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Aliases for HIST2H3D Gene

Aliases for HIST2H3D Gene

  • Histone Cluster 2, H3d 2 3
  • HIST2H3A HIST2H3C HIST2H3D 4
  • Histone 2, H3d 2
  • Histone H3/M 4
  • Histone H3/O 4
  • H3F2 4
  • H3FM 4

External Ids for HIST2H3D Gene

Previous GeneCards Identifiers for HIST2H3D Gene

  • GC01M148051
  • GC01M149784

Summaries for HIST2H3D Gene

Entrez Gene Summary for HIST2H3D Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H3 family. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST2H3D Gene

HIST2H3D (Histone Cluster 2, H3d) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Signaling by Rho GTPases. GO annotations related to this gene include protein heterodimerization activity and histone binding. An important paralog of this gene is HIST2H3A.

UniProtKB/Swiss-Prot for HIST2H3D 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

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST2H3D Gene

Genomics for HIST2H3D Gene

Regulatory Elements for HIST2H3D Gene

Genomic Location for HIST2H3D Gene

Chromosome:
1
Start:
149,813,225 bp from pter
End:
149,813,681 bp from pter
Size:
457 bases
Orientation:
Minus strand

Genomic View for HIST2H3D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST2H3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST2H3D Gene

Proteins for HIST2H3D Gene

  • Protein details for HIST2H3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q71DI3-H32_HUMAN
    Recommended name:
    Histone H3.2
    Protein Accession:
    Q71DI3
    Secondary Accessions:
    • A2BDF6
    • A6NFS4
    • Q6B053

    Protein attributes for HIST2H3D Gene

    Size:
    136 amino acids
    Molecular mass:
    15388 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. During nucleosome assembly the chaperone ASF1A interacts with the histone H3-H4 heterodimer.
    • 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. During nucleosome assembly the chaperone ASF1A interacts with the histone H3-H4 heterodimer.
    • 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. During nucleosome assembly the chaperone ASF1A interacts with the histone H3-H4 heterodimer.

    Three dimensional structures from OCA and Proteopedia for HIST2H3D Gene

neXtProt entry for HIST2H3D Gene

Proteomics data for HIST2H3D Gene at MOPED

Post-translational modifications for HIST2H3D 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 Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Ubiquitination at Lys 116
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST2H3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST2H3D Gene

Domains & Families for HIST2H3D Gene

Gene Families for HIST2H3D Gene

HGNC:

Protein Domains for HIST2H3D Gene

Suggested Antigen Peptide Sequences for HIST2H3D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q71DI3

UniProtKB/Swiss-Prot:

H32_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with HIST2H3D: view

Function for HIST2H3D Gene

Molecular function for HIST2H3D 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 HIST2H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 20580717
GO:0042393 histone binding IPI 25615412
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST2H3D: view

Phenotypes for HIST2H3D Gene

GenomeRNAi human phenotypes for HIST2H3D:
genes like me logo Genes that share phenotypes with HIST2H3D: view

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST2H3D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST2H3D Gene

Localization for HIST2H3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST2H3D Gene

Gene Ontology (GO) - Cellular Components for HIST2H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IDA 21636898
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0070062 extracellular exosome IDA 19199708
genes like me logo Genes that share ontologies with HIST2H3D: view

No data available for Subcellular locations from COMPARTMENTS for HIST2H3D Gene

Pathways & Interactions for HIST2H3D Gene

genes like me logo Genes that share pathways with HIST2H3D: view

Pathways by source for HIST2H3D Gene

1 BioSystems pathway for HIST2H3D Gene

Gene Ontology (GO) - Biological Process for HIST2H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006334 nucleosome assembly IDA 21636898
GO:0007264 small GTPase mediated signal transduction TAS --
GO:0007596 blood coagulation TAS --
GO:0010467 gene expression TAS --
genes like me logo Genes that share ontologies with HIST2H3D: view

No data available for SIGNOR curated interactions for HIST2H3D Gene

Drugs & Compounds for HIST2H3D Gene

No Compound Related Data Available

Transcripts for HIST2H3D Gene

mRNA/cDNA for HIST2H3D Gene

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

Unigene Clusters for HIST2H3D Gene

Histone cluster 2, H3d:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST2H3D

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST2H3D Gene

No ASD Table

Relevant External Links for HIST2H3D Gene

GeneLoc Exon Structure for
HIST2H3D
ECgene alternative splicing isoforms for
HIST2H3D

Expression for HIST2H3D Gene

mRNA expression in normal human tissues for HIST2H3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST2H3D Gene

This gene is overexpressed in Whole Blood (x5.5).

