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Aliases for H2AFX Gene

Aliases for H2AFX Gene

  • H2A Histone Family, Member X 2 3
  • H2AX 3 4 6
  • Histone H2A.X 3 4
  • H2A/X 3 4
  • H2AX Histone 3
  • Histone H2AX 3
  • H2A.X 3

External Ids for H2AFX Gene

Previous HGNC Symbols for H2AFX Gene

  • H2AX

Previous GeneCards Identifiers for H2AFX Gene

  • GC11U990060
  • GC11M120476
  • GC11M118998
  • GC11M118502
  • GC11M118469
  • GC11M114904
  • GC11M118964

Summaries for H2AFX Gene

Entrez Gene Summary for H2AFX Gene

  • 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 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, Jul 2008]

GeneCards Summary for H2AFX Gene

H2AFX (H2A Histone Family, Member X) is a Protein Coding gene. Diseases associated with H2AFX include vulvar intraepithelial neoplasia. Among its related pathways are Disease and Cell Cycle, Mitotic. GO annotations related to this gene include protein heterodimerization activity and histone binding. An important paralog of this gene is HIST1H2AM.

UniProtKB/Swiss-Prot for H2AFX Gene

  • Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.

Gene Wiki entry for H2AFX Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H2AFX Gene

Genomics for H2AFX Gene

Regulatory Elements for H2AFX Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for H2AFX Gene

Start:
119,093,854 bp from pter
End:
119,095,467 bp from pter
Size:
1,614 bases
Orientation:
Minus strand

Genomic View for H2AFX Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for H2AFX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AFX Gene

Proteins for H2AFX Gene

  • Protein details for H2AFX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P16104-H2AX_HUMAN
    Recommended name:
    Histone H2AX
    Protein Accession:
    P16104
    Secondary Accessions:
    • Q4ZGJ7
    • Q6IAS5

    Protein attributes for H2AFX Gene

    Size:
    143 amino acids
    Molecular mass:
    15145 Da
    Quaternary structure:
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts with numerous proteins required for DNA damage signaling and repair when phosphorylated on Ser-140. These include MDC1, TP53BP1, BRCA1 and the MRN complex, composed of MRE11A, RAD50, and NBN. Interaction with the MRN complex is mediated at least in part by NBN. Also interacts with DHX9/NDHII when phosphorylated on Ser-140 and MCPH1 when phosphorylated at Ser-140 or Tyr-143. Interacts with ARRB2; the interaction is detected in the nucleus upon OR1D2 stimulation.

    Three dimensional structures from OCA and Proteopedia for H2AFX Gene

neXtProt entry for H2AFX Gene

Proteomics data for H2AFX Gene at MOPED

Post-translational modifications for H2AFX Gene

  • Acetylation at Lys-37 increases in S and G2 phases. This modification has been proposed to play a role in DNA double-strand break repair (By similarity).
  • Monoubiquitination of Lys-120 (H2AXK119ub) by RING1 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression (By similarity). Following DNA double-strand breaks (DSBs), it is ubiquitinated through Lys-63 linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and Lys-63-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend Lys-63-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced Lys-63-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events.
  • Phosphorylated on Ser-140 (to form gamma-H2AX or H2AX139ph) in response to DNA double strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks, and may also occur during meiotic recombination events and immunoglobulin class switching in lymphocytes. Phosphorylation can extend up to several thousand nucleosomes from the actual site of the DSB and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Widespread phosphorylation may also serve to amplify the damage signal or aid repair of persistent lesions. Phosphorylation of Ser-140 (H2AX139ph) in response to ionizing radiation is mediated by both ATM and PRKDC while defects in DNA replication induce Ser-140 phosphorylation (H2AX139ph) subsequent to activation of ATR and PRKDC. Dephosphorylation of Ser-140 by PP2A is required for DNA DSB repair. In meiosis, Ser-140 phosphorylation (H2AX139ph) may occur at synaptonemal complexes during leptotene as an ATM-dependent response to the formation of programmed DSBs by SPO11. Ser-140 phosphorylation (H2AX139ph) may subsequently occurs at unsynapsed regions of both autosomes and the XY bivalent during zygotene, downstream of ATR and BRCA1 activation. Ser-140 phosphorylation (H2AX139ph) may also be required for transcriptional repression of unsynapsed chromatin and meiotic sex chromosome inactivation (MSCI), whereby the X and Y chromosomes condense in pachytene to form the heterochromatic XY-body. During immunoglobulin class switch recombination in lymphocytes, Ser-140 phosphorylation (H2AX139ph) may occur at sites of DNA-recombination subsequent to activation of the activation-induced cytidine deaminase AICDA. Phosphorylation at Tyr-143 (H2AXY142ph) by BAZ1B/WSTF determines the relative recruitment of either DNA repair or pro-apoptotic factors. Phosphorylation at Tyr-143 (H2AXY142ph) favors the recruitment of APBB1/FE65 and pro-apoptosis factors such as MAPK8/JNK1, triggering apoptosis. In contrast, dephosphorylation of Tyr-143 by EYA proteins (EYA1, EYA2, EYA3 or EYA4) favors the recruitment of MDC1-containing DNA repair complexes to the tail of phosphorylated Ser-140 (H2AX139ph).
  • Ubiquitination at Lys14, Lys16, Lys96, Lys119, Lys120, Lys128, and Lys135
  • Modification sites at PhosphoSitePlus

