prkdc protein kinase, DNA-activated, catalytic subunit [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: prkdcprovided by ZNC
Official Full Name: protein kinase, DNA-activated, catalytic subunitprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-9008
See related: Ensembl:ENSDARG00000075083 AllianceGenome:ZFIN:ZDB-GENE-030131-9008
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fa96e12; wu:fa96e12
Summary: Predicted to enable protein serine/threonine kinase activity. Acts upstream of or within B cell differentiation; T cell receptor V(D)J recombination; and immunoglobulin heavy chain V-D-J recombination. Predicted to be located in nucleolus. Predicted to be active in nucleus. Is expressed in kidney and spleen. 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, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 86

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (41348723..41396811, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (41068650..41116738, complement)

Chromosome 7 - NC_007118.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

zebrafish with mutations in recombination activating gene 2 (rag2), DNA-dependent protein kinase (prkdc), and janus kinase 3 (jak3), were characterized.
Title: Single-cell imaging of normal and malignant cell engraftment into optically clear prkdc-null SCID zebrafish.

Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

fa96e12.x1 (e-PCR)
- UniSTS:189731

G45317 (e-PCR)
- UniSTS:106119

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell differentiation	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
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining	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 immunoglobulin heavy chain V-D-J recombination	IMP Inferred from Mutant Phenotype more info	PubMed
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 phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-dependent protein kinase catalytic subunit

Names: protein kinase, DNA-activated, catalytic polypeptide

XP_009301676.1

EC 2.7.11.1

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007118.7 Reference GRCz11 Primary Assembly

Range

41348723..41396811 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009303401.2 → XP_009301676.1 DNA-dependent protein kinase catalytic subunit

UniProtKB/TrEMBL

A0A8M3B1E3, E7F4J7

Related

ENSDARP00000051678.4, ENSDART00000051679.8

Conserved Domains (4) summary

cd05172
Location:3713 → 4006

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

pfam02259
Location:3070 → 3465

FAT; FAT domain

pfam02260
Location:4089 → 4119

FATC; FATC domain

pfam08163
Location:1830 → 2211

NUC194; NUC194 domain