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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

H2AFB3 Gene

protein-coding   GIFtS: 43
GCID: GC0XM154689

H2A Histone Family, Member B3

(Previous names: H2A histone family, member B)
(Previous symbol: H2AFB)
  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)
About This Section

Aliases
H2A Histone Family, Member B31 2     H2A Barr Body-Deficient2 3
H2AFB1 2 3     H2A Histone Family, Member B1
H2A.Bbd2 3     Histone H2A-Bbd Type 2/32
H2ABBD2 3     Histone Variant H2A, Barr-Body Deficient2

External Ids:    HGNC: 144551   Entrez Gene: 837402   Ensembl: ENSG000001859787   OMIM: 3004455   UniProtKB: P0C5Z03   

Export aliases for H2AFB3 gene to outside databases

Previous GC identifers: GC0XP154174 GC0XM154342 GC0XP143154


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for H2AFB3 Gene:
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in
eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs
of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the
interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin
structures. This gene encodes a member of the histone H2A family. This gene is part of a region that is repeated
three times on chromosome X, once in intron 22 of the F8 gene and twice closer to the Xq telomere. This record
represents the most telomeric copy. (provided by RefSeq, Jul 2008)

GeneCards Summary for H2AFB3 Gene: 
H2AFB3 (H2A histone family, member B3) is a protein-coding gene. Diseases associated with H2AFB3 include systemic lupus erythematosus, and lupus erythematosus, and among its related super-pathways are Systemic lupus erythematosus. An important paralog of this gene is H2AFB1.

UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
Function: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with
active transcription and mRNA processing. 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. Nucleosomes containing this
histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively
transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome
components and are required for mRNA splicing. May participate in spermatogenesis




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NT_167198.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the H2AFB3 gene promoter:
         Pax-5   MyoD   Olf-1   AP-4   En-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for H2AFB3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat H2AFB3


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

Entrez Gene cytogenetic band: Xq28   Ensembl cytogenetic band:  Xq28   HGNC cytogenetic band: Xq28

H2AFB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H2AFB3 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM154689:  view genomic region     (about GC identifiers)

Start:
154,689,080 bp from pter      End:
154,689,596 bp from pter
Size:
517 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0 (See protein sequence)
Recommended Name: Histone H2A-Bbd type 2/3  
Size: 115 amino acids; 12713 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. May be incorporated into a proportion of nucleosomes,
replacing one or more H2A molecules
Subcellular location: Nucleus. Chromosome. Note=Associated with the active X chromosome and with autosomes, while
it is absent from the inactive X chromosome and excluded from Barr bodies
Miscellaneous: In contrast to other H2A histones, it does not contain the conserved residues that are the target
of post-translational modifications
Secondary accessions: A1L4E4 P98176 Q5TZB2 Q6FG78 Q96PR7

Explore the universe of human proteins at neXtProt for H2AFB3: NX_P0C5Z0

Explore proteomics data for H2AFB3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P0C5Z0

  • H2AFB3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    H2AFB3 Protein Expression
    REFSEQ proteins: NP_542451.1  
    ENSEMBL proteins: 
     ENSP00000358452  

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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000786nucleosome ----
    GO:0000788nuclear nucleosome ----
    GO:0005634nucleus ----
    GO:0035327transcriptionally active chromatin ----

    H2AFB3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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 P0C5Z0

    ProtoNet protein and cluster: P0C5Z0

    UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
    Domain: The docking domain is responsible for the weaker heterodimerization with H2B
    Similarity: Belongs to the histone H2A family


    H2AFB3 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: H2AB2_HUMAN, P0C5Z0
    Function: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with
    active transcription and mRNA processing. 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. Nucleosomes containing this
    histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively
    transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome
    components and are required for mRNA splicing. May participate in spermatogenesis

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0046982protein heterodimerization activity ----
         
    H2AFB3 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for H2AFB3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Alcoholism
    Alcoholism0.34
    Systemic lupus erythematosus0.34

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    2         Kegg Pathways  (Kegg details for H2AFB3):
        Alcoholism
    Systemic lupus erythematosus


    H2AFB3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for H2AFB3

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006334nucleosome assembly ----
    GO:0006397mRNA processing ----

    H2AFB3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for H2AFB3 (H2AB2)

    Search CenterWatch for drugs/clinical trials and news about H2AFB3 / H2AB2

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for H2AFB3 gene: 
    NM_080720.1  

    Unigene Cluster for H2AFB3:

    H2A histone family, member B3
    Hs.632841
    Unigene Representative Sequence: BC130510
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000369444(uc004fnk.3)
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat H2AFB3

    Additional mRNA sequence: 

    AF254576.1 BC101415.1 BC101417.1 BC101418.1 BC130510.1 

    2 DOTS entries:

    DT.121303715  DT.410848 

    16 AceView cDNA sequences:

    BM722299 AF254576 BU740141 AW183040 AI218259 AA428596 AA432232 AA703660 
    AA868831 AA993742 AA879431 AI018669 AI205744 AA912999 AI204297 AI218431 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    H2AFB3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    H2AFB3 Expression
    About this image


    See H2AFB3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for H2AFB3

    SOURCE GeneReport for Unigene cluster: Hs.632841

    UniProtKB/Swiss-Prot: H2AB2_HUMAN, P0C5Z0
    Tissue specificity: Present in mature sperm

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H2AFB3

    (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)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for H2AFB3 gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia HIST1H2AA6
    Histone H2A
    33(a)
    1 → many
    GL344481.1(11179-11601)
    worm
    (Caenorhabditis elegans)
    Secernentea htas-16
    Protein HTAS-1
    24(a)
    1 → many
    IV(9682984-9683532)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HTA26
    HTA16
    Histone H2A, core histone protein required for chr...
    Histone H2A, core histone protein required for chr...
    35(a)
    35(a)
    many ↔ many
    many ↔ many
    II(235394-235792)
    IV(915530-915928)
            Species with no ortholog for H2AFB3

    ENSEMBL Gene Tree for H2AFB3 (if available)
    TreeFam Gene Tree for H2AFB3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for H2AFB3 gene
    H2AFB21 2  H2AFB11 2  H2AFY22  H2AFX2  H2AFY2  
    18/25 SIMAP similar genes for H2AFB3 using alignment to 1 protein entry:     H2AB2_HUMAN(see all similar genes):
    H2AFB1    H2AFX    HIST1H2AA    HIST1H2AB    HIST1H2AC    HIST1H2AD
    HIST1H2AE    HIST1H2AG    HIST1H2AH    HIST1H2AI    HIST1H2AJ    HIST1H2AK
    HIST1H2AL    HIST1H2AM    HIST1H2APS4    HIST2H2AA3    HIST2H2AA4    HIST2H2AB

    H2AFB3 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    2 SNPs in H2AFB3 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1879793331,2
    --142657763(+) CAGTCC/TAGAAA 1 -- ds50010--------
    rs2009509591,2
    ----142657744(+) CGGGGA/GGGGGG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for H2AFB3 (154689080 - 154689596 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for H2AFB3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv508817CNV Insertion20534489
    esv29972CNV Gain17803354
    esv33784CNV Gain+Loss17666407
    nsv499361OTHER Inversion21111241
    nsv7470OTHER Inversion18451855

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 300445    OMIM disorders: --

    2 diseases for H2AFB3:    About MalaCards
    systemic lupus erythematosus    lupus erythematosus


    H2AFB3 for disorders           About GeneDecksing


    Export disorders for H2AFB3 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)
    About This Section

    PubMed articles for H2AFB3 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with H2AFB3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
    2. Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I. (PubMed id 16287874)1, 2 Okuwaki M.... Nagata K. (2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. (PubMed id 15257289)1, 2 Bao Y.... Luger K. (2004)
    5. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. (PubMed id 11266453)1, 2 Chadwick B.P. and Willard H.F. (2001)
    6. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (PubMed id 22795134)2 Tolstorukov M.Y....Park P.J. (2012)
    7. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. (PubMed id 20008104)2 Ishibashi T.... Ausio J. (2010)
    8. Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd. (PubMed id 18329190)2 Gonzalez-Romero R.... Eirin-Lopez J.M. (2008)
    9. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way. (PubMed id 17726088)2 Eirin-Lopez J.M.... Ausio J. (2008)
    10. Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. (PubMed id 16957777)2 Doyen C.M.... Dimitrov S. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
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    NCBI Bookshelf
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 83740 HGNC: 14455 AceView: H2AFB Ensembl:ENSG00000185978 euGenes: HUgn83740
    ECgene: H2AFB3 Kegg: 83740 H-InvDB: H2AFB3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for H2AFB3 Pharmacogenomics, SNPs, Pathways
    Wikipedia http://en.wikipedia.org/wiki/Histone_H2A

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for H2AFB3 gene:
    Search GeneIP for patents involving H2AFB3

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



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