Other Protein References for H2AFX Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for H2AFX (H2AX)

No data available for DME Specific Peptides for H2AFX Gene

Domains for H2AFX Gene

Gene Families for H2AFX Gene

HGNC:
  • RIH :Histones / Replication-independent

Protein Domains for H2AFX Gene

Suggested Antigen Peptide Sequences for H2AFX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P16104

UniProtKB/Swiss-Prot:

H2AX_HUMAN :
  • P16104
Domain:
  • The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AFX: view

Function for H2AFX Gene

Molecular function for H2AFX Gene

GENATLAS Biochemistry: histone family 2,replacement subtype,replication independent protein,species H2A-X
UniProtKB/Swiss-Prot Function: Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.

Gene Ontology (GO) - Molecular Function for H2AFX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding NAS 2587254
GO:0003684 damaged DNA binding IEA --
GO:0005515 protein binding IPI 12419185
GO:0019899 enzyme binding IPI 19234442
GO:0042393 histone binding IPI 19234442
genes like me logo Genes that share ontologies with H2AFX: view
genes like me logo Genes that share phenotypes with H2AFX: view

Animal Models for H2AFX Gene

MGI Knock Outs for H2AFX:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for H2AFX Gene

Localization for H2AFX Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AFX Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for H2AFX Gene COMPARTMENTS Subcellular localization image for H2AFX gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for H2AFX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 colocalizes_with chromosome, telomeric region IDA 15149599
GO:0000785 chromatin --
GO:0000786 nucleosome IEA --
GO:0000790 nuclear chromatin IEA --
GO:0000794 condensed nuclear chromosome IEA --
genes like me logo Genes that share ontologies with H2AFX: view

Pathways for H2AFX Gene

genes like me logo Genes that share pathways with H2AFX: view

Pathways by source for H2AFX Gene

1 Qiagen pathway for H2AFX Gene
2 Cell Signaling Technology pathways for H2AFX Gene
35 Reactome pathways for H2AFX Gene
2 KEGG pathways for H2AFX Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for H2AFX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000077 DNA damage checkpoint IDA 17974976
GO:0000724 double-strand break repair via homologous recombination TAS --
GO:0006281 DNA repair TAS --
GO:0006302 double-strand break repair TAS --
GO:0006334 nucleosome assembly NAS 2587254
genes like me logo Genes that share ontologies with H2AFX: view

Compounds for H2AFX Gene

(36) Novoseek inferred chemical compound relationships for H2AFX Gene

Compound -log(P) Hits PubMed IDs
7-hydroxystaurosporine 67.8 1
aphidicolin 60.3 4
topotecan 60.2 16
camptothecin 59.6 4
methylmethanesulfonate 57.7 2
genes like me logo Genes that share compounds with H2AFX: view

Transcripts for H2AFX Gene

mRNA/cDNA for H2AFX Gene

Unigene Clusters for H2AFX Gene

H2A histone family, member X:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for H2AFX

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for H2AFX Gene

No ASD Table

Relevant External Links for H2AFX Gene

GeneLoc Exon Structure for
H2AFX
ECgene alternative splicing isoforms for
H2AFX

Expression for H2AFX Gene

mRNA expression in normal human tissues for H2AFX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for H2AFX Gene

SOURCE GeneReport for Unigene cluster for H2AFX Gene Hs.477879

genes like me logo Genes that share expressions with H2AFX: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for H2AFX Gene

