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 H3-5 Gene

Aliases for H3-5 Gene

  • H3.5 Histone 2 3
  • H3 Histone Family Member 3C 2 3 5
  • H3 Histone, Family 3C 2 3
  • Histone H3.3C 3 4
  • Histone H3.5 3 4
  • H3F3C 3 5
  • Histone Variant H3.5 3
  • H3.5 3

External Ids for H3-5 Gene

Previous HGNC Symbols for H3-5 Gene

  • H3F3C

Summaries for H3-5 Gene

Entrez Gene Summary for H3-5 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 H3-5 Gene

H3-5 (H3.5 Histone) is a Protein Coding gene. Among its related pathways are Transcriptional misregulation in cancer and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. An important paralog of this gene is H3-3A.

UniProtKB/Swiss-Prot Summary for H3-5 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.

Additional gene information for H3-5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H3-5 Gene

Genomics for H3-5 Gene

GeneHancer (GH) Regulatory Elements for H3-5 Gene

Promoters and enhancers for H3-5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J031791 Promoter 0.4 Ensembl 500.7 +0.9 897 1.6 ZBTB33 H3-5 piR-53738 lnc-AMN1-2
GH12J031745 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 21.4 +43.0 42980 6.9 EP300 FOXK2 ZBTB40 ZNF217 ZSCAN5C TCF12 SP1 NCOR1 JUND FOS ENSG00000256843 ENSG00000257511 CAPRIN2 DDX11-AS1 H3-5 RESF1 BICD1 DNM1L ENSG00000223722 AMN1
GH12J032050 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 16.2 -260.5 -260509 3.7 ZSCAN5C TCF12 JUND FOS PHB2 AFF1 TRIM28 RFX1 HES1 CUX1 lnc-BICD1-2 RESF1 H3-5 DDX11 SINHCAF ENSG00000177340 AMN1 ETFBKMT piR-47675-022
GH12J031755 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 9.6 +33.6 33614 5.4 ZNF217 RBAK ZNF639 CLOCK HES1 TOE1 EP300 CTBP1 ZNF148 HDAC3 LOC105369724 DNM1L BICD1 CAPRIN2 AMN1 ENSG00000252204 DDX11 ENSG00000257511 DDX11-AS1 H3-5
GH12J031763 Enhancer 0.9 Ensembl ENCODE 13.2 +28.9 28897 1.2 RBAK JUND EP300 TRIM22 ZEB1 BCL11A ZNF316 ZNF184 TRIM24 FOS H3-5 RNU6-1069P LOC105369724 lnc-AMN1-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H3-5 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H3-5

Genomic Locations for H3-5 Gene

Genomic Locations for H3-5 Gene
chr12:31,791,185-31,792,298
(GRCh38/hg38)
Size:
1,114 bases
Orientation:
Minus strand
chr12:31,944,119-31,945,175
(GRCh37/hg19)
Size:
1,057 bases
Orientation:
Minus strand

Genomic View for H3-5 Gene

Genes around H3-5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3-5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3-5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3-5 Gene

Proteins for H3-5 Gene

  • Protein details for H3-5 Gene (UniProtKB/Swiss-Prot)

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

    Protein attributes for H3-5 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 H3-5 Gene

neXtProt entry for H3-5 Gene

Post-translational modifications for H3-5 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).
  • 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) 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 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-41 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin (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 (By similarity).
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Succinylated. Desuccinylation at Lys-122 (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 H3-5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H3-5 Gene

Domains & Families for H3-5 Gene

Gene Families for H3-5 Gene

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

Protein Domains for H3-5 Gene

Blocks:
  • Histone H3
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for H3-5 Gene

GenScript: Design optimal peptide antigens:
  • Histone variant H3.5 (E9P281_HUMAN)
  • Histone H3.3C (H3C_HUMAN)

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 H3-5: view

Function for H3-5 Gene

Molecular function for H3-5 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.

