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Aliases for H3F3A Gene

Aliases for H3F3A Gene

  • H3 Histone, Family 3A 2 3
  • H3F3 3 4 6
  • H3.3A 3 4
  • Histone H3.3 3
  • H3F3A H3F3B 4
  • H3.3B 4

External Ids for H3F3A Gene

Previous HGNC Symbols for H3F3A Gene

  • H3F3

Previous GeneCards Identifiers for H3F3A Gene

  • GC01P224732
  • GC01P222067
  • GC01P222656
  • GC01P223225
  • GC01P222557
  • GC01P224316
  • GC01P226249
  • GC01P196767

Summaries for H3F3A Gene

Entrez Gene Summary for H3F3A Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded is a replication-independent member of the histone H3 family. [provided by RefSeq, Jul 2008]

GeneCards Summary for H3F3A Gene

H3F3A (H3 Histone, Family 3A) is a Protein Coding gene. Among its related pathways are Disease and ERK Signaling. An important paralog of this gene is HIST2H3A.

UniProtKB/Swiss-Prot for H3F3A Gene

  • Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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 H3F3A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H3F3A Gene

Genomics for H3F3A Gene

Regulatory Elements for H3F3A Gene

Genomic Location for H3F3A Gene

Start:
226,061,851 bp from pter
End:
226,072,002 bp from pter
Size:
10,152 bases
Orientation:
Plus strand

Genomic View for H3F3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for H3F3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3F3A Gene

Proteins for H3F3A Gene

  • Protein details for H3F3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P84243-H33_HUMAN
    Recommended name:
    Histone H3.3
    Protein Accession:
    P84243
    Secondary Accessions:
    • P06351
    • P33155
    • Q5VV55
    • Q5VV56
    • Q66I33
    • Q9V3W4

    Protein attributes for H3F3A Gene

    Size:
    136 amino acids
    Molecular mass:
    15328 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. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes. Interacts with ZMYND11; when trimethylated at Lys-36 (H3.3K36me3).
    SequenceCaution:
    • Sequence=CAH73371.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for H3F3A Gene

neXtProt entry for H3F3A Gene

Proteomics data for H3F3A Gene at MOPED

Post-translational modifications for H3F3A 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).
  • 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 Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes.
  • Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me), Lys-37 and Lys-80. 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), which are linked to gene repression, are underrepresented. 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.
  • Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity).
  • Ubiquitination at Lys19, Lys24, Lys57, Lys65, Lys80, Lys116, and Lys123
  • Modification sites at PhosphoSitePlus

Other Protein References for H3F3A Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for H3F3A Gene

Domains for H3F3A Gene

Gene Families for H3F3A Gene

HGNC:
  • RIH :Histones / Replication-independent

Protein Domains for H3F3A Gene

Suggested Antigen Peptide Sequences for H3F3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P84243

UniProtKB/Swiss-Prot:

H33_HUMAN :
  • P84243
Domain:
  • Specific interaction of trimethylated form at Lys-36 (H3.3K36me3) with ZMYND11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3F3A: view

Function for H3F3A Gene

Molecular function for H3F3A Gene

GENATLAS Biochemistry: histone family 3,replacement subtype,replication independent protein,species H3.3A
UniProtKB/Swiss-Prot Function: Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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 H3F3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding IDA 19633671
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IDA 19633671
GO:0003677 DNA binding --
GO:0005515 protein binding IPI 19494831
GO:0031492 nucleosomal DNA binding IDA 19633671
genes like me logo Genes that share ontologies with H3F3A: view
genes like me logo Genes that share phenotypes with H3F3A: view

miRNA for H3F3A Gene

miRTarBase miRNAs that target H3F3A

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for H3F3A Gene

Localization for H3F3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3F3A Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for H3F3A Gene COMPARTMENTS Subcellular localization image for H3F3A gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for H3F3A 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 19633671
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 21630459
genes like me logo Genes that share ontologies with H3F3A: view

Pathways for H3F3A Gene

genes like me logo Genes that share pathways with H3F3A: view

Gene Ontology (GO) - Biological Process for H3F3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0007264 small GTPase mediated signal transduction TAS --
GO:0007596 blood coagulation TAS --
genes like me logo Genes that share ontologies with H3F3A: view

Transcripts for H3F3A Gene

Unigene Clusters for H3F3A Gene

H3 histone, family 3A:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for H3F3A Gene

No ASD Table

Relevant External Links for H3F3A Gene

GeneLoc Exon Structure for
H3F3A
ECgene alternative splicing isoforms for
H3F3A

Expression for H3F3A Gene

mRNA expression in normal human tissues for H3F3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for H3F3A Gene