Orthologs for H2AFX Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for H2AFX Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia H2AFX 36
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia H2AFX 35
  • 94.41 (n)
  • 99.3 (a)
H2AFX 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia H2AFX 36
  • 99 (a)
OneToOne
LOC489372 35
  • 95.57 (n)
  • 99.3 (a)
mouse
(Mus musculus)
Mammalia H2afx 35
  • 92.54 (n)
  • 97.2 (a)
H2afx 16
H2afx 36
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia H2AFX 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia H2AFX 36
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia H2afx 35
  • 92.07 (n)
  • 98.6 (a)
chicken
(Gallus gallus)
Aves H2AFX 35
  • 79.25 (n)
  • 88.11 (a)
H2AFX 36
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 81 (a)
OneToMany
-- 36
  • 80 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.18740 35
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487455 35
  • 74.1 (n)
  • 89.21 (a)
zebrafish
(Danio rerio)
Actinopterygii h2afx 35
  • 75.82 (n)
  • 88.73 (a)
h2afx 36
  • 89 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea his-51 37
  • 91 (a)
his-53 37
  • 91 (a)
his-65 37
  • 91 (a)
his-57 37
  • 91 (a)
his-61 37
  • 91 (a)
his-47 37
  • 91 (a)
his-30 37
  • 91 (a)
his-16 37
  • 91 (a)
his-43 37
  • 91 (a)
his-21 37
  • 91 (a)
his-12 37
  • 91 (a)
his-3 37
  • 91 (a)
his-33 37
  • 91 (a)
his-19 37
  • 91 (a)
his-68 37
  • 91 (a)
his-7 37
  • 91 (a)
his-35 37
  • 90 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons HTA12 35
  • 56.79 (n)
  • 67.41 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.836 35
corn
(Zea mays)
Liliopsida Zm.16259 35
rice
(Oryza sativa)
Liliopsida Os03g0279200 35
  • 75.26 (n)
  • 74.22 (a)
Species with no ortholog for H2AFX:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for H2AFX Gene

ENSEMBL:
Gene Tree for H2AFX (if available)
TreeFam:
Gene Tree for H2AFX (if available)

Paralogs for H2AFX Gene

genes like me logo Genes that share paralogs with H2AFX: view

Variants for H2AFX Gene

Sequence variations from dbSNP and Humsavar for H2AFX Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs7350 -- 119,094,338(-) ATCGC(C/T)GATTT utr-variant-3-prime
rs15301 -- 119,094,649(-) GCGGA(A/G)GACCC utr-variant-3-prime
rs1064180 -- 119,094,978(-) CAGGC(C/T)TCCCA reference, synonymous-codon
rs1064193 -- 119,094,628(-) GGGGG(A/T)GGCCG utr-variant-3-prime
rs1134734 -- 119,094,769(-) GCTCC(C/T)GTCCC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for H2AFX Gene

Variant ID Type Subtype PubMed ID
nsv898416 CNV Loss 21882294
nsv826102 CNV Gain 20364138

Relevant External Links for H2AFX Gene

HapMap Linkage Disequilibrium report
H2AFX

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H2AFX Gene

Disorders for H2AFX Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for H2AFX Gene including...

Search for H2AFX Gene in MalaCards »

(23) Novoseek inferred disease relationships for H2AFX Gene

Disease -log(P) Hits PubMed IDs
ataxia telangiectasia 87.6 30
nijmegen breakage syndrome 83.9 3
bloom syndrome 59.4 1
cancer 51 10
chromosomal aberrations 48.4 8

Relevant External Links for H2AFX

Genetic Association Database (GAD)
H2AFX
Human Genome Epidemiology (HuGE) Navigator
H2AFX
genes like me logo Genes that share disorders with H2AFX: view

No data available for UniProtKB/Swiss-Prot for H2AFX Gene

Publications for H2AFX Gene

  1. Megabase chromatin domains involved in DNA double-strand breaks in vivo. (PMID: 10477747) Rogakou E.P. … Bonner W.M. (J. Cell Biol. 1999) 3 4 23
  2. A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. (PMID: 10959836) Paull T.T. … Bonner W.M. (Curr. Biol. 2000) 3 4 23
  3. MDC1 is a mediator of the mammalian DNA damage checkpoint. (PMID: 12607005) Stewart G.S. … Elledge S.J. (Nature 2003) 3 4 23
  4. Accumulation of checkpoint protein 53BP1 at DNA breaks involves its binding to phosphorylated histone H2AX. (PMID: 12697768) Ward I.M. … Chen J. (J. Biol. Chem. 2003) 3 4 23
  5. DNA-PK is activated by nucleosomes and phosphorylates H2AX within the nucleosomes in an acetylation-dependent manner. (PMID: 14627815) Park E.-J. … Kwon J. (Nucleic Acids Res. 2003) 3 4 23

Products for H2AFX Gene

Sources for H2AFX Gene

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