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H2AFX Gene

protein-coding   GIFtS: 68
GCID: GC11M118964

H2A Histone Family, Member X


(Previous symbol: H2AX)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
H2A Histone Family, Member X1 2     H2A/X2
H2AX1 2 3 5     H2AX Histone2
Histone H2A.X2 3     Histone H2AX2
H2A.X2     H2a/x3

External Ids:    HGNC: 47391   Entrez Gene: 30142   Ensembl: ENSG000001884867   OMIM: 6017725   UniProtKB: P161043   

Export aliases for H2AFX gene to outside databases

Previous GC identifers: GC11U990060 GC11M120476 GC11M118998 GC11M118502 GC11M118469 GC11M114904


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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, and nijmegen breakage syndrome. GO annotations related to this gene include histone binding and protein heterodimerization activity. An important paralog of this gene is HIST3H2A.

UniProtKB/Swiss-Prot: H2AX_HUMAN, P16104
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 Wiki entry for H2AFX Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NC_018922.2  NT_033899.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the H2AFX gene promoter:
         c-Fos   GATA-3   p53   AP-1   GATA-2   GATA-1   YY1   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidH2AFX promoter sequence
   Search Chromatin IP Primers for H2AFX

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat H2AFX


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q23.3   Ensembl cytogenetic band:  11q23.3   HGNC cytogenetic band: 11q23.3

H2AFX Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H2AFX gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M118964:  view genomic region     (about GC identifiers)

Start:
118,964,564 bp from pter      End:
118,966,177 bp from pter
Size:
1,614 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: H2AX_HUMAN, P16104 (See protein sequence)
Recommended Name: Histone H2AX  
Size: 143 amino acids; 15145 Da
Subunit: 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
Developmental stage: Synthesized in G1 as well as in S-phase
6 PDB 3D structures from and Proteopedia for H2AFX:
2D31 (3D)        2DYP (3D)        3SHV (3D)        3SQD (3D)        3SZM (3D)        3U3Z (3D)    
Secondary accessions: Q4ZGJ7 Q6IAS5

Explore the universe of human proteins at neXtProt for H2AFX: NX_P16104

Explore proteomics data for H2AFX at MOPED

Post-translational modifications: 

  • 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)1
  • 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 events1
  • 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)1
  • Ubiquitination2 at Lys14, Lys16, Lys96, Lys119, Lys120, Lys128, Lys135
  • Modification sites at PhosphoSitePlus

  • See H2AFX Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002096.1  
    ENSEMBL proteins: 
     ENSP00000434024   ENSP00000364310  
    Reactome Protein details: P16104

    H2AFX Human Recombinant Protein Products:

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    Novus Biologicals H2AFX Proteins
    Novus Biologicals H2AFX Lysate
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for H2AFX

    H2AFX Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of H2AFX
    R&D Systems Antibodies for H2AFX (Histone H2AX)
    Cell Signaling Technology (CST) Antibodies for H2AFX  (H2AX)
    OriGene Antibodies for H2AFX
    OriGene Custom Antibody Services for H2AFX
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    Abcam antibodies for H2AFX
    Cloud-Clone Corp. Antibodies for H2AFX
    ThermoFisher Antibody for H2AFX
    LSBio Antibodies in human, mouse, rat for H2AFX

    H2AFX Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for H2AFX
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    Cloud-Clone Corp. ELISAs for H2AFX
    Cloud-Clone Corp. CLIAs for H2AFX


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RIH: Histones / Replication-independent

    3 InterPro protein domains:
     IPR009072 Histone-fold
     IPR007125 Histone_core_D
     IPR002119 Histone_H2A

    Graphical View of Domain Structure for InterPro Entry P16104

    ProtoNet protein and cluster: P16104

    1 Blocks protein domain: IPB002119 Histone H2A

    UniProtKB/Swiss-Prot: H2AX_HUMAN, P16104
    Domain: The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family
    Similarity: Belongs to the histone H2A family


    H2AFX for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: H2AX_HUMAN, P16104
    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

         Genatlas biochemistry entry for H2AFX:
    histone family 2,replacement subtype,replication independent protein,species H2A-X

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS2587254
    GO:0003684damaged DNA binding IEA--
    GO:0005515protein binding IPI12419185
    GO:0019899enzyme binding IPI19234442
    GO:0042393histone binding IPI19234442
         
