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... See more...

Aliases for H2AB3 Gene

Aliases for H2AB3 Gene

  • H2A.B Variant Histone 3 2 3 5
  • H2A Histone Family Member B3 2 3
  • Histone H2A-Bbd Type 2/3 3 4
  • H2A Barr Body-Deficient 3 4
  • H2A.Bbd 3 4
  • H2ABBD 3 4
  • H2AFB3 3 4
  • H2AFB 3 4
  • Histone Variant H2A, Barr-Body Deficient 3
  • H2A Histone Family, Member B3 2
  • H2A Histone Family, Member B 2
  • H2AFB2 4
  • H2AB2 3
  • H2AB3 5

External Ids for H2AB3 Gene

Previous HGNC Symbols for H2AB3 Gene

  • H2AFB
  • H2AFB3

Summaries for H2AB3 Gene

Entrez Gene Summary for H2AB3 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 H2AB3 Gene

H2AB3 (H2A.B Variant Histone 3) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Necroptosis. An important paralog of this gene is H2AB2.

UniProtKB/Swiss-Prot Summary for H2AB3 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.

Additional gene information for H2AB3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2AB3 Gene

Genomics for H2AB3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2AB3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ155466 Promoter 0.7 EPDnew Ensembl 0.4 -6.8 -6796 0.8 ENSG00000225393 TMLHE-AS1 H2AB3 SPRY3
GH0XJ155456 Promoter 0.3 Ensembl 0.7 +2.1 2104 3.4 F8A3 MIR1184-3 F8A1 H2AB3 F8A2
GH0XJ155611 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 0.1 -152.3 -152295 3 HNRNPL CREB1 PRDM10 ZNF629 ZNF692 PRDM1 ZSCAN4 RBFOX2 PATZ1 ZNF501 TMLHE SPRY3 lnc-H2AFB3-2 piR-61514-227 lnc-TMLHE-2 TMLHE-AS1 H2AB3
GH0XJ155577 Enhancer 0.3 Ensembl 0.1 -117.8 -117795 1.2 CTCF ZBTB40 TMLHE piR-61514-227 piR-32023-287 SPRY3 lnc-TMLHE-2 TMLHE-AS1 H2AB3
GH0XJ155557 Enhancer 0.2 Ensembl 0.2 -97.3 -97296 0.2 TMLHE piR-32023-287 MG828668-144 SPRY3 TMLHE-AS1 H2AB3 lnc-TMLHE-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2AB3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2AB3

Genomic Locations for H2AB3 Gene

Genomic Locations for H2AB3 Gene
chrX:155,459,415-155,460,005
(GRCh38/hg38)
Size:
591 bases
Orientation:
Minus strand
chrX:154,689,080-154,689,596
(GRCh37/hg19)
Size:
517 bases
Orientation:
Minus strand

Genomic View for H2AB3 Gene

Genes around H2AB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2AB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2AB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2AB3 Gene

Proteins for H2AB3 Gene

  • Protein details for H2AB3 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 H2AB3 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.
    Miscellaneous:
    • In contrast to other H2A histones, it does not contain the conserved residues that are the target of post-translational modifications.

    Three dimensional structures from OCA and Proteopedia for H2AB3 Gene

neXtProt entry for H2AB3 Gene

Post-translational modifications for H2AB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H2AB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2AB3 Gene

Domains & Families for H2AB3 Gene

Gene Families for H2AB3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for H2AB3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for H2AB3 Gene

GenScript: Design optimal peptide antigens:
  • H2A Barr body-deficient (H2AB2_HUMAN)

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 H2AB3: view

Function for H2AB3 Gene

Molecular function for H2AB3 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 H2AB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA 21873635
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2AB3: view
genes like me logo Genes that share phenotypes with H2AB3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AB3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for H2AB3 Gene

Localization for H2AB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2AB3 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. {ECO:0000269 PubMed:20008104}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for H2AB3 gene
Compartment Confidence
nucleus 5
mitochondrion 0

Gene Ontology (GO) - Cellular Components for H2AB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0000788 nuclear nucleosome IDA 22795134
GO:0000790 nuclear chromatin IBA 21873635
GO:0005634 nucleus IEA,HDA 21630459
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2AB3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H2AB3 Gene

Pathways & Interactions for H2AB3 Gene

genes like me logo Genes that share pathways with H2AB3: view

Pathways by source for H2AB3 Gene

3 KEGG pathways for H2AB3 Gene

Gene Ontology (GO) - Biological Process for H2AB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IBA 21873635
GO:0006334 nucleosome assembly IDA 22795134
GO:0006342 chromatin silencing IBA 21873635
GO:0006397 mRNA processing IMP 22795134
genes like me logo Genes that share ontologies with H2AB3: view

No data available for SIGNOR curated interactions for H2AB3 Gene

Drugs & Compounds for H2AB3 Gene

No Compound Related Data Available

Transcripts for H2AB3 Gene

mRNA/cDNA for H2AB3 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2AB3

Alternative Splicing Database (ASD) splice patterns (SP) for H2AB3 Gene

No ASD Table

Relevant External Links for H2AB3 Gene

GeneLoc Exon Structure for
H2AB3

Expression for H2AB3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2AB3

SOURCE GeneReport for Unigene cluster for H2AB3 Gene:

Hs.632841

mRNA Expression by UniProt/SwissProt for H2AB3 Gene:

P0C5Z0-H2AB2_HUMAN
Tissue specificity: Present in mature sperm.

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2AB3 Gene

Orthologs for H2AB3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2AB3 Gene

Organism Taxonomy Gene Similarity Type Details
Cow
(Bos Taurus)
Mammalia LOC528006 30
  • 73.21 (n)
Dog
(Canis familiaris)
Mammalia LOC102152481 30
  • 69.93 (n)
Mouse
(Mus musculus)
Mammalia H2afb3-ps 30
  • 64.87 (n)
H2ab1 17
H2ab2 17
H2ab3 17
Rat
(Rattus norvegicus)
Mammalia H2afb3 30
  • 63.8 (n)
Species where no ortholog for H2AB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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 H2AB3 Gene

ENSEMBL:
Gene Tree for H2AB3 (if available)
TreeFam:
Gene Tree for H2AB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2AB3: view image

Paralogs for H2AB3 Gene

Variants for H2AB3 Gene

Additional dbSNP identifiers (rs#s) for H2AB3 Gene

Structural Variations from Database of Genomic Variants (DGV) for H2AB3 Gene

Variant ID Type Subtype PubMed ID
dgv2549e212 CNV gain 25503493
esv29972 CNV gain 17803354
esv33784 CNV gain+loss 17666407
esv3577568 CNV gain 25503493
esv3577574 CNV gain 25503493
nsv1076287 CNV deletion 25765185
nsv499361 OTHER inversion 21111241
nsv508817 CNV insertion 20534489
nsv7470 OTHER inversion 18451855

Additional Variant Information for H2AB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2AB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for H2AB3 Gene

Disorders for H2AB3 Gene

No disorders were found for H2AB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2AB3 Gene

Publications for H2AB3 Gene

  1. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. (PMID: 22795134) Tolstorukov MY … Park PJ (Molecular cell 2012) 3 4
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4
  3. Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I. (PMID: 16287874) Okuwaki M … Nagata K (Molecular and cellular biology 2005) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. (PMID: 15257289) Bao Y … Luger K (The EMBO journal 2004) 3 4

Products for H2AB3 Gene

Sources for H2AB3 Gene