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Aliases for H3.Y Gene

Aliases for H3.Y Gene

  • Histone Cluster 2, H3c Pseudogene 3 5
  • H3 Histone, Family 3B (H3.3B) Pseudogene 3
  • Histone H3.Y 4

External Ids for H3.Y Gene

Previous GeneCards Identifiers for H3.Y Gene

  • GC05M017774
  • GC05M017783
  • GC05M017793
  • GC05M017802
  • GC05M017812
  • GC05M017822
  • GC05M017837
  • GC05M017851
  • GC05M017869
  • GC05M017883
  • GC05M018030
  • GC05M017898
  • GC05M017915
  • GC05M017930
  • GC05M017947
  • GC05M017964
  • GC05M017981
  • GC05M017998
  • GC05M018012

Summaries for H3.Y Gene

GeneCards Summary for H3.Y Gene

H3.Y (Histone Cluster 2, H3c Pseudogene) is a Protein Coding gene. An important paralog of this gene is ENSG00000268799.

UniProtKB/Swiss-Prot for H3.Y Gene

  • Primate-specific variant histone H3, which constitutes a core component of nucleosomes (PubMed:20819935, PubMed:27016736). Histone H3.Y-containing nucleosomes accumulate around transcription start sites and have flexible DNA ends, suggesting that they form relaxed chromatin that allows transcription factor access (PubMed:27016736). Histone H1 binds less efficiently to histone H3.Y-containing nucleosomes (PubMed:27016736). 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 (Probable).

Additional gene information for H3.Y Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H3.Y Gene

Genomics for H3.Y Gene

GeneHancer (GH) Regulatory Elements for H3.Y Gene

Promoters and enhancers for H3.Y 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
GH05J017667 Enhancer 0.4 Ensembl 0.4 -11.5 -11454 0.6 ATF7 CREB1 ATF2 ENSG00000274832 H3.Y
GH05J017664 Enhancer 0.2 Ensembl 0.4 -8.9 -8854 0.6 ENSG00000274832 H3.Y
- 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.Y on UCSC Golden Path with GeneCards custom track

Genomic Locations for H3.Y Gene

Genomic Locations for H3.Y Gene
chr5:17,654,870-17,655,847
(GRCh38/hg38)
Size:
978 bases
Orientation:
Minus strand
chr5:17,655,237-17,655,647
(GRCh37/hg19)
Size:
411 bases
Orientation:
Minus strand

Genomic View for H3.Y Gene

Genes around H3.Y on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3.Y 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.Y Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3.Y Gene

Proteins for H3.Y Gene

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

    Protein Symbol:
    P0DPK2-H3Y_HUMAN
    Recommended name:
    Histone H3.Y
    Protein Accession:
    P0DPK2

    Protein attributes for H3.Y Gene

    Size:
    136 amino acids
    Molecular mass:
    15423 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 (PubMed:20819935, PubMed:27016736). The octamer wraps approximately 147 bp of DNA (Probable). Interacts with HIRA, a chaperone required for its incorporation into nucleosomes (PubMed:28334823). Does not interact with DAXX chaperone (PubMed:28334823).

    Three dimensional structures from OCA and Proteopedia for H3.Y Gene

neXtProt entry for H3.Y Gene

Post-translational modifications for H3.Y 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).
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) impairs methylation and represses transcription.
  • Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) 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.
  • Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me), which are linked to gene repression, are underrepresented. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent acetylation of H3 and H4.
  • Phosphorylation at Thr-7 (H3T6ph) 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. Phosphorylation at Thr-12 (H3T11ph) is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me). Phosphorylation at Tyr-42 (H3Y41ph) promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Lysine deamination at Lys-5 (H3K4all) to form allysine. Allysine formation only takes place on H3K4me3 and results in gene repression.
  • 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.
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.

