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... See more...

Aliases for H3-4 Gene

Aliases for H3-4 Gene

  • H3.4 Histone 2 3 5
  • H3/G 2 3 4
  • H3t 2 3 4
  • H3 Histone Family, Member T 2 3
  • Histone Cluster 3 H3 2 3
  • Histone 3, H3 2 3
  • Histone H3.1t 3 4
  • Histone H3.4 3 4
  • HIST3H3 3 4
  • H3.4 2 3
  • H3FT 3 4
  • H3/T 3 4
  • Histone Cluster 3, H3 2
  • H3-4 5

External Ids for H3-4 Gene

Previous HGNC Symbols for H3-4 Gene

  • H3FT
  • HIST3H3

Summaries for H3-4 Gene

Entrez Gene Summary for H3-4 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 H3-4 Gene

H3-4 (H3.4 Histone) is a Protein Coding gene. Diseases associated with H3-4 include Colon Leiomyoma and Central Retinal Artery Occlusion. Among its related pathways are DNA Double-Strand Break Repair and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. An important paralog of this gene is H3C2.

UniProtKB/Swiss-Prot Summary for H3-4 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 H3-4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H3-4 Gene

Genomics for H3-4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H3-4 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 H3-4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H3-4

Genomic Locations for H3-4 Gene

Latest Assembly
chr1:228,424,845-228,425,360
(GRCh38/hg38)
Size:
516 bases
Orientation:
Minus strand

Previous Assembly
chr1:228,612,546-228,613,061
(GRCh37/hg19 by Entrez Gene)
Size:
516 bases
Orientation:
Minus strand

chr1:228,612,546-228,613,026
(GRCh37/hg19 by Ensembl)
Size:
481 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr1(PATCHES):16,044-16,559 (-)

Genomic View for H3-4 Gene

Genes around H3-4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3-4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3-4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3-4 Gene

Proteins for H3-4 Gene

  • Protein details for H3-4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16695-H31T_HUMAN
    Recommended name:
    Histone H3.1t
    Protein Accession:
    Q16695
    Secondary Accessions:
    • B2R5K3
    • Q6FGU4

    Protein attributes for H3-4 Gene

    Size:
    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 H3-4 Gene

neXtProt entry for H3-4 Gene

Post-translational modifications for H3-4 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).
  • 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 (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.
  • 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).
  • 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. It gives a specific tag for epigenetic transcription activation. Desuccinylation at Lys-123 (H3K122succ) by SIRT7 in response to DNA damage promotes chromatin condensation and double-strand breaks (DSBs) repair.
  • Serine ADP-ribosylation constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage. Serine ADP-ribosylation at Ser-11 (H3S10ADPr) is mutually exclusive with phosphorylation at Ser-11 (H3S10ph) and impairs acetylation at Lys-10 (H3K9ac).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H3-4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

No data available for DME Specific Peptides for H3-4 Gene

Domains & Families for H3-4 Gene

Gene Families for H3-4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for H3-4 Gene

InterPro:
Blocks:
  • Histone H3

Suggested Antigen Peptide Sequences for H3-4 Gene

GenScript: Design optimal peptide antigens:
  • H3/g (H31T_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q16695

UniProtKB/Swiss-Prot:

H31T_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3-4: view

Function for H3-4 Gene

Molecular function for H3-4 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 H3-4 Gene

Gene Ontology (GO) - Molecular Function for H3-4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 17537733
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H3-4: view
genes like me logo Genes that share phenotypes with H3-4: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H3-4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H3-4 Gene

Localization for H3-4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3-4 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 H3-4 gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for H3-4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region HDA 19135898
GO:0000786 nucleosome IDA 20498094
GO:0005634 nucleus IEA,HDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H3-4: view

Pathways & Interactions for H3-4 Gene

genes like me logo Genes that share pathways with H3-4: view

Pathways by source for H3-4 Gene

5 GeneGo (Thomson Reuters) pathways for H3-4 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 H3-4 Gene
  • Crosstalk Between CARM1 and ESRs
  • ERK Signaling
  • Interferon Pathway
  • MAPK Family Pathway
  • Nuclear Receptor Activation by Vitamin-A
1 GeneTex pathway for H3-4 Gene

SIGNOR curated interactions for H3-4 Gene

Is activated by:
Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for H3-4 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 --
genes like me logo Genes that share ontologies with H3-4: view

Drugs & Compounds for H3-4 Gene

No Compound Related Data Available

Transcripts for H3-4 Gene

mRNA/cDNA for H3-4 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H3-4

Alternative Splicing Database (ASD) splice patterns (SP) for H3-4 Gene

No ASD Table

Relevant External Links for H3-4 Gene

GeneLoc Exon Structure for
H3-4

Expression for H3-4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H3-4

SOURCE GeneReport for Unigene cluster for H3-4 Gene:

Hs.248171

mRNA Expression by UniProt/SwissProt for H3-4 Gene:

Q16695-H31T_HUMAN
Tissue specificity: Expressed in testicular cells.

Evidence on tissue expression from TISSUES for H3-4 Gene

  • Lung(4.4)
  • Skin(2.7)
  • Spleen(2.6)
  • Nervous system(2.5)
  • Intestine(2.5)
  • Kidney(2.4)
  • Adrenal gland(2.1)
  • Bone marrow(2.1)
  • Heart(2.1)
  • Liver(2.1)
  • Lymph node(2.1)
  • Muscle(2.1)
  • Pancreas(2.1)
  • Stomach(2.1)
  • Thyroid gland(2.1)

Primer products for research

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for H3-4 Gene

Orthologs for H3-4 Gene

This gene was present in the common ancestor of animals.

Orthologs for H3-4 Gene

Organism Taxonomy Gene Similarity Type Details
Cow
(Bos Taurus)
Mammalia -- 30
  • 97 (a)
ManyToMany
LOC518318 29
  • 81.13 (n)
Chimpanzee
(Pan troglodytes)
Mammalia -- 30
  • 97 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 92 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 94 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100493041 29
  • 82.84 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC570703 29
  • 81.13 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta His3:CG33860 29
  • 80.39 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 90 (a)
ManyToMany
-- 30
  • 90 (a)
ManyToMany
Species where no ortholog for H3-4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 H3-4 Gene

ENSEMBL:
Gene Tree for H3-4 (if available)
TreeFam:
Gene Tree for H3-4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H3-4: view image
Alliance of Genome Resources:
Additional Orthologs for H3-4

Paralogs for H3-4 Gene

genes like me logo Genes that share paralogs with H3-4: view

Variants for H3-4 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H3-4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for H3-4 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 H3-4 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 H3-4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H3-4
Leiden Open Variation Database (LOVD)
H3-4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H3-4 Gene

Disorders for H3-4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for H3-4 Gene - From: COP

Disorder Aliases PubMed IDs
colon leiomyoma
  • colonic leiomyoma
central retinal artery occlusion
- elite association - COSMIC cancer census association via MalaCards
Search H3-4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H3-4

genes like me logo Genes that share disorders with H3-4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H3-4 Gene

Publications for H3-4 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. A solitary human H3 histone gene on chromosome 1. (PMID: 8834248) Albig W … Doenecke D (Human genetics 1996) 2 3 4
  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
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  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

Products for H3-4 Gene

Sources for H3-4 Gene