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Aliases for HIST3H3 Gene

Aliases for HIST3H3 Gene

  • Histone Cluster 3 H3 2 3 5
  • H3 Histone Family, Member T 2 3
  • Histone 3, H3 2 3
  • H3FT 3 4
  • H3/G 3 4
  • H3/T 3 4
  • H3t 3 4
  • Histone Cluster 3, H3 2
  • Histone H3.1t 3
  • H3.4 3

External Ids for HIST3H3 Gene

Previous HGNC Symbols for HIST3H3 Gene

  • H3FT

Previous GeneCards Identifiers for HIST3H3 Gene

  • GC01M224351
  • GC01M224998
  • GC01M225587
  • GC01M224919
  • GC01M226679
  • GC01M228612
  • GC01M199127

Summaries for HIST3H3 Gene

Entrez Gene Summary for HIST3H3 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 H3 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is located separately from the other H3 genes that are in the histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST3H3 Gene

HIST3H3 (Histone Cluster 3 H3) is a Protein Coding gene. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and Mitotic Prophase. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and histone binding. An important paralog of this gene is HIST1H3I.

UniProtKB/Swiss-Prot for HIST3H3 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 HIST3H3 Gene

Additional gene information for HIST3H3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST3H3 Gene

Genomics for HIST3H3 Gene

GeneHancer (GH) Regulatory Elements for HIST3H3 Gene

Promoters and enhancers for HIST3H3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I228425 Promoter 0.6 EPDnew 550.8 -0.1 -53 0.1 ZBTB33 GC01M228428 HIST3H3 PIR49023 PIR35552 PIR36887 GC01M228427 RPL23AP15
GH01I227562 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 27.4 +861.5 861454 1.9 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 ZNF678 CICP26 C1orf35 HIST3H3 ENSG00000269890 IBA57 CDC42BPA SNAP47 MRPL57P2
GH01I229341 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 28.8 -917.6 -917574 3.8 ARNT ARID4B SIN3A FEZF1 ZNF2 POLR2B ZNF207 ZNF143 SP3 SP5 CCSAP NUP133 HIST3H3 URB2 RNU6-180P ACTA1 TMEM78 GC01M228906
GH01I228455 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 21.3 -32.6 -32576 4.2 CLOCK FEZF1 ZNF213 E2F8 ZNF143 SP3 ZFP41 ZNF610 GLIS1 NBN GC01M228457 HIST3H2A HIST3H2BB CICP26 C1orf35 ENSG00000269890 ZNF678 HIST3H3 LOC105373159 JMJD4
GH01I228781 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 28 -357.7 -357738 3.7 FEZF1 ZNF2 ZNF213 ZNF302 ZNF416 FOS KLF13 REST KAT8 MIER3 NUP133 CICP26 C1orf35 ENSG00000269890 HMGN2P19 ABCB10 HIST3H3 TAF5L URB2 LOC105373159
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HIST3H3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST3H3 gene promoter:

Genomic Locations for HIST3H3 Gene

Genomic Locations for HIST3H3 Gene
481 bases
Minus strand

Genomic View for HIST3H3 Gene

Genes around HIST3H3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST3H3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST3H3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST3H3 Gene

Proteins for HIST3H3 Gene

  • Protein details for HIST3H3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone H3.1t
    Protein Accession:
    Secondary Accessions:
    • B2R5K3
    • Q6FGU4

    Protein attributes for HIST3H3 Gene

    136 amino acids
    Molecular mass:
    15508 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.

    Three dimensional structures from OCA and Proteopedia for HIST3H3 Gene

neXtProt entry for HIST3H3 Gene

Post-translational modifications for HIST3H3 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 (By similarity).
  • 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 (By similarity).
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • 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 (By similarity).
  • 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 (By similarity).
  • Phosphorylated at Thr-4 (H3T3ph) by 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 MAP3K20 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 Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin (By similarity).
  • Ubiquitinated.

Other Protein References for HIST3H3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST3H3 Gene

Domains & Families for HIST3H3 Gene

Gene Families for HIST3H3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HIST3H3 Gene

Suggested Antigen Peptide Sequences for HIST3H3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the histone H3 family.
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with HIST3H3: view

Function for HIST3H3 Gene

Molecular function for HIST3H3 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.

