Format

Send to:

Choose Destination

XRCC4 X-ray repair cross complementing 4 [ Homo sapiens (human) ]

Gene ID: 7518, updated on 9-Dec-2018

Summary

Official Symbol
XRCC4provided by HGNC
Official Full Name
X-ray repair cross complementing 4provided by HGNC
Primary source
HGNC:HGNC:12831
See related
Ensembl:ENSG00000152422 MIM:194363
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
SSMED
Summary
The protein encoded by this gene functions together with DNA ligase IV and the DNA-dependent protein kinase in the repair of DNA double-strand breaks. This protein plays a role in both non-homologous end joining and the completion of V(D)J recombination. Mutations in this gene can cause short stature, microcephaly, and endocrine dysfunction (SSMED). Alternative splicing generates several transcript variants. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in testis (RPKM 2.7), lymph node (RPKM 2.1) and 25 other tissues See more
Orthologs

Genomic context

See XRCC4 in Genome Data Viewer
Location:
5q14.2
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (83077409..83370333)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (82373317..82649579)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379052 Neighboring gene transmembrane protein 167A Neighboring gene small Cajal body-specific RNA 18 Neighboring gene ribosomal protein L13 pseudogene 9 Neighboring gene coenzyme Q10B pseudogene 2 Neighboring gene uncharacterized LOC105379053 Neighboring gene ferritin heavy chain 1 pseudogene 9

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Short stature, microcephaly, and endocrine dysfunction
MedGen: C4225288 OMIM: 616541 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
NHGRI GWA Catalog
Meta-analysis identifies loci affecting levels of the potential osteoarthritis biomarkers sCOMP and uCTX-II with genome wide significance.
NHGRI GWA Catalog
Two-marker association tests yield new disease associations for coronary artery disease and hypertension.
NHGRI GWA Catalog

Pathways from BioSystems

  • 2-LTR circle formation, organism-specific biosystem (from REACTOME)
    2-LTR circle formation, organism-specific biosystemThe formation of 2-LTR circles requires the action of the cellular non-homologous DNA end-joining pathway. Specifically the cellular Ku, XRCC4 and ligase IV proteins are needed. Evidence for this i...
  • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
    DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Early Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
    Early Phase of HIV Life Cycle, organism-specific biosystemIn the early phase of HIV lifecycle, an active virion binds and enters a target cell mainly by specific interactions of the viral envelope proteins with host cell surface receptors. The virion core...
  • HIV Infection, organism-specific biosystem (from REACTOME)
    HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
  • HIV Life Cycle, organism-specific biosystem (from REACTOME)
    HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Integration of provirus, organism-specific biosystem (from REACTOME)
    Integration of provirus, organism-specific biosystemFor retroviral DNA to direct production of progeny virions it must become covalently integrated into the host cell chromosome (reviewed in Coffin et al. 1997; Hansen et al. 1998). Analyses of mutants...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Non-homologous end joining, organism-specific biosystem (from WikiPathways)
    Non-homologous end joining, organism-specific biosystem(From http://en.wikipedia.org/wiki/Non-homologous_end_joining) Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because...
  • Non-homologous end-joining, organism-specific biosystem (from KEGG)
    Non-homologous end-joining, organism-specific biosystemNonhomologous end joining (NHEJ) eliminates DNA double-strand breaks (DSBs) by direct ligation. NHEJ involves binding of the KU heterodimer to double-stranded DNA ends, recruitment of DNA-PKcs (MRX c...
  • Non-homologous end-joining, conserved biosystem (from KEGG)
    Non-homologous end-joining, conserved biosystemNonhomologous end joining (NHEJ) eliminates DNA double-strand breaks (DSBs) by direct ligation. NHEJ involves binding of the KU heterodimer to double-stranded DNA ends, recruitment of DNA-PKcs (MRX c...
  • Nonhomologous End-Joining (NHEJ), organism-specific biosystem (from REACTOME)
    Nonhomologous End-Joining (NHEJ), organism-specific biosystemThe nonhomologous end joining (NHEJ) pathway is initiated in response to the formation of DNA double-strand breaks (DSBs) induced by DNA-damaging agents, such as ionizing radiation. DNA DSBs are reco...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
    SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
  • SUMOylation, organism-specific biosystem (from REACTOME)
    SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
  • SUMOylation of DNA damage response and repair proteins, organism-specific biosystem (from REACTOME)
    SUMOylation of DNA damage response and repair proteins, organism-specific biosystemSeveral factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferr...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
DNA ligase IV complex IDA
Inferred from Direct Assay
more info
PubMed 
DNA-dependent protein kinase-DNA ligase 4 complex IDA
Inferred from Direct Assay
more info
PubMed 
NOT condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
nonhomologous end joining complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
DNA repair protein XRCC4
Names
X-ray repair complementing defective repair in Chinese hamster cells 4

NCBI Reference Sequences (RefSeq)

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

  1. NG_047086.1 RefSeqGene

    Range
    5001..281352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318012.1NP_001304941.1  DNA repair protein XRCC4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses alternate splice sites in the 5' UTR and in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. Variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    BC010655, BC016314, DA067761
    Consensus CDS
    CCDS4059.1
    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAQ8, Q7Z763
    Related
    ENSP00000421491.1, ENST00000511817.1
    Conserved Domains (1) summary
    pfam06632
    Location:2334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
  2. NM_001318013.1NP_001304942.1  DNA repair protein XRCC4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) has a distinct, shorter C-terminus than isoform 1.
    Source sequence(s)
    BC005259, DA067761
    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAP0
    Conserved Domains (1) summary
    pfam06632
    Location:2308
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
  3. NM_003401.4NP_003392.1  DNA repair protein XRCC4 isoform 1

    See identical proteins and their annotated locations for NP_003392.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    BC010655, BC016314, BT007216, DA067761, U40622
    Consensus CDS
    CCDS4058.1
    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAL0, Q7Z763
    Related
    ENSP00000379344.4, ENST00000396027.8
    Conserved Domains (1) summary
    pfam06632
    Location:2332
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
  4. NM_022406.3NP_071801.1  DNA repair protein XRCC4 isoform 2

    See identical proteins and their annotated locations for NP_071801.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. Variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    BC010655, BC016314, BT007216, DA067761
    Consensus CDS
    CCDS4059.1
    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAQ8, Q7Z763
    Related
    ENSP00000342011.6, ENST00000338635.10
    Conserved Domains (1) summary
    pfam06632
    Location:2334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
  5. NM_022550.3NP_072044.1  DNA repair protein XRCC4 isoform 1

    See identical proteins and their annotated locations for NP_072044.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    BC010655, BC016314, DA067761, U40622
    Consensus CDS
    CCDS4058.1
    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAL0, Q7Z763
    Related
    ENSP00000282268.3, ENST00000282268.7
    Conserved Domains (1) summary
    pfam06632
    Location:2332
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    83077409..83370333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009827.2XP_016865316.1  DNA repair protein XRCC4 isoform X2

  2. XM_017009828.2XP_016865317.1  DNA repair protein XRCC4 isoform X3

  3. XM_017009829.2XP_016865318.1  DNA repair protein XRCC4 isoform X4

    Conserved Domains (1) summary
    pfam06632
    Location:2252
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
  4. XM_011543626.1XP_011541928.1  DNA repair protein XRCC4 isoform X1

    See identical proteins and their annotated locations for XP_011541928.1

    UniProtKB/Swiss-Prot
    Q13426
    UniProtKB/TrEMBL
    A0A024RAQ8
    Conserved Domains (1) summary
    pfam06632
    Location:2334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
Support Center