-PK activity promotes the progression of TNBC via enhancing the immunosuppressive function of myeloid-derived suppressor cells.
Title: Regulation of DNA-PK activity promotes the progression of TNBC via enhancing the immunosuppressive function of myeloid-derived suppressor cells.
DNA-PKcs interacts with and phosphorylates Fis1 to induce mitochondrial fragmentation in tubular cells during acute kidney injury.
Title: DNA-PKcs interacts with and phosphorylates Fis1 to induce mitochondrial fragmentation in tubular cells during acute kidney injury.
DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells.
Title: DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells.
Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses.
Title: Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses.

Submit: New GeneRIF Correction See all GeneRIFs (103)

Variation

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Alleles

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

Spontaneous (3) 1 citation
Transgenic (1) 1 citation
Targeted (8) 1 citation
Chemically induced (ENU) (22)
Endonuclease-mediated (14) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D87521 (e-PCR)
- UniSTS:160530

RH131824 (e-PCR)
- UniSTS:215107

RH136293 (e-PCR)
- UniSTS:210286

AI326420 (e-PCR)
- UniSTS:180869

RH136614 (e-PCR)
- UniSTS:210594

06.MMHAP95FRB9.seq (e-PCR)
- UniSTS:122872

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

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Preferred Names: DNA-dependent protein kinase catalytic subunit

Names: DNA-PK catalytic subunit; doxorubicin nephropathy; severe combined immunodeficiency

NP_035289.2

EC 2.7.11.1

XP_006521924.1

EC 2.7.11.1

XP_017172381.1

EC 2.7.11.1

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)

NM_011159.2 → NP_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:3719 → 4014

PIKKc_DNA-PK; Catalytic domain of DNA-dependent protein kinase

pfam02259
Location:3024 → 3470

FAT; FAT domain

pfam02260
Location:4097 → 4128

FATC; FATC domain

pfam08163
Location:1812 → 2198

NUC194; NUC194 domain

pfam11728
Location:1766 → 1822

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

NC_000082.7 Reference GRCm39 C57BL/6J

Range

15455698..15660103

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (2) summary

pfam02259
Location:3089 → 3301

FAT; FAT domain

pfam08163
Location:1813 → 2198

NUC194; NUC194 domain
XM_017316892.3 → XP_017172381.1 DNA-dependent protein kinase catalytic subunit isoform X2

Conserved Domains (2) summary

pfam02259
Location:3089 → 3301

FAT; FAT domain

pfam08163
Location:1813 → 2198

NUC194; NUC194 domain