Other Protein References for H3.Y Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H3.Y Gene

Domains & Families for H3.Y Gene

Protein Domains for H3.Y Gene

Graphical View of Domain Structure for InterPro Entry

P0DPK2

UniProtKB/Swiss-Prot:

H3Y_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3.Y: view

No data available for Gene Families and Suggested Antigen Peptide Sequences for H3.Y Gene

Function for H3.Y Gene

Molecular function for H3.Y Gene

UniProtKB/Swiss-Prot Function:
Primate-specific variant histone H3, which constitutes a core component of nucleosomes (PubMed:20819935, PubMed:27016736). Histone H3.Y-containing nucleosomes accumulate around transcription start sites and have flexible DNA ends, suggesting that they form relaxed chromatin that allows transcription factor access (PubMed:27016736). Histone H1 binds less efficiently to histone H3.Y-containing nucleosomes (PubMed:27016736). 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 (Probable).

Gene Ontology (GO) - Molecular Function for H3.Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0031492 nucleosomal DNA binding IDA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H3.Y: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for H3.Y Gene

Localization for H3.Y Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3.Y Gene

Nucleus. Chromosome. Note=Histone H3.Y-containing nucleosomes are depleted from repressive post-translational histone modifications (PubMed:28334823). Histone H3.Y-containing nucleosomes accumulate around transcription start sites (PubMed:27016736). {ECO:0000269 PubMed:27016736, ECO:0000269 PubMed:28334823}.

Gene Ontology (GO) - Cellular Components for H3.Y Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000788 nuclear nucleosome IDA --
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H3.Y: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for H3.Y Gene

Pathways & Interactions for H3.Y Gene

PathCards logo

SuperPathways for H3.Y Gene

No Data Available

Interacting Proteins for H3.Y Gene

Gene Ontology (GO) - Biological Process for H3.Y Gene

None

No data available for Pathways by source and SIGNOR curated interactions for H3.Y Gene

Drugs & Compounds for H3.Y Gene

No Compound Related Data Available

Transcripts for H3.Y Gene

mRNA/cDNA for H3.Y Gene

(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for H3.Y Gene

No ASD Table

Relevant External Links for H3.Y Gene

GeneLoc Exon Structure for
H3.Y

Expression for H3.Y Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for H3.Y Gene

mRNA Expression by UniProt/SwissProt for H3.Y Gene:

P0DPK2-H3Y_HUMAN
Tissue specificity: Expressed at low level in some tissues, such as testis and brain.
genes like me logo Genes that share expression patterns with H3.Y: view

No data available for 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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H3.Y Gene

Orthologs for H3.Y Gene

Evolution for H3.Y Gene

ENSEMBL:
Gene Tree for H3.Y (if available)
TreeFam:
Gene Tree for H3.Y (if available)

No data available for Orthologs for H3.Y Gene

Paralogs for H3.Y Gene

Variants for H3.Y Gene

Sequence variations from dbSNP and Humsavar for H3.Y Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000556394 -- 17,656,807(-) T/G upstream_transcript_variant
rs1002636228 -- 17,655,556(-) T/C 5_prime_UTR_variant
rs1002650037 -- 17,656,511(-) C/T upstream_transcript_variant
rs1002924602 -- 17,656,258(-) G/A upstream_transcript_variant
rs1003515078 -- 17,654,854(-) C/A downstream_transcript_variant

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Structural Variations from Database of Genomic Variants (DGV) , Variation tolerance and Additional Variant Information for H3.Y Gene

Disorders for H3.Y Gene

No disorders were found for H3.Y Gene.

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

Publications for H3.Y Gene

  1. H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements. (PMID: 28334823) Zink LM … Hake SB (Nucleic acids research 2017) 3 4 58
  2. Structure and function of human histone H3.Y nucleosome. (PMID: 27016736) Kujirai T … Kurumizaka H (Nucleic acids research 2016) 3 4 58
  3. Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. (PMID: 20819935) Wiedemann SM … Hake SB (The Journal of cell biology 2010) 3 4 58
  4. Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y. (PMID: 28118111) Kujirai T … Kurumizaka H (Nucleus (Austin, Tex.) 2017) 4 58
  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 (Neurotoxicity research 2015) 3 58

No data available for External Links for H3.Y Gene

Products for H3.Y Gene

Sources for H3.Y Gene

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