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Aliases for H2AFB3 Gene

Aliases for H2AFB3 Gene

  • H2A Histone Family, Member B3 2 3
  • H2A Barr Body-Deficient 3 4
  • H2A.Bbd 3 4
  • H2ABBD 3 4
  • H2AFB 3 4
  • Histone Variant H2A, Barr-Body Deficient 3
  • H2A Histone Family, Member B 2
  • H2AFB2 H2AFB3 4

External Ids for H2AFB3 Gene

Previous HGNC Symbols for H2AFB3 Gene

  • H2AFB

Previous GeneCards Identifiers for H2AFB3 Gene

  • GC0XP154174
  • GC0XM154342
  • GC0XM154689
  • GC0XP143154

Summaries for H2AFB3 Gene

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 replication-independent histone that is 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, Oct 2015]

GeneCards Summary for H2AFB3 Gene

H2AFB3 (H2A Histone Family, Member B3) is a Protein Coding gene. Among its related pathways are RNA Polymerase I Promoter Opening. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is H2AFB2.

UniProtKB/Swiss-Prot for H2AFB3 Gene

  • 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H2AFB3 Gene

Genomics for H2AFB3 Gene

Regulatory Elements for H2AFB3 Gene

Genomic Location for H2AFB3 Gene

Chromosome:
X
Start:
155,459,415 bp from pter
End:
155,460,005 bp from pter
Size:
591 bases
Orientation:
Minus strand

Genomic View for H2AFB3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for H2AFB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AFB3 Gene

Proteins for H2AFB3 Gene

  • Protein details for H2AFB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0C5Z0-H2AB2_HUMAN
    Recommended name:
    Histone H2A-Bbd type 2/3
    Protein Accession:
    P0C5Z0
    Secondary Accessions:
    • A1L4E4
    • P98176
    • Q5TZB2
    • Q6FG78
    • Q96PR7

    Protein attributes for H2AFB3 Gene

    Size:
    115 amino acids
    Molecular mass:
    12713 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. May be incorporated into a proportion of nucleosomes, replacing one or more H2A molecules
    • 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
    Miscellaneous:
    • In contrast to other H2A histones, it does not contain the conserved residues that are the target of post-translational modifications

neXtProt entry for H2AFB3 Gene

Proteomics data for H2AFB3 Gene at MOPED

Post-translational modifications for H2AFB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H2AFB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AFB3 Gene

Domains & Families for H2AFB3 Gene

Gene Families for H2AFB3 Gene

HGNC:

Protein Domains for H2AFB3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for H2AFB3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P0C5Z0

UniProtKB/Swiss-Prot:

H2AB2_HUMAN :
  • The docking domain is responsible for the weaker heterodimerization with H2B.
  • Belongs to the histone H2A family.
Domain:
  • The docking domain is responsible for the weaker heterodimerization with H2B.
Family:
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with H2AFB3: view

Function for H2AFB3 Gene

Molecular function for H2AFB3 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for H2AFB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AFB3: view
genes like me logo Genes that share phenotypes with H2AFB3: view

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for H2AFB3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for H2AFB3 Gene

Localization for H2AFB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AFB3 Gene

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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for H2AFB3 Gene COMPARTMENTS Subcellular localization image for H2AFB3 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for H2AFB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome --
GO:0000788 nuclear nucleosome IDA 22795134
GO:0005634 nucleus IDA 21630459
GO:0035327 transcriptionally active chromatin IDA 22795134
genes like me logo Genes that share ontologies with H2AFB3: view

Pathways & Interactions for H2AFB3 Gene

SuperPathways for H2AFB3 Gene

genes like me logo Genes that share pathways with H2AFB3: view

Pathways by source for H2AFB3 Gene

2 KEGG pathways for H2AFB3 Gene

Interacting Proteins for H2AFB3 Gene

Gene Ontology (GO) - Biological Process for H2AFB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IDA 22795134
GO:0006342 chromatin silencing IBA --
GO:0006397 mRNA processing IMP 22795134
genes like me logo Genes that share ontologies with H2AFB3: view