This gene is overexpressed in Whole Blood (11.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for H3F3A Gene

SOURCE GeneReport for Unigene cluster for H3F3A Gene Hs.533624

genes like me logo Genes that share expressions with H3F3A: view

No data available for mRNA Expression by UniProt/SwissProt for H3F3A Gene

Orthologs for H3F3A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for H3F3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia H3F3C 36
  • 100 (a)
OneToOne
HIST1H3A 35
  • 100 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia H3F3A 35
  • 98.28 (n)
  • 100 (a)
H3F3C 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 95 (a)
ManyToMany
H3F3B 35
  • 97.55 (n)
  • 100 (a)
mouse
(Mus musculus)
Mammalia H3f3a 35
  • 96.08 (n)
  • 100 (a)
H3f3a 16
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 94 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia LOC100361558 35
  • 95.59 (n)
  • 100 (a)
chicken
(Gallus gallus)
Aves H3-IX 36
  • 100 (a)
OneToOne
LOC100859629 35
  • 79.17 (n)
  • 100 (a)
lizard
(Anolis carolinensis)
Reptilia H3F3A 36
  • 100 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.8034 35
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101730642 35
  • 77.21 (n)
  • 97.06 (a)
Str.6553 35
zebrafish
(Danio rerio)
Actinopterygii H3F3A 36
  • 99 (a)
OneToOne
LOC565028 35
  • 79.66 (n)
  • 97.06 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33857 35
  • 79.17 (n)
  • 97.06 (a)
His3.3B 37
  • 100 (a)
His3.3A 37
  • 100 (a)
worm
(Caenorhabditis elegans)
Secernentea his-71 36
  • 99 (a)
OneToMany
W05B10.1 37
  • 93 (a)
his-69 37
  • 88 (a)
his-72 37
  • 98 (a)
his-71 37
  • 99 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHT1 36
  • 90 (a)
ManyToMany
HHT2 36
  • 90 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 36
  • 100 (a)
OneToMany
Species with no ortholog for H3F3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 (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)

Evolution for H3F3A Gene

ENSEMBL:
Gene Tree for H3F3A (if available)
TreeFam:
Gene Tree for H3F3A (if available)

Paralogs for H3F3A Gene

Pseudogenes.org Pseudogenes for H3F3A Gene

genes like me logo Genes that share paralogs with H3F3A: view

Variants for H3F3A Gene

Sequence variations from dbSNP and Humsavar for H3F3A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs1136219 -- 226,064,288(+) GTTTG(G/T)TAGTT intron-variant
rs1511056 -- 226,065,426(-) AATTC(A/C)TCAAA intron-variant
rs1533114 -- 226,066,335(-) CCCCC(A/G)ATCTT intron-variant
rs1849032 -- 226,065,615(-) CATAA(A/C)TAGCA intron-variant
rs2036870 -- 226,064,531(-) ATTAT(A/G)TGGAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for H3F3A Gene

Variant ID Type Subtype PubMed ID
nsv832747 CNV Gain 17160897
nsv873232 CNV Gain 21882294

Relevant External Links for H3F3A Gene

HapMap Linkage Disequilibrium report
H3F3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H3F3A Gene

Disorders for H3F3A Gene

(2) University of Copenhagen DISEASES for H3F3A Gene

Relevant External Links for H3F3A

Genetic Association Database (GAD)
H3F3A
Human Genome Epidemiology (HuGE) Navigator
H3F3A
genes like me logo Genes that share disorders with H3F3A: view

No data available for UniProtKB/Swiss-Prot for H3F3A Gene

Publications for H3F3A Gene

  1. The human replacement histone H3.3B gene (H3F3B). (PMID: 8586426) Albig W. … Doenecke D. (Genomics 1995) 3 4 23
  2. Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family. (PMID: 3031613) Wells D. … Kedes L. (Nucleic Acids Res. 1987) 2 3 4
  3. Human spleen histone H3. Isolation and amino acid sequence. (PMID: 7309716) Ohe Y. … Iwai K. (J. Biochem. 1981) 3 4
  4. Differential expression of human replacement and cell cycle dependent H3 histone genes. (PMID: 12909349) Frank D. … Albig W. (Gene 2003) 3 23
  5. Structure of a human histone cDNA: evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated mRNAs. (PMID: 2859593) Wells D. … Kedes L. (Proc. Natl. Acad. Sci. U.S.A. 1985) 3 4

Products for H3F3A Gene

  • Addgene plasmids for H3F3A

Sources for H3F3A Gene

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