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Aliases for H3F3C Gene

Aliases for H3F3C Gene

  • H3 Histone, Family 3C 2 3
  • Histone H3.5 3 4
  • Histone Variant H3.5 3
  • Histone H3.3C 3
  • H3.5 3

External Ids for H3F3C Gene

Previous GeneCards Identifiers for H3F3C Gene

  • GC12M031838
  • GC12M031944
  • GC12M031696

Summaries for H3F3C Gene

GeneCards Summary for H3F3C Gene

H3F3C (H3 Histone, Family 3C) is a Protein Coding gene. Diseases associated with H3F3C include corneal granular dystrophy and lattice corneal dystrophy. Among its related pathways are Transcriptional misregulation in cancer and RNA Polymerase I Promoter Opening. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is HIST2H3A.

UniProtKB/Swiss-Prot for H3F3C 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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H3F3C Gene

Genomics for H3F3C Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for H3F3C Gene

Start:
31,791,185 bp from pter
End:
31,792,241 bp from pter
Size:
1,057 bases
Orientation:
Minus strand

Genomic View for H3F3C Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for H3F3C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3F3C Gene

No data available for Regulatory Elements for H3F3C Gene

Proteins for H3F3C Gene

  • Protein details for H3F3C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6NXT2-H3C_HUMAN
    Recommended name:
    Histone H3.3C
    Protein Accession:
    Q6NXT2
    Secondary Accessions:
    • E9P281

    Protein attributes for H3F3C Gene

    Size:
    135 amino acids
    Molecular mass:
    15214 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 H3F3C Gene

neXtProt entry for H3F3C Gene

Proteomics data for H3F3C Gene at MOPED

Post-translational modifications for H3F3C 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-122 (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).
  • 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) is linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. 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) requires 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-56 (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 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-41 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin (By similarity).
  • Ubiquitination at Lys19, Lys24, Lys56, Lys64, and Lys122
  • Modification sites at PhosphoSitePlus

Other Protein References for H3F3C Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H3F3C Gene

Domains for H3F3C Gene

Gene Families for H3F3C Gene

HGNC:
  • RIH :Histones / Replication-independent

Protein Domains for H3F3C Gene

Suggested Antigen Peptide Sequences for H3F3C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6NXT2

UniProtKB/Swiss-Prot:

H3C_HUMAN :
  • Q6NXT2
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3F3C: view

Function for H3F3C Gene

Molecular function for H3F3C 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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.

Gene Ontology (GO) - Molecular Function for H3F3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0005515 protein binding IPI 25416956
GO:0031492 nucleosomal DNA binding IDA 21274551
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H3F3C: view

Animal Model Products

miRNA for H3F3C Gene

miRTarBase miRNAs that target H3F3C

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for H3F3C Gene

Localization for H3F3C Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3F3C Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for H3F3C Gene COMPARTMENTS Subcellular localization image for H3F3C gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for H3F3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005719 nuclear euchromatin IDA 21274551
genes like me logo Genes that share ontologies with H3F3C: view

Pathways for H3F3C Gene

genes like me logo Genes that share pathways with H3F3C: view

Pathways by source for H3F3C Gene

Gene Ontology (GO) - Biological Process for H3F3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030307 positive regulation of cell growth IMP 21274551
genes like me logo Genes that share ontologies with H3F3C: view

Transcripts for H3F3C Gene

mRNA/cDNA for H3F3C Gene

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

Unigene Clusters for H3F3C Gene

H3 histone, family 3C:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for H3F3C

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for H3F3C Gene

No ASD Table

Relevant External Links for H3F3C Gene

GeneLoc Exon Structure for
H3F3C
ECgene alternative splicing isoforms for
H3F3C

Expression for H3F3C Gene

mRNA expression in normal human tissues for H3F3C Gene

mRNA differential expression in normal tissues according to GTEx for H3F3C Gene

This gene is overexpressed in Testis (7.1) and Whole Blood (5.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for H3F3C Gene

SOURCE GeneReport for Unigene cluster for H3F3C Gene Hs.448697

mRNA Expression by UniProt/SwissProt for H3F3C Gene

Q6NXT2-H3C_HUMAN
Tissue specificity: Specifically expressed in the seminiferous tubules of testis.
genes like me logo Genes that share expressions with H3F3C: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for H3F3C Gene