Phenotypes From GWAS Catalog for H3-5 Gene

Gene Ontology (GO) - Molecular Function for H3-5 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 H3-5: view
genes like me logo Genes that share phenotypes with H3-5: view

Animal Model Products

CRISPR Products

miRNA for H3-5 Gene

miRTarBase miRNAs that target H3-5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H3-5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H3-5 Gene

Localization for H3-5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3-5 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 H3-5 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for H3-5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IBA 21873635
GO:0005694 chromosome IEA --
GO:0005719 nuclear euchromatin IDA 21274551
genes like me logo Genes that share ontologies with H3-5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H3-5 Gene

Pathways & Interactions for H3-5 Gene

genes like me logo Genes that share pathways with H3-5: view

Pathways by source for H3-5 Gene

Gene Ontology (GO) - Biological Process for H3-5 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 H3-5: view

No data available for SIGNOR curated interactions for H3-5 Gene

Drugs & Compounds for H3-5 Gene

No Compound Related Data Available

Transcripts for H3-5 Gene

mRNA/cDNA for H3-5 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H3-5

Alternative Splicing Database (ASD) splice patterns (SP) for H3-5 Gene

No ASD Table

Relevant External Links for H3-5 Gene

GeneLoc Exon Structure for
H3-5

Expression for H3-5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H3-5

SOURCE GeneReport for Unigene cluster for H3-5 Gene:

Hs.448697

mRNA Expression by UniProt/SwissProt for H3-5 Gene:

Q6NXT2-H3C_HUMAN
Tissue specificity: Specifically expressed in the seminiferous tubules of testis.

Evidence on tissue expression from TISSUES for H3-5 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)

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 H3-5 Gene

Orthologs for H3-5 Gene

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

Orthologs for H3-5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia H3F3C 30
  • 99.26 (n)
mouse
(Mus musculus)
Mammalia H3f3b 31
  • 96 (a)
ManyToMany
Gm12657 17 30
  • 75.8 (n)
dog
(Canis familiaris)
Mammalia H3F3C 31
  • 96 (a)
OneToOne
LOC612779 30
  • 75.06 (n)
cow
(Bos Taurus)
Mammalia H3F3A 31
  • 96 (a)
OneToOne
LOC100297725 30
  • 76.3 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 91 (a)
ManyToMany
chicken
(Gallus gallus)
Aves H3-IX 31
  • 96 (a)
ManyToMany
H3F3C 30
  • 78.52 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 96 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101731074 30
  • 81.48 (n)
zebrafish
(Danio rerio)
Actinopterygii h3f3a 31
  • 96 (a)
OneToOne
h3f3c 30
  • 83.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3.3B 31
  • 96 (a)
ManyToMany
His3:CG33839 30
  • 76.79 (n)
worm
(Caenorhabditis elegans)
Secernentea his-71 31 30
  • 74.32 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHT2 31
  • 86 (a)
ManyToMany
HHT1 31 30
  • 68.89 (n)
ManyToMany
CSE4 33
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER013W 30
  • 71.36 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 31
  • 96 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU01635 30
  • 74.63 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hht2 30
  • 70.86 (n)
Species where no ortholog for H3-5 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 H3-5 Gene

ENSEMBL:
Gene Tree for H3-5 (if available)
TreeFam:
Gene Tree for H3-5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H3-5: view image

Paralogs for H3-5 Gene

genes like me logo Genes that share paralogs with H3-5: view

Variants for H3-5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H3-5 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs3759295 - p.His39Arg

Additional dbSNP identifiers (rs#s) for H3-5 Gene

Structural Variations from Database of Genomic Variants (DGV) for H3-5 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 H3-5 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)

Additional Variant Information for H3-5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H3-5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H3-5 Gene

Disorders for H3-5 Gene

No disorders were found for H3-5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for H3-5 Gene

Publications for H3-5 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 54
  2. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer SE … Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team (Nature 2006) 3 4 54
  3. 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 54
  4. Insights into the ubiquitin-proteasome system of human embryonic stem cells. (PMID: 29511261) Saez I … Vilchez D (Scientific reports 2018) 3 54
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54

Products for H3-5 Gene

Sources for H3-5 Gene