XRCC5 X-ray repair cross complementing 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: XRCC5provided by HGNC
Official Full Name: X-ray repair cross complementing 5provided by HGNC
Primary source: HGNC:HGNC:12833
See related: Ensembl:ENSG00000079246 MIM:194364
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KU80; KUB2; Ku86; NFIV; KARP1; KARP-1
Summary: The protein encoded by this gene is the 80-kilodalton subunit of the Ku heterodimer protein which is also known as ATP-dependant DNA helicase II or DNA repair protein XRCC5. Ku is the DNA-binding component of the DNA-dependent protein kinase, and it functions together with the DNA ligase IV-XRCC4 complex in the repair of DNA double-strand break by non-homologous end joining and the completion of V(D)J recombination events. This gene functionally complements Chinese hamster xrs-6, a mutant defective in DNA double-strand break repair and in ability to undergo V(D)J recombination. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 87.8), lymph node (RPKM 70.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q35

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	2	NC_000002.12 (216109348..216206293)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (216974071..217071016)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

XRCC5/6 polymorphisms and their interactions with smoking, alcohol consumption, and sleep satisfaction in breast cancer risk: A Chinese multi-center study.
Title: XRCC5/6 polymorphisms and their interactions with smoking, alcohol consumption, and sleep satisfaction in breast cancer risk: A Chinese multi-center study.
miR-623 suppresses cell proliferation, migration and invasion through direct inhibition of XRCC5 in breast cancer.
Title: miR-623 suppresses cell proliferation, migration and invasion through direct inhibition of XRCC5 in breast cancer.
CDK-mediated Yku80 Phosphorylation Regulates the Balance Between Non-homologous End Joining (NHEJ) and Homologous Directed Recombination (HDR).
Title: CDK-mediated Yku80 Phosphorylation Regulates the Balance Between Non-homologous End Joining (NHEJ) and Homologous Directed Recombination (HDR).
Overexpression of miR-623 suppresses progression of hepatocellular carcinoma via regulating the PI3K/Akt signaling pathway by targeting XRCC5.
Title: Overexpression of miR-623 suppresses progression of hepatocellular carcinoma via regulating the PI3K/Akt signaling pathway by targeting XRCC5.
ATM antagonizes NHEJ proteins assembly and DNA-ends synapsis at single-ended DNA double strand breaks.
Title: ATM antagonizes NHEJ proteins assembly and DNA-ends synapsis at single-ended DNA double strand breaks.
High expression of XRCC5 is associated with metastasis through Wnt signaling pathway and predicts poor prognosis in patients with hepatocellular carcinoma.
Title: High expression of XRCC5 is associated with metastasis through Wnt signaling pathway and predicts poor prognosis in patients with hepatocellular carcinoma.
Ligand binding characteristics of the Ku80 von Willebrand domain.
Title: Ligand binding characteristics of the Ku80 von Willebrand domain.
Ku80 negatively regulates the expression of OCT4 via competitive binding to SALL4 and promoting lysosomal degradation of OCT4.
Title: Ku80 negatively regulates the expression of OCT4 via competitive binding to SALL4 and promoting lysosomal degradation of OCT4.
Using a combination of biotin identification and affinity purification coupled to mass spectrometry, this is the first report that comprehensively characterizes the Ku protein interaction landscape, revealing new cellular processes and protein complexes involving the Ku complexcomposed of( Ku70 and Ku80).
Title: Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells.
Ku80 promoted melanoma growth and regulated antitumor activity of melatonin by targeting HIF1-alpha dependent PDK-1 signaling pathway.
Title: Ku80 promotes melanoma growth and regulates antitumor effect of melatonin by targeting HIF1-α dependent PDK-1 signaling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (167)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Ku protein binds to HIV-1 TAR RNA and is involved in the stimulation of the elongation property of RNA polymerase II as well as the activation of several transcription factors, suggesting a role in HIV-1 gene expression and Tat transactivation	PubMed
integrase	gag-pol	Ku80 associates with viral preintegration complexes containing HIV-1 Integrase	PubMed
	gag-pol	DNA-PK, along with Ku70 and Ku80, is proposed to play a role in retroviral DNA integration and protects cells against toxicity induced by HIV-1 Integrase or integration	PubMed
matrix	gag	HIV-1 MA interacts with XRCC5 (Ku80)	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

