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Aliases for HIST3H2A Gene

Aliases for HIST3H2A Gene

  • Histone Cluster 3 H2A 2 3 5
  • Histone Cluster 3, H2a 2
  • Histone 3, H2a 2

External Ids for HIST3H2A Gene

Previous GeneCards Identifiers for HIST3H2A Gene

  • GC01M224383
  • GC01M225030
  • GC01M225619
  • GC01M224951
  • GC01M226711
  • GC01M228645
  • GC01M199159

Summaries for HIST3H2A Gene

Entrez Gene Summary for HIST3H2A 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 is intronless and encodes a replication-dependent histone that is a member of the histone H2A family. Transcripts from this gene contain a palindromic termination element. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST3H2A Gene

HIST3H2A (Histone Cluster 3 H2A) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Deubiquitination. GO annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST1H2AC.

UniProtKB/Swiss-Prot for HIST3H2A Gene

  • Core component of nucleosome. 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.

Gene Wiki entry for HIST3H2A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST3H2A Gene

Genomics for HIST3H2A Gene

Regulatory Elements for HIST3H2A Gene

Enhancers for HIST3H2A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G228500 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.2 -43.0 -43028 1.8 PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 ZNF48 ZNF766 ELK1 ZNF143 REST HIST3H3 HIST3H2A HIST3H2BB RPL23AP15 CICP26 OBSCN-AS1 OBSCN C1orf35 RNF187 LOC105373124
GH01G228377 1.5 Ensembl ENCODE dbSUPER 11.2 +79.2 79172 1.8 AGO1 SIN3A ZNF2 ZNF121 GLIS2 KLF7 SP3 TSHZ1 REST ZNF623 TRIM11 ENSG00000231563 RPL23AP15 HIST3H2BB HIST3H2A OBSCN-AS1 OBSCN ENSG00000270104 LOC101927401
GH01G228130 1.3 Ensembl ENCODE 10.9 +326.3 326262 2.0 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 ZNF2 ZNF143 FOS ZNF548 CICP26 C1orf35 ENSG00000269890 OBSCN OBSCN-AS1 HIST3H3 RPL23AP15 HIST3H2BB HIST3H2A ENSG00000231563
GH01G228212 1.3 ENCODE dbSUPER 10.8 +242.9 242891 4.8 AGO1 ARID4B SIN3A YBX1 ZNF2 CBX5 ZNF143 KLF13 ZNF263 SP3 OBSCN RPL23AP15 HIST3H2A HIST3H2BB OBSCN-AS1 PIR37830
GH01G228137 1.4 ENCODE dbSUPER 10 +315.8 315809 8.8 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 OBSCN CICP26 ENSG00000269890 OBSCN-AS1 FAM96AP2 MRPL55 C1orf35 ENSG00000231563 RPL23AP15 HIST3H2BB
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST3H2A on UCSC Golden Path with GeneCards custom track

Promoters for HIST3H2A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000257116 -227 3001 CREB3L1 AGO1 FEZF1 YBX1 ZNF143 ZNF263 MCM3 SP3 ZFP41 ZNF610

Genomic Location for HIST3H2A Gene

228,456,979 bp from pter
228,457,873 bp from pter
895 bases
Minus strand

Genomic View for HIST3H2A Gene

Genes around HIST3H2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST3H2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST3H2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST3H2A Gene

Proteins for HIST3H2A Gene

  • Protein details for HIST3H2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone H2A type 3
    Protein Accession:
    Secondary Accessions:
    • B2R4S4

    Protein attributes for HIST3H2A Gene

    130 amino acids
    Molecular mass:
    14121 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.

neXtProt entry for HIST3H2A Gene

Post-translational modifications for HIST3H2A Gene

  • Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
  • Deiminated on Arg-4 in granulocytes upon calcium entry.
  • Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239).
  • Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM27 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of Lys-27 of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Monoubiquitination of Lys-120 (H2AK119Ub) by TRIM27 may promote transformation of cells in a number of breast cancers (PubMed:25470042). 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.
  • Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by VPRBP is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription.
  • Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • Ubiquitination at posLast=1414 and isoforms=16
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST3H2A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST3H2A Gene

Domains & Families for HIST3H2A Gene

Gene Families for HIST3H2A Gene

Protein Domains for HIST3H2A Gene

Suggested Antigen Peptide Sequences for HIST3H2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the histone H2A family.
  • Belongs to the histone H2A family.
genes like me logo Genes that share domains with HIST3H2A: view

Function for HIST3H2A Gene

Molecular function for HIST3H2A Gene

UniProtKB/Swiss-Prot Function:
Core component of nucleosome. 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.

Gene Ontology (GO) - Molecular Function for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IDA 22334663
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST3H2A: view
genes like me logo Genes that share phenotypes with HIST3H2A: view

Animal Model Products

miRNA for HIST3H2A Gene

miRTarBase miRNAs that target HIST3H2A

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST3H2A Gene

Localization for HIST3H2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST3H2A Gene

Nucleus. Chromosome.