No data available for SIGNOR curated interactions for H2AFB3 Gene

Drugs & Compounds for H2AFB3 Gene

No Compound Related Data Available

Transcripts for H2AFB3 Gene

mRNA/cDNA for H2AFB3 Gene

(1) REFSEQ mRNAs :
(16) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for H2AFB3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for H2AFB3 Gene

No ASD Table

Relevant External Links for H2AFB3 Gene

GeneLoc Exon Structure for
H2AFB3
ECgene alternative splicing isoforms for
H2AFB3

Expression for H2AFB3 Gene

mRNA expression in normal human tissues for H2AFB3 Gene

Protein differential expression in normal tissues from HIPED for H2AFB3 Gene

This gene is overexpressed in Testis (36.4) and Ovary (32.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for H2AFB3 Gene



SOURCE GeneReport for Unigene cluster for H2AFB3 Gene Hs.632841

mRNA Expression by UniProt/SwissProt for H2AFB3 Gene

P0C5Z0-H2AB2_HUMAN
Tissue specificity: Present in mature sperm.
genes like me logo Genes that share expression patterns with H2AFB3: view

Protein tissue co-expression partners for H2AFB3 Gene

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for H2AFB3 Gene

Orthologs for H2AFB3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2AFB3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC528006 35
  • 73.21 (n)
  • 65.42 (a)
dog
(Canis familiaris)
Mammalia LOC102152481 35
  • 69.93 (n)
  • 58.7 (a)
mouse
(Mus musculus)
Mammalia H2afb3-ps 35
  • 64.87 (n)
  • 60.22 (a)
rat
(Rattus norvegicus)
Mammalia H2afb3 35
  • 63.8 (n)
  • 60.22 (a)
Species with no ortholog for H2AFB3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for H2AFB3 Gene

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

Paralogs for H2AFB3 Gene

Paralogs for H2AFB3 Gene

genes like me logo Genes that share paralogs with H2AFB3: view

Variants for H2AFB3 Gene

Sequence variations from dbSNP and Humsavar for H2AFB3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs5983725 -- 155,461,485(-) gggcc(A/G)agaag upstream-variant-2KB
rs12389952 -- 155,461,387(+) cagaa(C/T)ggtaa upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for H2AFB3 Gene

Variant ID Type Subtype PubMed ID
esv33784 CNV Gain+Loss 17666407
esv29972 CNV Gain 17803354
nsv508817 CNV Insertion 20534489
nsv7470 OTHER Inversion 18451855
nsv499361 OTHER Inversion 21111241

Relevant External Links for H2AFB3 Gene

HapMap Linkage Disequilibrium report
H2AFB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for H2AFB3 Gene

Disorders for H2AFB3 Gene

Relevant External Links for H2AFB3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
H2AFB3
genes like me logo Genes that share disorders with H2AFB3: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2AFB3 Gene

Publications for H2AFB3 Gene

  1. Histone variant H2ABbd confers lower stability to the nucleosome. (PMID: 15192699) Gautier T. … Dimitrov S. (EMBO Rep. 2004) 23 67
  2. Mammal-specific H2A variant, H2ABbd, is involved in apoptotic induction via activation of NF-I_B signaling pathway. (PMID: 24584930) Goshima T. … Nakanishi M. (J. Biol. Chem. 2014) 67
  3. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (PMID: 22795134) Tolstorukov M.Y. … Park P.J. (Mol. Cell 2012) 67
  4. Proteomic characterization of the human sperm nucleus. (PMID: 21630459) de Mateo S. … Oliva R. (Proteomics 2011) 67
  5. H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. (PMID: 20008104) Ishibashi T. … Ausio J. (Nucleic Acids Res. 2010) 67

Products for H2AFB3 Gene

Sources for H2AFB3 Gene

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