    H2AFX for ontologies           About GeneDecksing


    Phenotypes:
         10 MGI mutant phenotypes (inferred from 3 alleles(MGI details for H2afx):
     cardiovascular system  cellular  endocrine/exocrine gland  growth/size/body  hematopoietic system 
     immune system  mortality/aging  reproductive system  tumorigenesis  vision/eye 

    H2AFX for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for H2AFX: H2afxtm1Nus H2afxtm1Fwa

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for H2AFX
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for H2AFX

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for H2AFX
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for H2AFX

    miRNA
    Products:
        
    miRTarBase miRNAs that target H2AFX:
    hsa-let-7d-5p (MIRT051722), hsa-mir-16-5p (MIRT051262), hsa-mir-320a (MIRT044465), hsa-mir-138-5p (MIRT006493), hsa-mir-328-3p (MIRT019531), hsa-mir-484 (MIRT042120), hsa-mir-24-3p (MIRT030383)

    Block miRNA regulation of human, mouse, rat H2AFX using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate H2AFX (see all 13):
    hsa-miR-22 hsa-miR-4264 hsa-miR-328 hsa-miR-938 hsa-miR-218 hsa-miR-1291 hsa-miR-455-3p hsa-miR-501-5p
    SwitchGear 3'UTR luciferase reporter plasmidH2AFX 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for H2AFX
    Predesigned siRNA for gene silencing in human, mouse, rat H2AFX

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for H2AFX

    Clone
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    OriGene ORF clones in mouse, rat for H2AFX
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: H2AFX (NM_002105)
    Sino Biological Human cDNA Clone for H2AFX
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for H2AFX
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat H2AFX

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    Browse ESI BIO Cell Lines and PureStem Progenitors for H2AFX 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H2AFX


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    H2AX_HUMAN, P16104: Nucleus. Chromosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton3
    cytosol3
    mitochondrion2

    Gene Ontology (GO): Selected cellular component terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000781colocalizes with chromosome, telomeric region IDA15149599
    GO:0000785chromatin ----
    GO:0000786nucleosome IEA--
    GO:0000790nuclear chromatin IEA--
    GO:0000794condensed nuclear chromosome IEA--

    H2AFX for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for H2AFX About   (see all 17)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Packaging Of Telomere Ends
    Packaging Of Telomere Ends0.66
    Nucleosome assembly0.59
    Meiotic Synapsis0.66
    Deposition of New CENPA-containing Nucleosomes at the Centromere0.59
    DNA Damage/Telomere Stress Induced Senescence0.65
    Signal transduction Activin A signaling regulation0.40
    Telomere Maintenance0.64
    Histone modification0.31
    2RNA Polymerase I Promoter Opening
    RNA Polymerase I Transcription0.78
    RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription0.73
    RNA Polymerase I Chain Elongation0.78
    Amyloids0.68
    RNA Polymerase I Promoter Clearance0.78
    Mitotic Prophase0.56
    RNA Polymerase I Promoter Opening0.78
    Systemic lupus erythematosus0.40
    3Homologous Recombination Repair
    Homologous Recombination Repair0.70
    Recruitment of repair and signaling proteins to double-strand breaks0.00
    Double-Strand Break Repair0.70
    Homologous recombination repair of replication-independent double-strand breaks0.00
    ATM mediated response to DNA double-strand break0.31
    ATM mediated phosphorylation of repair proteins0.00
    4Cellular Senescence
    Cellular Senescence0.81
    Oxidative Stress Induced Senescence0.64
    Cellular responses to stress0.81
    Senescence-Associated Secretory Phenotype (SASP)0.57
    5Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    M Phase0.62
    Cell Cycle0.90

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for H2AFX
        ATM Pathway

    2 Cell Signaling Technology (CST) Pathways for H2AFX
        Chromatin Regulation / Acetylation
    DNA Damage

    2 GeneGo (Thomson Reuters) Pathways for H2AFX
        DNA damage Role of Brca1 and Brca2 in DNA repair
    Signal transduction Activin A signaling regulation

    3 BioSystems Pathways for H2AFX
        DNA damage response
    miRNAs involved in DDR
    Proteasome Degradation


    Selected Reactome Pathways for H2AFX (see all 19)
        Recruitment of repair and signaling proteins to double-strand breaks
    NoRC negatively regulates rRNA expression
    formation of the beta-catenin:TCF transactivating complex
    PRC2 methylates histones and DNA
    RNA Polymerase I Chain Elongation


