prkdc.L protein kinase, DNA-activated, catalytic subunit L homeolog [Xenopus laevis (African clawed frog)] - Gene

Summary

Official Symbol: prkdc.L
Official Full Name: protein kinase, DNA-activated, catalytic subunit L homeolog
Primary source: Xenbase:XB-GENE-866368
Locus tag: XELAEV_18031990mg
See related: EnsemblRapid:ENSXLAG00005032729 AllianceGenome:Xenbase:XB-GENE-866368
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Xenopus laevis
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as: hyrc; p350; dnapk; dnpk1; hyrc1; prkdc; xrcc7; prkdc-A; dna-pkcs
Summary: Predicted to enable histone H2AXS139 kinase activity. Acts upstream of or within double-strand break repair via nonhomologous end joining. Predicted to be located in nucleolus. Predicted to be part of nonhomologous end joining complex. 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, Jan 2025]
Annotation information: Annotation category: partial on reference assembly
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 6L

Exon count:: 86

Annotation release	Status	Assembly	Chr	Location
101	current	Xenopus_laevis_v10.1 (GCF_017654675.1)	6L	NC_054381.1 (120706143..120801989, complement)
100	previous assembly	Xenopus_laevis_v2 (GCF_001663975.1)	6L	NC_030734.1 (113587593..113683545, complement)

Chromosome 6L - NC_054381.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ku80 is susceptible to proteolytic degradation when not dimerized with Ku70; dimer induces DNA-PK activity; evidence that interacting domain(s) of Xenopus DNA-PKcs is conserved so as to interact with human Ku, reconstituting a functional holoenzyme
Title: Exogenously expressed human Ku70 stabilizes Ku80 in Xenopus oocytes and induces heterologous DNA-PK catalytic activity.
These results suggest that potential mechanisms occurring outside of the nucleus might activate DNA-PK, and therefore, could reveal novel functions of this enzyme.
Title: DNase I-resistant DNA-dependent protein kinase activity in Xenopus oocytes.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by Xenbase

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	IEA Inferred from Electronic Annotation more info
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	ISS Inferred from Sequence or Structural Similarity 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 serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mitotic G1 DNA damage checkpoint signaling	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within ribosome biogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of nonhomologous end joining complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IEA Inferred from Electronic Annotation 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: DNA-PK catalytic subunit; protein kinase, DNA-activated, catalytic polypeptide L homeolog

NP_001079070.1

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_001085601.1 → NP_001079070.1 DNA-dependent protein kinase catalytic subunit

Status: PROVISIONAL

Source sequence(s)

AB016434

UniProtKB/Swiss-Prot

O57402, Q9DEI1

UniProtKB/TrEMBL

A0A974HG54

Related

ENSXLAP00005098120.1, ENSXLAT00005099927.1

Conserved Domains (4) summary

cd05172
Location:3736 → 4033

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

pfam02259
Location:3045 → 3487

FAT; FAT domain

pfam02260
Location:4115 → 4146

FATC; FATC domain

pfam08163
Location:1837 → 2223

NUC194; NUC194 domain

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

NC_054381.1 Reference Xenopus_laevis_v10.1 Primary Assembly

Range

120706143..120801989 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)