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Aliases for H3F3C Gene

Aliases for H3F3C Gene

  • H3 Histone Family Member 3C 2 3 5
  • 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

Entrez Gene Summary for H3F3C 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 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. [provided by RefSeq, Oct 2015]

GeneCards Summary for H3F3C Gene

H3F3C (H3 Histone Family Member 3C) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Transcriptional misregulation in cancer. GO annotations related to this gene include protein heterodimerization activity and nucleosomal DNA binding. An important paralog of this gene is H3F3A.

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 CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H3F3C Gene

Genomics for H3F3C Gene

Regulatory Elements for H3F3C Gene

Enhancers for H3F3C Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G031745 2.1 FANTOM5 Ensembl ENCODE dbSUPER 12.8 +42.9 42910 6.9 MLX CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC KIAA1551 H3F3C DSPA2D LOC100420981 DDX11-AS1 AMN1 ENSG00000256843
GH12G031714 1.8 VISTA Ensembl ENCODE dbSUPER 10.9 +76.5 76540 3.0 HDGF PKNOX1 FOXA2 ARNT YY1 ZNF766 CBX5 ZNF207 FOS ZHX2 H3F3C FLJ13224 KIAA1551 FAM60A STMN1P1 GC12P031714
GH12G031316 1.7 Ensembl ENCODE dbSUPER 10.7 +470.2 470186 10.8 HDGF PKNOX1 FOXA2 CREB3L1 ARNT AGO1 WRNIP1 SIN3A ARID4B DMAP1 FLJ13224 H3F3C IPO8 FAM60A KIAA1551 DENND5B DENND5B-AS1 RNU5F-4P ENSG00000256176
GH12G031755 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.6 +35.2 35196 2.1 HDAC1 TBL1XR1 TCF12 SCRT2 SIRT6 SMARCC1 USF2 ZEB2 ZNF579 ZNF589 AMN1 ENSG00000252204 H3F3C DSPA2D LOC105369724
GH12G031726 1.4 ENCODE dbSUPER 10.9 +63.8 63764 3.9 HDGF PKNOX1 MLX CREB3L1 ARNT ZFP64 WRNIP1 ARID4B SIN3A DMAP1 H3F3C FLJ13224 BICD1 KIAA1551 FAM60A DDX11-AS1 AK4P3 ENSG00000276900 LOC105369722
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around H3F3C on UCSC Golden Path with GeneCards custom track

Genomic Location for H3F3C Gene

Chromosome:
12
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

Genes around H3F3C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3F3C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3F3C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

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).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H3F3C Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H3F3C Gene

Domains & Families for H3F3C Gene

Gene Families for H3F3C Gene

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 :
  • Belongs to the histone H3 family.
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 IEA --
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
genes like me logo Genes that share phenotypes with H3F3C: view

Animal Model Products

miRNA for H3F3C Gene

miRTarBase miRNAs that target H3F3C

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
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 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:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005719 nuclear euchromatin IDA 21274551
genes like me logo Genes that share ontologies with H3F3C: view

Pathways & Interactions 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

No data available for SIGNOR curated interactions for H3F3C Gene

Drugs & Compounds for H3F3C Gene

No Compound Related Data Available

Transcripts for H3F3C Gene

mRNA/cDNA for H3F3C Gene

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

Unigene Clusters for H3F3C Gene

H3 histone, family 3C:
Representative Sequences:

Inhibitory RNA Products

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for H3F3C Gene

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

This gene is overexpressed in Testis (x7.1) and Whole Blood (x5.1).

Protein differential expression in normal tissues from HIPED for H3F3C Gene

This gene is overexpressed in Heart (39.0), Urine (10.5), and Testis (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for H3F3C Gene



Protein tissue co-expression partners for H3F3C Gene

NURSA nuclear receptor signaling pathways regulating expression of H3F3C Gene:

H3F3C

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.

Evidence on tissue expression from TISSUES for H3F3C Gene

  • Nervous system(4)
  • Pancreas(3.4)
  • Skin(2.7)
  • Eye(2.6)
  • Spleen(2.6)
  • Blood(2.5)
  • Lung(2.2)
  • Thyroid gland(2.1)
  • Bone marrow(2)
genes like me logo Genes that share expression patterns with H3F3C: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34
  • 99.26 (n)
cow
(Bos Taurus)
Mammalia H3F3A 35
  • 96 (a)
OneToOne
LOC100297725 34
  • 76.3 (n)
dog
(Canis familiaris)
Mammalia H3F3C 35
  • 96 (a)
OneToOne
LOC612779 34
  • 75.06 (n)
mouse
(Mus musculus)
Mammalia H3f3b 35
  • 96 (a)
ManyToMany
Gm12657 34 16
  • 75.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 91 (a)
ManyToMany
chicken
(Gallus gallus)
Aves H3-IX 35
  • 96 (a)
ManyToMany
H3F3C 34
  • 78.52 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 96 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101731074 34
  • 81.48 (n)
zebrafish
(Danio rerio)
Actinopterygii h3f3a 35
  • 96 (a)
OneToOne
h3f3c 34
  • 83.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3.3B 35
  • 96 (a)
ManyToMany
His3:CG33839 34
  • 76.79 (n)
worm
(Caenorhabditis elegans)
Secernentea his-71 34 35
  • 74.32 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHT2 35
  • 86 (a)
ManyToMany
HHT1 34 35
  • 68.89 (n)
CSE4 37
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER013W 34
  • 71.36 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 35
  • 96 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU01635 34
  • 74.63 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hht2 34
  • 70.86 (n)
Species where no ortholog for H3F3C was found in the sources mined by GeneCards:
  • 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

Variants for H3F3C Gene

Sequence variations from dbSNP and Humsavar for H3F3C Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000549714 -- 31,793,464(+) CAGGT(A/G)TGGTG upstream-variant-2KB
rs1001172982 -- 31,793,754(+) AATAA(C/T)GAAAA upstream-variant-2KB
rs1001648883 -- 31,791,538(+) AAATA(C/T)CACGC utr-variant-3-prime
rs1003067887 -- 31,792,420(+) AGTGG(A/C)GTGAT upstream-variant-2KB
rs1004397396 -- 31,793,249(+) CTGCC(A/T)CCACA upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv3580219 CNV loss 25503493
nsv519112 CNV loss 19592680
nsv522362 CNV loss 19592680
nsv523907 CNV loss 19592680
nsv558100 CNV gain 21841781
nsv558101 CNV gain 21841781
nsv558138 CNV loss 21841781
nsv663 CNV deletion 18451855
nsv8940 CNV gain 18304495
nsv983306 CNV duplication 23825009

Variation tolerance for H3F3C Gene

Residual Variation Intolerance Score: 84.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.73; 73.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for H3F3C Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H3F3C

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

Disorders for H3F3C Gene

Relevant External Links for H3F3C

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
H3F3C

No disorders were found for H3F3C Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 64
  2. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer S.E. … Gibbs R.A. (Nature 2006) 3 4 64
  3. 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 64
  4. Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. (PMID: 26779285) Urahama T. … Kurumizaka H. (Epigenetics Chromatin 2016) 3 64
  5. A comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation pathways and histone variants. (PMID: 25362550) Sadakierska-Chudy A. … Filip M. (Neurotox Res 2015) 3 64

Products for H3F3C Gene

Sources for H3F3C Gene

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