    2 Kegg Pathways  (Kegg details for H2AFX):
        Alcoholism
    Systemic lupus erythematosus


    H2AFX for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including H2AFX: 
              DNA Damage Signaling Pathway in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for H2AFX

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for H2AFX (P161041, 2, 3 ENSP000003643104) via UniProtKB, MINT, STRING, and/or I2D (see all 732)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST3H3Q166951, 2, 3, ENSP000003556574EBI-494830,EBI-358900 MINT-7914854 MINT-7914438 MINT-7914390 MINT-7914502 MINT-7914490 MINT-7914370 MINT-7914453 MINT-7914423 MINT-7914408 MINT-7914478 MINT-7914465 I2D: score=1 STRING: ENSP00000355657
    SMARCA4P515321, 2, 3, ENSP000003507204EBI-494830,EBI-302489 MINT-7914854 MINT-7914589 MINT-7914654 MINT-7914952 MINT-7914515 MINT-7914936 MINT-7914564 MINT-7914353 MINT-7914632 I2D: score=2 STRING: ENSP00000350720
    ENSG00000224587Q146761, 2, 3EBI-494830,EBI-495644 MINT-6805304 I2D: score=4 
    ENSG00000225589Q146761, 2, 3EBI-494830,EBI-495644 MINT-6805304 I2D: score=4 
    ENSG00000228575Q146761, 2, 3EBI-494830,EBI-495644 MINT-6805304 I2D: score=4 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000077DNA damage checkpoint IDA17974976
    GO:0000724double-strand break repair via homologous recombination TAS--
    GO:0006281DNA repair TAS--
    GO:0006302double-strand break repair TAS--
    GO:0006334nucleosome assembly NAS2587254

    H2AFX for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for H2AFX (H2AX)

    Selected Novoseek inferred chemical compound relationships for H2AFX gene (see all 36)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    7-hydroxystaurosporine 67.8 1 17406032 (1)
    aphidicolin 60.3 6 17169990 (1), 18616816 (1), 15655354 (1), 16672000 (1)
    topotecan 60.2 17 18459160 (5), 16426422 (3), 18802408 (2), 16760673 (2) (see all 8)
    camptothecin 59.6 4 18285460 (1), 19557000 (1), 16407843 (1), 14504478 (1)
    methylmethanesulfonate 57.7 2 14643438 (1), 15381075 (1)
    etoposide 57.1 12 19516899 (2), 18922022 (1), 18285460 (1), 19109557 (1) (see all 9)
    adozelesin 56.8 1 14643438 (1)
    calicheamicin 54.2 3 19516899 (2), 12606118 (1)
    mitoxantrone 51.5 14 16760673 (4), 18459160 (4), 18802408 (2), 16184611 (1) (see all 7)
    wortmannin 49.2 4 15389585 (2), 20205745 (1), 17167777 (1)



    H2AFX for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for H2AFX gene: 
    NM_002105.2  

    Unigene Cluster for H2AFX:

    H2A histone family, member X
    Hs.477879  [show with all ESTs]
    Unigene Representative Sequence: BM917453
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000530167(uc001pvg.3) ENST00000375167
    miRNA
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    hsa-miR-22 hsa-miR-4264 hsa-miR-328 hsa-miR-938 hsa-miR-218 hsa-miR-1291 hsa-miR-455-3p hsa-miR-501-5p
    SwitchGear 3'UTR luciferase reporter plasmidH2AFX 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat H2AFX
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    Additional mRNA sequence: 

    BC004915.2 BC011694.2 BC013416.2 CR457079.1 X14850.1 

    10 DOTS entries:

    DT.95318297  DT.40219073  DT.95318293  DT.120752112  DT.100785924  DT.100785920  DT.95318235  DT.120752100 
    DT.95318305  DT.317312 

    Selected AceView cDNA sequences (see all 434):

    BU736476 AI273251 BM840793 BM841758 BM844983 AI126730 CD671486 AI424667 
    AW949942 BQ277985 BM762587 BM128191 BM766690 BM929922 BM767129 AI346292 
    BM699266 BM766729 BM840436 BU615689 AI521429 BM767105 AW731660 BF797344 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    H2AFX expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAAGAGCTG
    H2AFX Expression
    About this image


