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 ... See more...

Aliases for H3-3B Gene

Aliases for H3-3B Gene

  • H3.3 Histone B 2 3
  • H3 Histone Family Member 3B 2 3 5
  • H3F3B 3 4 5
  • H3 Histone, Family 3B (H3.3B) 2 3
  • H3.3B 3 4
  • H3 Histone, Family 3B 2
  • Histone H3.3 3
  • H3-3A 3
  • H3.3A 4
  • H3F3A 4
  • H3F3 4

External Ids for H3-3B Gene

Previous HGNC Symbols for H3-3B Gene

  • H3F3B

Previous GeneCards Identifiers for H3-3B Gene

  • GC17M075778

Summaries for H3-3B Gene

Entrez Gene Summary for H3-3B 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 by this gene is a replication-independent histone that is a member of the histone H3 family. Pseudogenes of this gene have been identified on the X chromosome, and on chromosomes 5, 13 and 17. [provided by RefSeq, Oct 2015]

CIViC Summary for H3-3B Gene

GeneCards Summary for H3-3B Gene

H3-3B (H3.3 Histone B) is a Protein Coding gene. Diseases associated with H3-3B include Chondroblastoma and Clear Cell Chondrosarcoma. Among its related pathways are Signaling by Wnt and ERK Signaling. An important paralog of this gene is H3-3A.

UniProtKB/Swiss-Prot Summary for H3-3B 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.

Additional gene information for H3-3B Gene

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H3-3B Gene

Genomics for H3-3B Gene

GeneHancer (GH) Regulatory Elements for H3-3B Gene

Promoters and enhancers for H3-3B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H3-3B on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H3-3B

Genomic Locations for H3-3B Gene

Genomic Locations for H3-3B Gene
chr17:75,776,434-75,785,893
(GRCh38/hg38)
Size:
9,460 bases
Orientation:
Minus strand
chr17:73,772,515-73,781,974
(GRCh37/hg19)
Size:
9,460 bases
Orientation:
Minus strand

Genomic View for H3-3B Gene

Genes around H3-3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3-3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3-3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3-3B Gene

Proteins for H3-3B Gene

  • Protein details for H3-3B 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 H3-3B 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).

    Three dimensional structures from OCA and Proteopedia for H3-3B Gene

neXtProt entry for H3-3B Gene

Post-translational modifications for H3-3B 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.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • 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.
  • 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.
  • 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. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes.
  • Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity).
  • 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.
  • 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.
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Succinylation at Lys-80 (H3K79succ) by KAT2A takes place with a maximum frequency around the transcription start sites of genes (PubMed:29211711). It gives a specific tag for epigenetic transcription activation (PubMed:29211711). Desuccinylation at Lys-123 (H3K122succ) by SIRT7 in response to DNA damage promotes chromatin condensation and double-strand breaks (DSBs) repair (PubMed:27436229).
  • Serine ADP-ribosylation constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (PubMed:29480802). Serine ADP-ribosylation at Ser-11 (H3S10ADPr) is mutually exclusive with phosphorylation at Ser-11 (H3S10ph) and impairs acetylation at Lys-10 (H3K9ac) (PubMed:30257210).
  • Ubiquitination at Lys116
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for H3-3B Gene

Domains & Families for H3-3B Gene

Gene Families for H3-3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for H3-3B Gene

Suggested Antigen Peptide Sequences for H3-3B Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92171, Homo sapiens H3 histone, family 3A (H3F3A), mRNA (B2R4P9_HUMAN)
  • Histone H3.3 (H33_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P84243

UniProtKB/Swiss-Prot:

H33_HUMAN :
  • 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.
  • Belongs to the histone H3 family.
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 H3-3B: view

Function for H3-3B Gene

Molecular function for H3-3B Gene

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.

Phenotypes From GWAS Catalog for H3-3B Gene

Gene Ontology (GO) - Molecular Function for H3-3B 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 IEA --
GO:0005515 protein binding IPI 19494831
GO:0031492 nucleosomal DNA binding IDA 19633671
genes like me logo Genes that share ontologies with H3-3B: view
genes like me logo Genes that share phenotypes with H3-3B: view

Animal Models for H3-3B Gene

MGI Knock Outs for H3-3B:

miRNA for H3-3B Gene

miRTarBase miRNAs that target H3-3B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for H3-3B Gene

Localization for H3-3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3-3B Gene

Nucleus. Chromosome.