Protein differential expression in normal tissues from HIPED for HIST2H3D Gene

This gene is overexpressed in Heart (35.7) and Urine (21.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HIST2H3D Gene



SOURCE GeneReport for Unigene cluster for HIST2H3D Gene Hs.712062

genes like me logo Genes that share expression patterns with HIST2H3D: view

Protein tissue co-expression partners for HIST2H3D Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for HIST2H3D Gene

Orthologs for HIST2H3D Gene

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

Orthologs for HIST2H3D Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC531990 35
  • 91.67 (n)
  • 99.26 (a)
-- 36
  • 99 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hist1h3c 35
  • 90.2 (n)
  • 100 (a)
Hist1h3f 36
  • 100 (a)
ManyToMany
chimpanzee
(Pan troglodytes)
Mammalia LOC746430 35
  • 97.06 (n)
  • 100 (a)
rat
(Rattus norvegicus)
Mammalia LOC684762 35
  • 88.73 (n)
  • 100 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 98 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HIST2H3D 36
  • 95 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC770022 35
  • 92.16 (n)
  • 100 (a)
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 100 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495338 35
  • 83.82 (n)
  • 100 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC564732 35
  • 83.33 (n)
  • 100 (a)
HIST2H3D 36
  • 100 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33851 35
  • 81.62 (n)
  • 100 (a)
His3:CG31613 36
  • 100 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CSE4 38
Species with no ortholog for HIST2H3D:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)

Evolution for HIST2H3D Gene

ENSEMBL:
Gene Tree for HIST2H3D (if available)
TreeFam:
Gene Tree for HIST2H3D (if available)

Paralogs for HIST2H3D Gene

(16) SIMAP similar genes for HIST2H3D Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for HIST2H3D Gene

genes like me logo Genes that share paralogs with HIST2H3D: view

Variants for HIST2H3D Gene

Sequence variations from dbSNP and Humsavar for HIST2H3D Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs594135 -- 149,815,536(+) cccac(A/G)caccc upstream-variant-2KB
rs663980 -- 149,815,189(-) ATTAC(A/C)GTTTC upstream-variant-2KB
rs2749309 -- 149,815,581(+) ATTGC(A/T)TGATG upstream-variant-2KB
rs2788825 -- 149,815,320(+) gcctc(C/T)gcctc upstream-variant-2KB
rs2788826 -- 149,815,373(+) gggac(A/T)atagg upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST2H3D Gene

Variant ID Type Subtype PubMed ID
dgv117e1 CNV Complex 17122850
nsv428235 CNV Gain 18775914
esv2750807 CNV Gain 17911159
dgv123e1 CNV Complex 17122850
dgv125e1 CNV Complex 17122850
dgv126e1 CNV Complex 17122850
nsv872384 CNV Gain 21882294
esv21909 CNV Gain 19812545
nsv824564 CNV Gain 20364138
nsv831503 CNV Gain 17160897
nsv469694 CNV Loss 16826518
nsv831525 CNV Gain 17160897
essv23032 CNV CNV 17122850
esv1007634 OTHER Inversion 20482838
nsv7182 OTHER Inversion 18451855

Variation tolerance for HIST2H3D Gene

Residual Variation Intolerance Score: 67.97% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.24; 5.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST2H3D Gene

HapMap Linkage Disequilibrium report
HIST2H3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST2H3D Gene

Disorders for HIST2H3D Gene

Relevant External Links for HIST2H3D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST2H3D
genes like me logo Genes that share disorders with HIST2H3D: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST2H3D Gene

Publications for HIST2H3D Gene

  1. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome A.S. … Carapito C. (Proteomics 2015) 67
  2. Human tNASP promotes in vitro nucleosome assembly with histone H3.3. (PMID: 25615412) Kato D. … Kurumizaka H. (Biochemistry 2015) 67
  3. Identifying biological pathways that underlie primordial short stature using network analysis. (PMID: 24711643) Hanson D. … Clayton P.E. (J. Mol. Endocrinol. 2014) 67
  4. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. (PMID: 23415232) Tropberger P. … Schneider R. (Cell 2013) 67
  5. Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA. (PMID: 22387026) Yu Y. … Grunstein M. (Mol. Cell 2012) 67

Products for HIST2H3D Gene

Sources for HIST2H3D Gene

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