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H2AX H2A.X variant histone [ Homo sapiens (human) ]

Gene ID: 3014, updated on 17-Jun-2024

Summary

Official Symbol
H2AXprovided by HGNC
Official Full Name
H2A.X variant histoneprovided by HGNC
Primary source
HGNC:HGNC:4739
See related
Ensembl:ENSG00000188486 MIM:601772; AllianceGenome:HGNC:4739
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
H2A.X; H2A/X; H2AFX
Summary
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-independent histone that is a member of the histone H2A family, and generates two transcripts through the use of the conserved stem-loop termination motif, and the polyA addition motif. [provided by RefSeq, Oct 2015]
Orthologs
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Genomic context

See H2AX in Genome Data Viewer
Location:
11q23.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119093874..119095465, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119114257..119115848, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118964584..118966175, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5620 Neighboring gene VPS11 core subunit of CORVET and HOPS complexes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118955192-118955889 Neighboring gene hydroxymethylbilane synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118963458-118963970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965105-118965668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965669-118966232 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118966233-118966796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118966797-118967358 Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:118972216-118973415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3969 Neighboring gene C2CD2 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3970 Neighboring gene histone H4 transcription factor

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness PubMed
Vpr vpr Soluble HIV-1 Vpr induces a DNA damage response by forming H2AX- and 53BP1-containing DNA repair foci PubMed
vpr HIV-1 Vpr expression in HeLa cells and human primary CD4+ lymphocytes induces phosphorylation of H2AFX and formation of nuclear foci containing H2AFX and BRCA1 PubMed
vpr Recruitment of a catalytically active CRL4A (VPRBP) complex is required to observe HIV-1 Vpr-interacting unknown cellular ubiquitinated proteins. Phosphorylation of H2AX requires Vpr-induced K48 residue polyubiquitination PubMed
vpr HIV-1 Vpr binds DCAF1 and activates the DNA damage response in renal tubule epithelial cells, in which gamma H2AX-positive nuclei are abundant compared to the control PubMed
integrase gag-pol HIV-1 IN-mediated proviral DNA integration triggers cell death during HIV-1 infection. The mechanism of killing during viral integration involves activation of DNA-PK, which causes phosphorylation of p53 and histone gammaH2AX PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
enables chromatin-protein adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables damaged DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nucleosomal DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables structural constituent of chromatin IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in DNA damage checkpoint signaling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA damage response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular senescence IEA
Inferred from Electronic Annotation
more info
 
involved_in cerebral cortex development IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair NAS
Non-traceable Author Statement
more info
PubMed 
involved_in double-strand break repair via homologous recombination IEA
Inferred from Electronic Annotation
more info
 
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of DNA repair NAS
Non-traceable Author Statement
more info
PubMed 
involved_in protein localization to site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to ionizing radiation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in XY body IEA
Inferred from Electronic Annotation
more info
 
located_in centrosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in condensed nuclear chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular exosome HDA PubMed 
located_in male germ cell nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
part_of nucleosome IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in replication fork IEA
Inferred from Electronic Annotation
more info
 
located_in site of DNA damage IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone H2AX
Names
H2A histone family member X
H2AX histone
histone H2A.x

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)

  1. NM_002105.3NP_002096.1  histone H2AX

    See identical proteins and their annotated locations for NP_002096.1

    Status: REVIEWED

    Source sequence(s)
    AP003391
    Consensus CDS
    CCDS8410.1
    UniProtKB/Swiss-Prot
    P16104, Q4ZGJ7, Q6IAS5
    UniProtKB/TrEMBL
    B2R5B3
    Related
    ENSP00000434024.1, ENST00000530167.2
    Conserved Domains (1) summary
    PTZ00017
    Location:1131
    PTZ00017; histone H2A; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119093874..119095465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119114257..119115848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)