Subcellular locations from

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 HIST3H2A gene
Compartment Confidence
extracellular 5
nucleus 5

Gene Ontology (GO) - Cellular Components for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000788 nuclear nucleosome IDA 22334663
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0070062 extracellular exosome IDA 23533145
genes like me logo Genes that share ontologies with HIST3H2A: view

Pathways & Interactions for HIST3H2A Gene

genes like me logo Genes that share pathways with HIST3H2A: view

Pathways by source for HIST3H2A Gene

Gene Ontology (GO) - Biological Process for HIST3H2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006337 nucleosome disassembly IMP 22334663
GO:0006342 chromatin silencing IBA --
GO:0070914 UV-damage excision repair IMP 22334663
genes like me logo Genes that share ontologies with HIST3H2A: view

No data available for SIGNOR curated interactions for HIST3H2A Gene

Drugs & Compounds for HIST3H2A Gene

(1) Drugs for HIST3H2A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with HIST3H2A: view

Transcripts for HIST3H2A Gene

mRNA/cDNA for HIST3H2A Gene

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

Unigene Clusters for HIST3H2A Gene

Histone cluster 3, H2a:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST3H2A Gene

No ASD Table

Relevant External Links for HIST3H2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIST3H2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST3H2A Gene

mRNA differential expression in normal tissues according to GTEx for HIST3H2A Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.8) and Brain - Cerebellum (x4.8).

Protein differential expression in normal tissues from HIPED for HIST3H2A Gene

This gene is overexpressed in Saliva (40.6) and Heart (18.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HIST3H2A Gene

Protein tissue co-expression partners for HIST3H2A Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST3H2A Gene:


SOURCE GeneReport for Unigene cluster for HIST3H2A Gene:


Evidence on tissue expression from TISSUES for HIST3H2A Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with HIST3H2A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST3H2A Gene

Orthologs for HIST3H2A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST3H2A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HIST3H2A 34 35
  • 99.74 (n)
(Canis familiaris)
Mammalia HIST3H2A 35
  • 99 (a)
(Bos Taurus)
Mammalia HIST3H2A 35
  • 98 (a)
LOC614881 34
  • 83.08 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 94 (a)
-- 35
  • 94 (a)
-- 35
  • 94 (a)
-- 35
  • 91 (a)
-- 35
  • 91 (a)
(Mus musculus)
Mammalia Hist3h2a 34 16 35
  • 86.67 (n)
(Rattus norvegicus)
Mammalia Hist1h2aa 34
  • 84.36 (n)
(Gallus gallus)
Aves H2A-VII 35
  • 97 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 98 (a)
(Hordeum vulgare)
Liliopsida Hv.8481 34
(Oryza sativa)
Liliopsida Os.12821 34
Species where no ortholog for HIST3H2A was found in the sources mined by GeneCards:
  • 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)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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)
  • 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 HIST3H2A Gene

Gene Tree for HIST3H2A (if available)
Gene Tree for HIST3H2A (if available)

Paralogs for HIST3H2A Gene

Variants for HIST3H2A Gene

Sequence variations from dbSNP and Humsavar for HIST3H2A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000238442 -- 228,458,768(+) AGTAA(C/T)GTTGG downstream-variant-500B, upstream-variant-2KB
rs1001050817 -- 228,458,095(+) CCGAG(C/G)GCCGC upstream-variant-2KB
rs1002053230 -- 228,457,188(+) TTCCC(-/TGT)TGTTA downstream-variant-500B, upstream-variant-2KB
rs1002084351 -- 228,457,042(+) TTGAT(G/T)ACCAC downstream-variant-500B, upstream-variant-2KB
rs1003133451 -- 228,457,383(+) AAGAG(A/C)CTTTA upstream-variant-2KB, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for HIST3H2A Gene

Variant ID Type Subtype PubMed ID
esv32853 CNV gain 17666407
nsv1013500 CNV gain 25217958
nsv517545 CNV loss 19592680
nsv523935 CNV loss 19592680
nsv549296 CNV gain 21841781
nsv826908 CNV gain 20364138
nsv827019 CNV loss 20364138
nsv945354 CNV duplication 23825009

Variation tolerance for HIST3H2A Gene

Residual Variation Intolerance Score: 37.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.24; 5.31% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST3H2A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST3H2A Gene

Disorders for HIST3H2A Gene

Relevant External Links for HIST3H2A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HIST3H2A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST3H2A Gene

Publications for HIST3H2A Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
  2. DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. (PMID: 16702407) Bergink S. … Dantuma N.P. (Genes Dev. 2006) 3 4 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  4. Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. (PMID: 15823041) Hagiwara T. … Yamada M. (Biochemistry 2005) 3 4 64
  5. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. (PMID: 16359901) Cao R. … Zhang Y. (Mol. Cell 2005) 3 4 64

Products for HIST3H2A Gene

Sources for HIST3H2A Gene

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