Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HIST1H3A Gene

Aliases for HIST1H3A Gene

  • Histone Cluster 1, H3a 2 3
  • H3FA 3 4 6
  • H3 Histone Family, Member A 2 3
  • Histone 1, H3a 2 3
  • Histone H3/A 3 4
  • Histone H3.1 3
  • Histone H3/B 4
  • Histone H3/C 4
  • Histone H3/D 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/I 4
  • Histone H3/J 4
  • Histone H3/K 4
  • Histone H3/L 4
  • H3FC 4
  • H3FB 4
  • H3FD 4
  • H3FF 4
  • H3FH 4
  • H3FI 4
  • H3FJ 4
  • H3FK 4
  • H3FL 4
  • H3/A 3

External Ids for HIST1H3A Gene

Previous Symbols for HIST1H3A Gene

  • H3FA

Summaries for HIST1H3A Gene

Entrez Gene Summary for HIST1H3A Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an 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 member of the histone H3 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Jul 2008]

GeneCards Summary for HIST1H3A Gene

HIST1H3A (Histone Cluster 1, H3a) is a Protein Coding gene. Among its related pathways are Disease and ERK Signaling.

UniProtKB/Swiss-Prot for HIST1H3A 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 HIST1H3A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3A Gene

Genomics for HIST1H3A Gene

Genomic Location for HIST1H3A Gene

26,020,490 bp from pter
26,020,958 bp from pter
469 bases
Plus strand

Genomic View for HIST1H3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3A Gene

Regulatory Elements for HIST1H3A Gene

Proteins for HIST1H3A Gene

  • Protein details for HIST1H3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone H3.1
    Protein Accession:
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3A Gene

    136 amino acids
    Molecular mass:
    15404 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.
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2)

    Three dimensional structures from OCA and Proteopedia for HIST1H3A Gene

neXtProt entry for HIST1H3A Gene

Proteomics data for HIST1H3A Gene at MOPED

Post-translational modifications for HIST1H3A Gene

  • Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability.
  • Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3 of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • 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.
  • Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression (PubMed:22483618).
  • Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at Lys-120. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication.
  • Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins.
  • Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Thr-12 (H3T11ph) by chromatin-associated CHEK1 regulates the transcription of cell cycle regulatory genes by modulating acetylation of Lys-10 (H3K9ac). Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys19, Lys24, Lys57, Lys65, Lys80, Lys116, and Lys123

Other Protein References for HIST1H3A Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3A Gene

Domains for HIST1H3A Gene

Gene Families for HIST1H3A Gene

  • HIST :Histones / Replication-dependent

Protein Domains for HIST1H3A Gene


  • Belongs to the histone H3 family.:
    • P68431
genes like me logo Genes that share domains with HIST1H3A: view

Function for HIST1H3A Gene

Molecular function for HIST1H3A 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 HIST1H3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 10949293
GO:0042393 histone binding IPI 20498094
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H3A: view

miRNA for HIST1H3A Gene

miRTarBase miRNAs that target HIST1H3A

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for HIST1H3A Gene

Localization for HIST1H3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H3A Gene

Nucleus. Chromosome.

Subcellular locations from

Jensen Localization Image for HIST1H3A Gene COMPARTMENTS Subcellular localization image for HIST1H3A gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2

Gene Ontology (GO) - Cellular Components for HIST1H3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000786 nucleosome IDA 21636898
GO:0000788 nuclear nucleosome IDA 20498094
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 21630459
genes like me logo Genes that share ontologies with HIST1H3A: view

Pathways for HIST1H3A Gene

genes like me logo Genes that share pathways with HIST1H3A: view

Pathways by source for HIST1H3A Gene

Gene Ontology (GO) - Biological Process for HIST1H3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
genes like me logo Genes that share ontologies with HIST1H3A: view

Transcripts for HIST1H3A Gene

mRNA/cDNA for HIST1H3A Gene

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

Unigene Clusters for HIST1H3A Gene

Histone cluster 1, H3a:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H3A Gene

No ASD Table

Relevant External Links for HIST1H3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIST1H3A Gene

mRNA expression in normal human tissues for HIST1H3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H3A Gene

This gene is overexpressed in Testis (14.1) and Whole Blood (4.8).

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for HIST1H3A Gene

SOURCE GeneReport for Unigene cluster for HIST1H3A Gene Hs.546315

genes like me logo Genes that share expressions with HIST1H3A: view

Orthologs for HIST1H3A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC471886 36
  • 85.54 (n)
  • 100 (a)
(Bos Taurus)
Mammalia LOC788077 36
  • 85.29 (n)
  • 99.26 (a)
(Canis familiaris)
Mammalia LOC608586 36
  • 85.78 (n)
  • 99.26 (a)
(Mus musculus)
Mammalia Hist1h3a 16
Hist1h3d 36
  • 86.52 (n)
  • 99.26 (a)
(Rattus norvegicus)
Mammalia LOC102549173 36
  • 85.54 (n)
  • 99.26 (a)
(Gallus gallus)
Aves LOC768333 36
  • 86.52 (n)
  • 99.26 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495788 36
  • 81.62 (n)
  • 99.26 (a)
(Danio rerio)
Actinopterygii zgc:113984 36
  • 82.11 (n)
  • 99.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33833 36
  • 80.15 (n)
  • 99.26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons HTR11 36
  • 65.93 (n)
  • 92.65 (a)
Species with no ortholog for HIST1H3A:
  • 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)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIST1H3A Gene

Gene Tree for HIST1H3A (if available)
Gene Tree for HIST1H3A (if available)

Paralogs for HIST1H3A Gene

Selected SIMAP similar genes for HIST1H3A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H3A: view

No data available for Paralogs for HIST1H3A Gene

Variants for HIST1H3A Gene

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3A Gene

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914
nsv509122 CNV Insertion 20534489

Relevant External Links for HIST1H3A Gene

HapMap Linkage Disequilibrium report

No data available for Sequence variations from dbSNP and Humsavar for HIST1H3A Gene

Disorders for HIST1H3A Gene

No disorders were found for HIST1H3A Gene.

No data available for UniProtKB/Swiss-Prot for HIST1H3A Gene

Publications for HIST1H3A Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 3 4
  3. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W. … Doenecke D. (Hum. Genet. 1997) 3 4
  4. JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. (PMID: 19783980) Dawson M.A. … Kouzarides T. (Nature 2009) 3 4
  5. Ligand-dependent activation of the farnesoid X-receptor directs arginine methylation of histone H3 by CARM1. (PMID: 15471871) Ananthanarayanan M. … Walsh M.J. (J. Biol. Chem. 2004) 3 4

Products for HIST1H3A Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate HIST1H3A
  • 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
  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H3A
  • Block miRNA regulation of HIST1H3A using miScript Target Protectors

Sources for HIST1H3A Gene

Back to Top