    H2AFX expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Thymus (Hematopoietic System)
             Double Negative 2 Thymocytes Thymus
     
     Blood (Cardiovascular System)
             Double Negative 2 Thymocytes Thymus
    H2AFX Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    H2AFX Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.477879
        Pathway & Disease-focused RT2 Profiler PCR Array including H2AFX: 
              DNA Damage Signaling Pathway in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H2AFX

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for H2AFX gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia H2afx1 , 5 H2A histone family, member X1, 5 92.54(n)1
    97.2(a)1
      9 (24.84 cM)5
    152701  NM_010436.21  NP_034566.11 
     443346945 
    chicken
    (Gallus gallus)
    Aves H2AFX1 H2A histone family, member X 79.25(n)
    88.11(a)
      100857391  XM_004947917.1  XP_004947974.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Histone H2A
    81(a)
    80(a)
    1 ↔ many
    1 ↔ many
    2(192891563-192891991)
    2(192904087-192904521)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.187402 Xenopus laevis transcribed sequence with strong similarity more 81.47(n)    BI477765.1 
    zebrafish
    (Danio rerio)
    Actinopterygii h2afx1 H2A histone family, member X 75.82(n)
    88.73(a)
      394048  NM_201073.1  NP_957367.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons HTA121 HTA12 56.79(n)
    67.41(a)
      831891  NM_120334.2  NP_195876.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g02792001 Os03g0279200 75.26(n)
    74.22(a)
      4332433  NM_001056266.1  NP_001049731.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for H2AFX gene
    HIST3H2A2  HIST1H2AD2  HIST2H2AA32  HIST2H2AB2  HIST1H2AI2  HIST1H2AG2  HIST1H2AC2  HIST1H2AH2  
    HIST1H2AM2  HIST1H2AJ2  HIST1H2AA2  HIST2H2AA42  HIST1H2AE2  HIST1H2AB2  HIST2H2AC2  HIST1H2AK2  
    HIST1H2AL2  H2AFJ2  
    Selected SIMAP similar genes for H2AFX using alignment to 1 protein entry:     H2AX_HUMAN(see all similar genes):
    HIST1H2AA    HIST2H2AB    H2AFJ    HIST1H2AB    HIST1H2AC    HIST1H2AD
    HIST1H2AE    HIST1H2AG    HIST1H2AH    HIST1H2AI    HIST1H2AJ    HIST1H2AK
    HIST1H2AL    HIST1H2AM    HIST2H2AA3    HIST2H2AA4    HIST2H2AC    HIST3H2A

    H2AFX for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for H2AFX (see all 46)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1810686311,2
    --118964956(+) CGTCCC/TGGCCC 1 -- ut310--------
    rs38249441,2
    C,F,H--118964964(-) CTGCGC/ATGGGG 1 -- ut31 ese312Minor allele frequency- A:0.01NS EA NA 1128
    rs73501,2
    C,F,A--118965048(-) ATCGCC/TGATTT 1 -- ut3111Minor allele frequency- T:0.34MN NS NA WA EA 728
    rs10641931,2
    C,F--118965338(-) GGGGGA/TGGCCG 1 -- ut315Minor allele frequency- T:0.22MN NA EA 428
    rs582325061,2
    C--118965353(+) AGGCTC/TGGGTC 1 -- ut311Minor allele frequency- T:0.50WA 2
    rs11347341,2
    C,F--118965479(-) GCTCCC/TGTCCC 1 -- ut313Minor allele frequency- T:0.50NA 6
    rs2019247521,2
    --118965658(+) CGGCCA/GCGGCG 1 -- ut310--------
    rs10641801,2
    C--118965688(-) CAGGCC/TTCCCA 2 A syn1 ese32Minor allele frequency- T:0.00MN EU 1267
    rs2011472061,2
    --118965753(+) CTTGGC/GCAGCA 2 P A mis10--------
    rs1417986411,2
    F--118965823(+) TTGTTG/TAGCTC 2 L syn11Minor allele frequency- T:0.00NA 4478

    HapMap Linkage Disequilibrium report for H2AFX (118964564 - 118966177 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for H2AFX:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv898416CNV Loss21882294
    nsv826102CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing H2AFX
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601772    OMIM disorders: --