Phenotypes From GWAS Catalog for HIST3H3 Gene

Gene Ontology (GO) - Molecular Function for HIST3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 17537733
GO:0031492 nucleosomal DNA binding IBA --
GO:0042393 histone binding IPI --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST3H3: view
genes like me logo Genes that share phenotypes with HIST3H3: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST3H3 Gene

Localization for HIST3H3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST3H3 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 HIST3H3 gene
Compartment Confidence
extracellular 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HIST3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 nuclear chromosome, telomeric region HDA 19135898
GO:0000786 nucleosome IDA 25615412
GO:0000788 nuclear nucleosome IDA 20498094
GO:0005634 nucleus HDA,IEA 21630459
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with HIST3H3: view

Pathways & Interactions for HIST3H3 Gene

genes like me logo Genes that share pathways with HIST3H3: view

Gene Ontology (GO) - Biological Process for HIST3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
GO:0006334 nucleosome assembly IMP 20498094
GO:0016233 telomere capping TAS --
GO:0032460 negative regulation of protein oligomerization IMP 20498094
GO:0051290 protein heterotetramerization IDA 20498094
genes like me logo Genes that share ontologies with HIST3H3: view

No data available for SIGNOR curated interactions for HIST3H3 Gene

Drugs & Compounds for HIST3H3 Gene

No Compound Related Data Available

Transcripts for HIST3H3 Gene

mRNA/cDNA for HIST3H3 Gene

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

Unigene Clusters for HIST3H3 Gene

Histone cluster 3, H3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST3H3 Gene

No ASD Table

Relevant External Links for HIST3H3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIST3H3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST3H3 Gene

mRNA differential expression in normal tissues according to GTEx for HIST3H3 Gene

This gene is overexpressed in Testis (x26.8).

Protein differential expression in normal tissues from HIPED for HIST3H3 Gene

This gene is overexpressed in Tlymphocyte (14.5), Peripheral blood mononuclear cells (12.0), Nasal epithelium (10.3), Monocytes (8.9), Blymphocyte (7.5), and Neutrophil (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HIST3H3 Gene

Protein tissue co-expression partners for HIST3H3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST3H3 Gene:


SOURCE GeneReport for Unigene cluster for HIST3H3 Gene:


mRNA Expression by UniProt/SwissProt for HIST3H3 Gene:

Tissue specificity: Expressed in testicular cells.

Evidence on tissue expression from TISSUES for HIST3H3 Gene

  • Lung(4.4)
  • Adrenal gland(2.1)
  • Bone marrow(2.1)
  • Heart(2.1)
  • Intestine(2.1)
  • Kidney(2.1)
  • Liver(2.1)
  • Lymph node(2.1)
  • Muscle(2.1)
  • Pancreas(2.1)
  • Skin(2.1)
  • Spleen(2.1)
  • Stomach(2.1)
  • Thyroid gland(2.1)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with HIST3H3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST3H3 Gene

Orthologs for HIST3H3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HIST3H3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia -- 34
  • 97 (a)
LOC518318 33
  • 81.13 (n)
(Pan troglodytes)
Mammalia -- 34
  • 97 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493041 33
  • 82.84 (n)
(Danio rerio)
Actinopterygii LOC570703 33
  • 81.13 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33860 33
  • 80.39 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 90 (a)
-- 34
  • 90 (a)
Species where no ortholog for HIST3H3 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIST3H3 Gene

Gene Tree for HIST3H3 (if available)
Gene Tree for HIST3H3 (if available)

Paralogs for HIST3H3 Gene

Variants for HIST3H3 Gene

Sequence variations from dbSNP and Humsavar for HIST3H3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000042512 -- 228,425,096(-) T/G coding_sequence_variant, missense_variant
rs1001475235 -- 228,425,492(-) T/A upstream_transcript_variant
rs1001607156 -- 228,425,038(-) C/G coding_sequence_variant, synonymous_variant
rs1003379877 -- 228,426,947(-) C/G upstream_transcript_variant
rs1003801489 -- 228,425,092(-) G/ coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for HIST3H3 Gene

Variant ID Type Subtype PubMed ID
esv32853 CNV gain 17666407
nsv1013500 CNV gain 25217958
nsv508697 CNV deletion 20534489
nsv517545 CNV loss 19592680
nsv523935 CNV loss 19592680
nsv549296 CNV gain 21841781
nsv826908 CNV gain 20364138
nsv827019 CNV loss 20364138

Variation tolerance for HIST3H3 Gene

Residual Variation Intolerance Score: 58.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.73; 46.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIST3H3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST3H3 Gene

Disorders for HIST3H3 Gene

Additional Disease Information for HIST3H3

No disorders were found for HIST3H3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST3H3 Gene

Publications for HIST3H3 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 58
  2. A solitary human H3 histone gene on chromosome 1. (PMID: 8834248) Albig W … Doenecke D (Human genetics 1996) 2 3 4 58
  3. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. (PMID: 20850016) Vermeulen M … Mann M (Cell 2010) 3 4 58
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  5. 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 58

Products for HIST3H3 Gene

Sources for HIST3H3 Gene

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