HSC2AF082 (e-PCR)
- UniSTS:79121

PMC22716P1 (e-PCR)
- UniSTS:272151

RH104285 (e-PCR)
- UniSTS:98610

G67228 (e-PCR)
- UniSTS:186433

G67229 (e-PCR)
- UniSTS:186434

G67230 (e-PCR)
- UniSTS:186435

G67232 (e-PCR)
- UniSTS:186436

G67231 (e-PCR)
- UniSTS:186437

D2S2881 (e-PCR)
- UniSTS:26736

A004W06 (e-PCR)
- UniSTS:30865

SHGC-33338 (e-PCR)
- UniSTS:32425

SHGC-11966 (e-PCR)
- UniSTS:16811

D2S2382 (e-PCR), detects polymorphism
- UniSTS:8379

D2S2606 (e-PCR)
- UniSTS:58598

XRCC5_1894 (e-PCR)
- UniSTS:281081

PMC117391P1 (e-PCR)
- UniSTS:270331

PMC117391P2 (e-PCR)
- UniSTS:270332

Homology

Homologs of the XRCC5 gene: The XRCC5 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, mosquito, S.pombe, M.oryzae, N.crassa, A.thaliana, and frog.
Orthologs from Annotation Pipeline: 420 organisms have orthologs with human gene XRCC5
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to 5'-deoxyribose-5-phosphate lyase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	NAS Non-traceable Author Statement more info	PubMed
contributes_to DNA end binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA end binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables U3 snoRNA binding	IDA Inferred from Direct Assay more info	PubMed
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	PubMed
contributes_to double-stranded telomeric DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme activator activity	TAS Traceable Author Statement more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables protein C-terminus binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables telomeric DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables telomeric DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables telomeric DNA binding	TAS Traceable Author Statement more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in DNA recombination	TAS Traceable Author Statement more info	PubMed
involved_in activation of innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in cellular hyperosmotic salinity response	IEA Inferred from Electronic Annotation more info
involved_in cellular response to DNA damage stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to X-ray	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cellular response to fatty acid	IEA Inferred from Electronic Annotation more info
involved_in cellular response to gamma radiation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cellular response to gamma radiation	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in double-strand break repair via nonhomologous end joining	IDA Inferred from Direct Assay more info	PubMed
involved_in 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	TAS Traceable Author Statement more info	PubMed
involved_in hematopoietic stem cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of t-circle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription, DNA-templated	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of catalytic activity	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of telomerase activity	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of telomere maintenance via telomerase	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to chromosome, telomeric region	TAS Traceable Author Statement more info	PubMed
involved_in regulation of smooth muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of telomere maintenance	TAS Traceable Author Statement more info	PubMed
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in small-subunit processome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
part_of DNA-dependent protein kinase complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Ku70:Ku80 complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of Ku70:Ku80 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Ku70:Ku80 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Ku70:Ku80 complex	TAS Traceable Author Statement more info	PubMed
located_in chromosome, telomeric region	HDA more info	PubMed
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
part_of nonhomologous end joining complex	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear telomere cap complex	TAS Traceable Author Statement more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info
part_of protein-DNA complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule lumen	TAS Traceable Author Statement more info
located_in site of DNA damage	IMP Inferred from Mutant Phenotype more info	PubMed
part_of small-subunit processome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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

Names: 86 kDa subunit of Ku antigen; ATP-dependent DNA helicase 2 subunit 2; ATP-dependent DNA helicase II 80 kDa subunit; CTC box-binding factor 85 kDa subunit; CTC85; CTCBF; DNA repair protein XRCC5; Ku autoantigen, 80kDa; Ku86 autoantigen related protein 1; TLAA; X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining); lupus Ku autoantigen protein p86; nuclear factor IV; thyroid-lupus autoantigen

NP_066964.1

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.

Genomic

NG_029780.1 RefSeqGene

Range

5052..101997

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_021141.4 → NP_066964.1 X-ray repair cross-complementing protein 5

See identical proteins and their annotated locations for NP_066964.1

Status: REVIEWED

Source sequence(s)

BG717693, BP375944, BU184024, M30938, X57500

Consensus CDS

CCDS2402.1

UniProtKB/Swiss-Prot

P13010

Related

ENSP00000375977.2, ENST00000392132.7

Conserved Domains (3) summary

cd00873
Location:244 → 543

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:593 → 705

Ku_PK_bind; Ku C terminal domain like