Xrcc5 X-ray repair cross complementing 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xrcc5provided by RGD
Official Full Name: X-ray repair cross complementing 5provided by RGD
Primary source: RGD:3976
See related: Ensembl:ENSRNOG00000016105 AllianceGenome:RGD:3976
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
Also known as: Ku80; Kup80
Summary: Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular hyperosmotic salinity response; cellular response to X-ray; and cellular response to fatty acid. Located in cytoplasm and nucleus. Part of protein-containing complex. Human ortholog(s) of this gene implicated in chronic obstructive pulmonary disease and multiple myeloma. Orthologous to human XRCC5 (X-ray repair cross complementing 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 154.4), Kidney (RPKM 147.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q33

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (81404507..81493293)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (73955216..74044020)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (79659275..79748050)

Chromosome 9 - NC_086027.1 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?

The radiosensitizing effect of beclin-1 knockdown may result from the disruption of nuclear translocation and DNA binding activity of Ku proteins and consequent attenuation of double strand break repair.
Title: Blockage of Autophagy in C6 Glioma Cells Enhanced Radiosensitivity Possibly by Attenuating DNA-PK-Dependent DSB Due to Limited Ku Nuclear Translocation and DNA Binding.
Sp1, Sp2 and Sp4 transcription factors play a role in activating cholesterol desmolase gene transcription in the nervous system, and Ku antigen may further augment this activation
Title: Transcriptional regulation of P450scc gene expression in the embryonic rodent nervous system.

Submit: New GeneRIF Correction

General gene information

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Markers

D9Mco23 (e-PCR)
- UniSTS:518912

RH143010 (e-PCR)
- UniSTS:232257

RH141867 (e-PCR)
- UniSTS:223859

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to 5'-deoxyribose-5-phosphate lyase activity	ISO Inferred from Sequence Orthology more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
contributes_to DNA end binding	ISO Inferred from Sequence Orthology more info
enables DNA end binding	ISO Inferred from Sequence Orthology more info
enables DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables U3 snoRNA binding	ISO Inferred from Sequence Orthology more info
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
contributes_to double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to double-stranded telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables telomeric DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in activation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in cellular hyperosmotic salinity response	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to X-ray	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to fatty acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to gamma radiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology 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
involved_in double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hematopoietic stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hematopoietic stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of t-circle formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomere maintenance via telomerase	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 xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in small-subunit processome assembly	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor 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 DNA-dependent protein kinase-DNA ligase 4 complex	TAS Traceable Author Statement more info	PubMed
part_of Ku70:Ku80 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Ku70:Ku80 complex	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	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	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of protein-DNA complex	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info
located_in site of DNA damage	ISO Inferred from Sequence Orthology more info
part_of small-subunit processome	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: X-ray repair cross-complementing protein 5

Names: Ku autoantigen, 80kD); X-ray repair complementing defective repair in Chinese hamster cells 5; X-ray repair cross complementation (double-strand-break rejoining; X-ray repair cross complementation (double-strand-break rejoining; Ku autoantigen, 80kD)

NP_803154.2

EC 3.6.4.-

XP_063123455.1

EC 3.6.4.-

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_177419.3 → NP_803154.2 X-ray repair cross-complementing protein 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A6KFI3, G3V817, Q6P7P8

Related

ENSRNOP00000021656.3, ENSRNOT00000021656.5

Conserved Domains (3) summary

cd00873
Location:246 → 542

KU80; Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the ...

pfam03731
Location:9 → 244

Ku_N; Ku70/Ku80 N-terminal alpha/beta domain

pfam08785
Location:594 → 707

Ku_PK_bind; Ku C terminal domain like