    Selected diseases for H2AFX (see all 51):    
    About MalaCards
    vulvar intraepithelial neoplasia    nijmegen breakage syndrome    seckel syndrome    bloom syndrome
    riddle syndrome    ataxia telangiectasia    fanconi's anemia    werner syndrome
    t cell deficiency    sporadic breast cancer    testicular cancer    mantle cell lymphoma
    ataxia    diffuse large b-cell lymphoma    gastrointestinal stromal tumor    osteosarcoma
    b-cell lymphomas    malignant glioma    breast cancer    non-hodgkin lymphoma

    5 diseases from the University of Copenhagen DISEASES database for H2AFX:
    Cancer     Ataxia telangiectasia     Nijmegen breakage syndrome     Fanconi's anemia
    Werner syndrome

    H2AFX for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for H2AFX gene (see all 23)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ataxia telangiectasia 87.6 34 15059890 (2), 16360120 (1), 16567133 (1), 18560558 (1) (see all 29)
    nijmegen breakage syndrome 83.9 3 14712078 (1), 17183606 (1), 20173316 (1)
    bloom syndrome 59.4 1 14712078 (1)
    cancer 51 11 12914701 (1), 14712078 (1), 18616816 (1), 15610743 (1) (see all 10)
    chromosomal aberrations 48.4 8 16093433 (1), 16618761 (1), 16394631 (1), 17471025 (1) (see all 8)
    tumors 39 30 12914700 (3), 12914701 (2), 19190126 (2), 15279782 (1) (see all 23)
    fanconis anemia 32.9 1 17471025 (1)
    lung carcinoma 31.3 4 16820894 (1), 16760673 (1), 18459160 (1), 19658174 (1)
    osteosarcoma 18.7 1 17015833 (1)
    solid tumor 13.8 1 12914700 (1)

    Genetic Association Database (GAD): H2AFX
    Human Genome Epidemiology (HuGE) Navigator: H2AFX (7 documents)

    Export disorders for H2AFX gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for H2AFX gene, integrated from 10 sources (see all 541):
    (articles sorted by number of sources associating them with H2AFX)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. ATM and DNA-PK function redundantly to phosphorylate H2AX after exposure to ionizing radiation. (PubMed id 15059890)1, 2, 9 Stiff T....Jeggo P.A. (Cancer Res. 2004)
    2. Accumulation of checkpoint protein 53BP1 at DNA breaks involves its binding to phosphorylated histone H2AX. (PubMed id 12697768)1, 2, 9 Ward I.M.... Chen J. (J. Biol. Chem. 2003)
    3. DNA-PK is activated by nucleosomes and phosphorylates H2AX within the nucleosomes in an acetylation-dependent manner. (PubMed id 14627815)1, 2, 9 Park E.-J.... Kwon J. (Nucleic Acids Res. 2003)
    4. A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. (PubMed id 10959836)1, 2, 9 Paull T.T....Bonner W.M. (Curr. Biol. 2000)
    5. Absence of the H2AX mutations in idiopathic infertile men with spermatogenic impairment. (PubMed id 18536151)1, 4, 9 Zhang W....Zhang S. (Syst Biol Reprod Med 2008)
    6. MDC1 is a mediator of the mammalian DNA damage checkpoint. (PubMed id 12607005)1, 2, 9 Stewart G.S.... Elledge S.J. (Nature 2003)
    7. Doxorubicin activates ATM-dependent phosphorylation of multiple downstream targets in part through the generation of reactive oxygen species. (PubMed id 15489221)1, 2, 9 Kurz E.U.... Lees-Miller S.P. (J. Biol. Chem. 2004)
    8. Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions. (PubMed id 19234442)1, 2, 9 Cook P.J.... Rosenfeld M.G. (Nature 2009)
    9. The Fanconi anemia family of genes and its correlation with breast cancer susceptibility and breast cancer features. (PubMed id 19536649)1, 4, 9 Barroso E....Ribas G. (Breast Cancer Res. Treat. 2009)
    10. Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients. (PubMed id 19638463)1, 4, 9 Pugh T.J....Moore R.A. (Clin. Cancer Res. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3014 HGNC: 4739 AceView: H2AFX Ensembl:ENSG00000188486 euGenes: HUgn3014
    ECgene: H2AFX Kegg: 3014 H-InvDB: H2AFX

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for H2AFX Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for H2AFX Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/h2afx/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for H2AFX gene:
    Search GeneIP for patents involving H2AFX

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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