Prkdc protein kinase, DNA-activated, catalytic subunit [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prkdcprovided by RGD
Official Full Name: protein kinase, DNA-activated, catalytic subunitprovided by RGD
Primary source: RGD:1308982
See related: EnsemblRapid:ENSRNOG00000025028 AllianceGenome:RGD:1308982
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including RNA polymerase II-specific DNA-binding transcription factor binding activity; nucleic acid binding activity; and protein serine/threonine kinase activity. Involved in several processes, including hematopoietic or lymphoid organ development; negative regulation of metabolic process; and negative regulation of response to gamma radiation. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of several cellular components, including nucleus; protein-DNA complex; and small-subunit processome. Predicted to be active in chromatin and nucleus. Used to study severe combined immunodeficiency. 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, Dec 2024]
Expression: Biased expression in Thymus (RPKM 176.7), Spleen (RPKM 150.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q23

Exon count:: 87

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (98544952..98762499, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (85040790..85258357, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (89293547..89510948, complement)

Chromosome 11 - NC_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DNA repair protein DNA-PK protects PC12 cells from oxidative stress-induced apoptosis involving AKT phosphorylation.
Title: DNA repair protein DNA-PK protects PC12 cells from oxidative stress-induced apoptosis involving AKT phosphorylation.
Abeta mediates inhibition of the DNA-PK-dependent nonhomologous end joining pathway contributing to the accumulation of DSBs that, if not efficiently repaired, may lead to the neuronal loss observed in AD.
Title: Sublethal doses of β-amyloid peptide abrogate DNA-dependent protein kinase activity.
the pancreatic duodenal homeobox-1 protein is regulated by DNA-dependent protein kinase
Title: Regulation of the pancreatic duodenal homeobox-1 protein by DNA-dependent protein kinase.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
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 Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables U3 snoRNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	ISO Inferred from Sequence Orthology more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
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 ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell lineage commitment	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell differentiation in thymus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell lineage commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell receptor V(D)J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in activation of innate immune response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
involved_in cellular response to insulin stimulus	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ectopic germ cell programmed cell death	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immature B cell differentiation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymphocyte differentiation	ISO Inferred from Sequence Orthology more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of immunoglobulin production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of response to gamma radiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peptidyl-serine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in 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 positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of developmental growth	IMP Inferred from Mutant Phenotype more info	PubMed
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fibroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of immune system process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of lymphocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of platelet formation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of translation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pro-B cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of hematopoietic stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to activity	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to gamma radiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in small-subunit processome assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somitogenesis	ISO Inferred from Sequence Orthology more info
involved_in spleen development	IMP Inferred from Mutant Phenotype more info	PubMed
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	ISO Inferred from Sequence Orthology more info
involved_in thymus development	IMP Inferred from Mutant Phenotype more info	PubMed

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
is_active_in 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	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: protein kinase, DNA activated, catalytic polypeptide

NP_001101797.2

EC 2.7.11.1

XP_008767155.1

EC 2.7.11.1

XP_017453703.1

EC 2.7.11.1

XP_038944465.1

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_001108327.2 → NP_001101797.2 DNA-dependent protein kinase catalytic subunit

Status: VALIDATED

Source sequence(s)

BF400782, JAXUCZ010000011

UniProtKB/TrEMBL

A0A8I6ADM3, D3ZTN0

Related

ENSRNOP00000037412.6, ENSRNOT00000035247.9

Conserved Domains (5) summary

COG5032
Location:3457 → 4013

TEL1; Phosphatidylinositol kinase or protein kinase, PI-3 family [Signal transduction mechanisms]

cd05172
Location:3717 → 4012

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

pfam02259
Location:3087 → 3471

FAT; FAT domain

pfam02260
Location:4096 → 4126

FATC; FATC domain

pfam08163
Location:1813 → 2196

NUC194; NUC194 domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086029.1 Reference GRCr8

Range

98544952..98762499 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039088537.2 → XP_038944465.1 DNA-dependent protein kinase catalytic subunit isoform X2

UniProtKB/TrEMBL

A0A8I5ZT26

Conserved Domains (5) summary

COG5032
Location:3314 → 3870

TEL1; Phosphatidylinositol kinase or protein kinase, PI-3 family [Signal transduction mechanisms]

cd05172
Location:3574 → 3869

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

pfam02259
Location:2944 → 3328

FAT; FAT domain

pfam02260
Location:3953 → 3983

FATC; FATC domain

pfam08163
Location:1670 → 2053

NUC194; NUC194 domain
XM_008768933.4 → XP_008767155.1 DNA-dependent protein kinase catalytic subunit isoform X1

See identical proteins and their annotated locations for XP_008767155.1

UniProtKB/TrEMBL

A0A8I6ADM3

Conserved Domains (4) summary

cd05172
Location:3717 → 4011

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

pfam02259
Location:3022 → 3471

FAT; FAT domain

pfam02260
Location:4095 → 4125

FATC; FATC domain

pfam08163
Location:1811 → 2196

NUC194; NUC194 domain
XM_017598214.3 → XP_017453703.1 DNA-dependent protein kinase catalytic subunit isoform X3

UniProtKB/TrEMBL

A0A8I5ZT26