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 H3-3B gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 2
plasma membrane 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for H3-3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000784 nuclear chromosome, telomeric region IDA 20110566
GO:0000786 nucleosome IEA,IDA 21636898
GO:0000788 nuclear nucleosome IDA 19633671
GO:0001740 Barr body IEA --
genes like me logo Genes that share ontologies with H3-3B: view

Pathways & Interactions for H3-3B Gene

PathCards logo

SuperPathways for H3-3B Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence (REACTOME)
3 Cell Cycle, Mitotic
.60
4 Mitotic Prophase
5 Development NOTCH1-mediated pathway for NF-KB activity modulation
.55
.55
.31
genes like me logo Genes that share pathways with H3-3B: view

Pathways by source for H3-3B Gene

5 GeneGo (Thomson Reuters) pathways for H3-3B Gene
  • Cell cycle_Chromosome condensation in prometaphase
  • Development Notch Signaling Pathway
  • Development NOTCH1-mediated pathway for NF-KB activity modulation
  • Signal transduction Activin A signaling regulation
  • Transcription Sin3 and NuRD in transcription regulation
8 Qiagen pathways for H3-3B Gene
  • Crosstalk Between CARM1 and ESRs
  • ERK Signaling
  • Interferon Pathway
  • MAPK Family Pathway
  • Nuclear Receptor Activation by Vitamin-A
1 GeneTex pathway for H3-3B Gene

Gene Ontology (GO) - Biological Process for H3-3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0001649 osteoblast differentiation IEA --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0006997 nucleus organization IEA --
genes like me logo Genes that share ontologies with H3-3B: view

No data available for SIGNOR curated interactions for H3-3B Gene

Drugs & Compounds for H3-3B Gene

No Compound Related Data Available

Transcripts for H3-3B Gene

mRNA/cDNA for H3-3B Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for H3-3B Gene

No ASD Table

Relevant External Links for H3-3B Gene

GeneLoc Exon Structure for
H3-3B

Expression for H3-3B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H3-3B

SOURCE GeneReport for Unigene cluster for H3-3B Gene:

Hs.180877

Evidence on tissue expression from TISSUES for H3-3B Gene

  • Nervous system(5)
  • Eye(4.9)
  • Liver(4.8)
  • Lung(4.8)
  • Pancreas(4.6)
  • Blood(4.5)
  • Skin(4.5)
  • Kidney(3.9)
  • Intestine(3.8)
  • Bone(3.4)
  • Muscle(3.4)
  • Stomach(3.2)
  • Heart(3.1)
  • Spleen(2.3)
No Expression Related Data Available

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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for H3-3B Gene

Orthologs for H3-3B Gene

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

Orthologs for H3-3B Gene

Organism Taxonomy Gene Similarity Type Details
oppossum
(Monodelphis domestica)
Mammalia H3F3B 31
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia H3F3A 31
  • 100 (a)
OneToOne
H3F3B 30
  • 92.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia H3F3B 31
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia H3f3a 31
  • 100 (a)
OneToOne
H3f3b 17 30
  • 91.91 (n)
chimpanzee
(Pan troglodytes)
Mammalia H3F3C 31
  • 100 (a)
OneToOne
H3F3B 30
  • 99.02 (n)
rat
(Rattus norvegicus)
Mammalia H3f3b 30
  • 91.91 (n)
dog
(Canis familiaris)
Mammalia H3F3B 31 30
  • 78.19 (n)
OneToOne
chicken
(Gallus gallus)
Aves H3-IX 31
  • 100 (a)
OneToOne
H3F3B 30
  • 88.24 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 100 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101730642 30
  • 82.35 (n)
zebrafish
(Danio rerio)
Actinopterygii h3f3a 31
  • 100 (a)
OneToMany
H3F3B (1 of 3) 31
  • 100 (a)
OneToMany
H3F3B (3 of 3) 31
  • 100 (a)
OneToMany
LOC565028 30
  • 80.64 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3.3A 31
  • 100 (a)
OneToOne
His3:CG33857 30
  • 77.7 (n)
worm
(Caenorhabditis elegans)
Secernentea his-71 31
  • 99 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHT2 31
  • 90 (a)
ManyToMany
HHT1 31
  • 90 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 31
  • 100 (a)
OneToOne
Species where no ortholog for H3-3B 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)
  • 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)
  • 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 H3-3B Gene

ENSEMBL:
Gene Tree for H3-3B (if available)
TreeFam:
Gene Tree for H3-3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H3-3B: view image

Paralogs for H3-3B Gene

Pseudogenes.org Pseudogenes for H3-3B Gene