Orthologs for H3F3C Gene

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

Orthologs for H3F3C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia H3F3C 35
  • 99.26 (n)
  • 99.26 (a)
cow
(Bos Taurus)
Mammalia H3F3A 36
  • 96 (a)
OneToOne
LOC100297725 35
  • 76.3 (n)
  • 94.81 (a)
dog
(Canis familiaris)
Mammalia H3F3C 36
  • 96 (a)
OneToOne
LOC612779 35
  • 75.06 (n)
  • 91.85 (a)
mouse
(Mus musculus)
Mammalia Gm12657 35
  • 75.8 (n)
  • 93.33 (a)
H3f3b 36
  • 96 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 91 (a)
ManyToMany
chicken
(Gallus gallus)
Aves H3-IX 36
  • 96 (a)
ManyToMany
H3F3C 35
  • 78.52 (n)
  • 95.56 (a)
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 96 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101731074 35
  • 81.48 (n)
  • 94.81 (a)
zebrafish
(Danio rerio)
Actinopterygii h3f3a 36
  • 96 (a)
OneToOne
h3f3c 35
  • 83.21 (n)
  • 96.3 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3.3B 36
  • 96 (a)
ManyToMany
His3:CG33839 35
  • 76.79 (n)
  • 94.81 (a)
worm
(Caenorhabditis elegans)
Secernentea his-71 35
  • 74.32 (n)
  • 95.56 (a)
his-71 36
  • 95 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER013W 35
  • 71.36 (n)
  • 86.67 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CSE4 38
HHT1 35
  • 68.89 (n)
  • 86.67 (a)
HHT1 36
  • 86 (a)
ManyToMany
HHT2 36
  • 86 (a)
ManyToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU01635 35
  • 74.63 (n)
  • 88.06 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hht2 35
  • 70.86 (n)
  • 88.15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 36
  • 96 (a)
OneToMany
Species with no ortholog for H3F3C:
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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)
  • 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)

Evolution for H3F3C Gene

ENSEMBL:
Gene Tree for H3F3C (if available)
TreeFam:
Gene Tree for H3F3C (if available)

Paralogs for H3F3C Gene

genes like me logo Genes that share paralogs with H3F3C: view

Variants for H3F3C Gene

Sequence variations from dbSNP and Humsavar for H3F3C Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type MAF
rs1797735 -- 31,794,047(-) AATTG(C/T)TTATA upstream-variant-2KB
rs1797737 -- 31,793,112(-) tctcc(A/C)aaaaa upstream-variant-2KB
rs1797738 -- 31,790,771(-) TCTGC(C/T)GGTTA downstream-variant-500B
rs1797820 -- 31,793,285(-) CCCCC(A/G)TCTCT upstream-variant-2KB
rs1797821 -- 31,792,688(-) TGTGA(A/C)GGAGG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for H3F3C Gene

Variant ID Type Subtype PubMed ID
nsv898966 CNV Gain 21882294
nsv8940 CNV Gain 18304495
nsv522362 CNV Loss 19592680
nsv663 CNV Loss 18451855
nsv523907 CNV Loss 19592680
nsv519112 CNV Loss 19592680

Relevant External Links for H3F3C Gene

HapMap Linkage Disequilibrium report
H3F3C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H3F3C Gene

Disorders for H3F3C Gene

MalaCards: The human disease database

MalaCards: The human disease database. (2) Diseases for H3F3C Gene including...

Search for H3F3C Gene in MalaCards »

(2) University of Copenhagen DISEASES for H3F3C Gene

genes like me logo Genes that share disorders with H3F3C: view

No data available for UniProtKB/Swiss-Prot for H3F3C Gene

Publications for H3F3C Gene

  1. H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes. (PMID: 21274551) Schenk R. … Postberg J. (Chromosoma 2011) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  3. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer S.E. … Gibbs R.A. (Nature 2006) 3 4
  4. The human monocytic leukemia zinc finger histone acetyltransferase domain contains DNA-binding activity implicated in chromatin targeting. (PMID: 17925393) Holbert M.A. … Marmorstein R. (J. Biol. Chem. 2007) 3
  5. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L. … Andersson-Svahn H. (Mol. Cell Proteomics 2008) 3

Products for H3F3C Gene

Sources for H3F3C Gene

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