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Aliases for HIST1H3F Gene

Aliases for HIST1H3F Gene

  • Histone Cluster 1, H3f 2 3
  • H3 Histone Family, Member I 2 3
  • Histone 1, H3f 2 3
  • Histone H3/I 3 4
  • H3FI 3 4
  • HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J 4
  • Histone H3.1 3
  • Histone H3/A 4
  • Histone H3/B 4
  • Histone H3/C 4
  • Histone H3/D 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/J 4
  • Histone H3/K 4
  • Histone H3/L 4
  • H3FC 4
  • H3FA 4
  • H3FB 4
  • H3FD 4
  • H3FF 4
  • H3FH 4
  • H3FJ 4
  • H3FK 4
  • H3FL 4
  • H3/I 3

External Ids for HIST1H3F Gene

Previous Symbols for HIST1H3F Gene

  • H3FI

Summaries for HIST1H3F Gene

Entrez Gene Summary for HIST1H3F 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 HIST1H3F Gene

HIST1H3F (Histone Cluster 1, H3f) is a Protein Coding gene. Among its related pathways are Disease and ERK Signaling. GO annotations related to this gene include protein heterodimerization activity.

UniProtKB/Swiss-Prot for HIST1H3F 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 HIST1H3F Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3F Gene

Genomics for HIST1H3F Gene

Genomic Location for HIST1H3F Gene

Start:
26,250,142 bp from pter
End:
26,250,607 bp from pter
Size:
466 bases
Orientation:
Minus strand

Genomic View for HIST1H3F Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H3F Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3F Gene

Regulatory Elements for HIST1H3F Gene

Proteins for HIST1H3F Gene

  • Protein details for HIST1H3F Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P68431-H31_HUMAN
    Recommended name:
    Histone H3.1
    Protein Accession:
    P68431
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3F Gene

    Size:
    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.
    Miscellaneous:
    • 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 HIST1H3F Gene

neXtProt entry for HIST1H3F Gene

Proteomics data for HIST1H3F Gene at MOPED

Post-translational modifications for HIST1H3F 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 HIST1H3F Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3F Gene

Domains for HIST1H3F Gene

Gene Families for HIST1H3F Gene

HGNC:
  • HIST :Histones / Replication-dependent

Protein Domains for HIST1H3F Gene

UniProtKB/Swiss-Prot:

H31_HUMAN
Family:
  • Belongs to the histone H3 family.:
    • P68431
genes like me logo Genes that share domains with HIST1H3F: view

Function for HIST1H3F Gene

Molecular function for HIST1H3F 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 HIST1H3F 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 HIST1H3F: view

Phenotypes for HIST1H3F Gene

GenomeRNAi human phenotypes for HIST1H3F:
genes like me logo Genes that share phenotypes with HIST1H3F: view

miRNA for HIST1H3F Gene

miRTarBase miRNAs that target HIST1H3F

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for HIST1H3F Gene

Localization for HIST1H3F Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H3F Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HIST1H3F Gene COMPARTMENTS Subcellular localization image for HIST1H3F gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2

Gene Ontology (GO) - Cellular Components for HIST1H3F 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 HIST1H3F: view

Pathways for HIST1H3F Gene

genes like me logo Genes that share pathways with HIST1H3F: view

Gene Ontology (GO) - Biological Process for HIST1H3F 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 HIST1H3F: view

Transcripts for HIST1H3F Gene

mRNA/cDNA for HIST1H3F Gene

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

Unigene Clusters for HIST1H3F Gene

Histone cluster 1, H3f:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H3F Gene

No ASD Table

Relevant External Links for HIST1H3F Gene

GeneLoc Exon Structure for
HIST1H3F
ECgene alternative splicing isoforms for
HIST1H3F

Expression for HIST1H3F Gene

mRNA expression in normal human tissues for HIST1H3F Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H3F Gene

This gene is overexpressed in Whole Blood (7.1), Colon - Transverse (5.1), and Esophagus - Mucosa (4.3).

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for HIST1H3F Gene

SOURCE GeneReport for Unigene cluster for HIST1H3F Gene Hs.247814

genes like me logo Genes that share expressions with HIST1H3F: view

Orthologs for HIST1H3F Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H3F Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Hist1h3f 16
Hist1h3i 36
  • 86.76 (n)
  • 100 (a)
rat
(Rattus norvegicus)
Mammalia LOC682330 36
  • 85.05 (n)
  • 100 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497984 36
  • 83.58 (n)
  • 99.26 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012559 36
  • 82.6 (n)
  • 99.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33818 36
  • 80.15 (n)
  • 99.26 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.7493 36
Species with no ortholog for HIST1H3F:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • 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)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HIST1H3F Gene

ENSEMBL:
Gene Tree for HIST1H3F (if available)
TreeFam:
Gene Tree for HIST1H3F (if available)

Paralogs for HIST1H3F Gene

Selected SIMAP similar genes for HIST1H3F Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H3F: view

No data available for Paralogs for HIST1H3F Gene

Variants for HIST1H3F Gene

Sequence variations from dbSNP and Humsavar for HIST1H3F Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs181931096 -- 26,252,580(+) GAAAA(A/T)TTTAA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3F Gene

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914

Relevant External Links for HIST1H3F Gene

HapMap Linkage Disequilibrium report
HIST1H3F

Disorders for HIST1H3F Gene

No disorders were found for HIST1H3F Gene.

No data available for UniProtKB/Swiss-Prot for HIST1H3F Gene

Publications for HIST1H3F Gene

  1. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 3 4
  2. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 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. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. (PMID: 11242053) Lachner M. … Jenuwein T. (Nature 2001) 3 4
  5. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 3 4

Products for HIST1H3F Gene

Sources for HIST1H3F Gene

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