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Aliases for HIST1H3D Gene

Aliases for HIST1H3D Gene

  • Histone Cluster 1, H3d 2 3
  • H3FB 3 4 6
  • H3 Histone Family, Member B 2 3
  • Histone 1, H3d 2 3
  • Histone H3/B 3 4
  • HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J 4
  • Histone H3.1 3
  • Histone H3/A 4
  • Histone H3/C 4
  • Histone H3/D 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/I 4
  • Histone H3/J 4
  • Histone H3/K 4
  • Histone H3/L 4
  • H3FC 4
  • H3FA 4
  • H3FD 4
  • H3FF 4
  • H3FH 4
  • H3FI 4
  • H3FJ 4
  • H3FK 4
  • H3FL 4
  • H3/B 3

External Ids for HIST1H3D Gene

Previous HGNC Symbols for HIST1H3D Gene

  • H3FB

Previous GeneCards Identifiers for HIST1H3D Gene

  • GC06M026254
  • GC06M026306
  • GC06M026310
  • GC06M026312
  • GC06M026314
  • GC06M026197
  • GC06M026140

Summaries for HIST1H3D Gene

Entrez Gene Summary for HIST1H3D 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 member of the histone H3 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Jul 2008]

GeneCards Summary for HIST1H3D Gene

HIST1H3D (Histone Cluster 1, H3d) is a Protein Coding gene. Among its related pathways are Disease and ERK Signaling. An important paralog of this gene is HIST2H3A.

UniProtKB/Swiss-Prot for HIST1H3D 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

Gene Wiki entry for HIST1H3D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3D Gene

Genomics for HIST1H3D Gene

Regulatory Elements for HIST1H3D Gene

Epigenetics Products

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

Genomic Location for HIST1H3D Gene

Start:
26,196,784 bp from pter
End:
26,199,293 bp from pter
Size:
2,510 bases
Orientation:
Minus strand

Genomic View for HIST1H3D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3D Gene

Proteins for HIST1H3D Gene

  • Protein details for HIST1H3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P68431-H31_HUMAN
    Recommended name:
    Histone H3.1
    Protein Accession:
    P68431
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3D Gene

    Size:
    136 amino acids
    Molecular mass:
    15404 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.
    Miscellaneous:
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2)

    Three dimensional structures from OCA and Proteopedia for HIST1H3D Gene

neXtProt entry for HIST1H3D Gene

Proteomics data for HIST1H3D Gene at MOPED

Post-translational modifications for HIST1H3D 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 Thr-12 (H3T11ph) by chromatin-associated CHEK1 regulates the transcription of cell cycle regulatory genes by modulating acetylation of Lys-10 (H3K9ac). Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Ubiquitination at Lys19, Lys24, Lys57, Lys65, Lys80, Lys116, and Lys123
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H3D Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3D Gene

Domains for HIST1H3D Gene

Gene Families for HIST1H3D Gene

HGNC:
  • HIST :Histones / Replication-dependent

Protein Domains for HIST1H3D Gene

Graphical View of Domain Structure for InterPro Entry

P68431

UniProtKB/Swiss-Prot:

H31_HUMAN :
  • P68431
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with HIST1H3D: view

No data available for Suggested Antigen Peptide Sequences for HIST1H3D Gene

Function for HIST1H3D Gene

Molecular function for HIST1H3D 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 HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 10949293
GO:0042393 histone binding IPI 20498094
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H3D: view
genes like me logo Genes that share phenotypes with HIST1H3D: view

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H3D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for HIST1H3D Gene

Localization for HIST1H3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H3D Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HIST1H3D Gene COMPARTMENTS Subcellular localization image for HIST1H3D gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2

Gene Ontology (GO) - Cellular Components for HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000786 nucleosome IDA 21636898
GO:0000788 nuclear nucleosome IDA 20498094
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 21630459
genes like me logo Genes that share ontologies with HIST1H3D: view

Pathways for HIST1H3D Gene

genes like me logo Genes that share pathways with HIST1H3D: view

Gene Ontology (GO) - Biological Process for HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
genes like me logo Genes that share ontologies with HIST1H3D: view

Transcripts for HIST1H3D Gene

mRNA/cDNA for HIST1H3D Gene

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

Unigene Clusters for HIST1H3D Gene

Histone cluster 1, H3d:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H3D

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 HIST1H3D Gene

No ASD Table

Relevant External Links for HIST1H3D Gene

GeneLoc Exon Structure for
HIST1H3D
ECgene alternative splicing isoforms for
HIST1H3D

Expression for HIST1H3D Gene

mRNA expression in normal human tissues for HIST1H3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H3D Gene

This gene is overexpressed in Whole Blood (20.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HIST1H3D Gene

SOURCE GeneReport for Unigene cluster for HIST1H3D Gene Hs.532144

genes like me logo Genes that share expressions with HIST1H3D: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for HIST1H3D Gene

Orthologs for HIST1H3D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 36
  • 100 (a)
ManyToMany
LOC462506 35
  • 87.75 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia -- 36
  • 100 (a)
ManyToMany
LOC525511 35
  • 89.46 (n)
  • 100 (a)
dog
(Canis familiaris)
Mammalia -- 36
  • 100 (a)
OneToMany
LOC100684574 35
  • 88.48 (n)
  • 100 (a)
mouse
(Mus musculus)
Mammalia Hist1h3a 35
  • 87.75 (n)
  • 100 (a)
Hist1h3d 16
Hist1h3i 36
  • 100 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 94 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia LOC691496 35
  • 83.09 (n)
  • 97.79 (a)
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 96 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487139 35
  • 85.29 (n)
  • 99.26 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100329422 35
  • 84.31 (n)
  • 99.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33848 35
  • 81.37 (n)
  • 99.26 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CSE4 38
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10591 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15445 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 93 (a)
ManyToMany
-- 36
  • 93 (a)
ManyToMany
Species with no ortholog for HIST1H3D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 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 HIST1H3D Gene

ENSEMBL:
Gene Tree for HIST1H3D (if available)
TreeFam:
Gene Tree for HIST1H3D (if available)

Paralogs for HIST1H3D Gene

Selected SIMAP similar genes for HIST1H3D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H3D: view

Variants for HIST1H3D Gene

Sequence variations from dbSNP and Humsavar for HIST1H3D Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs1056031 -- 26,196,885(-) ATGCC(C/G)AAGGA reference, synonymous-codon
rs41266801 -- 26,197,265(+) CTAAA(A/C)CCTGC utr-variant-5-prime
rs67575965 -- 26,196,365(+) CAGGC(A/G)GTGTT downstream-variant-500B
rs74526984 -- 26,196,785(+) AAGGT(G/T)GTTGG utr-variant-3-prime
rs76511383 -- 26,197,412(+) ATGTA(A/G)ACCAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3D Gene

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914
dgv375n21 CNV Loss 19592680
nsv883490 CNV Loss 21882294

Relevant External Links for HIST1H3D Gene

HapMap Linkage Disequilibrium report
HIST1H3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H3D Gene

Disorders for HIST1H3D Gene

No disorders were found for HIST1H3D Gene.

No data available for UniProtKB/Swiss-Prot for HIST1H3D Gene

Publications for HIST1H3D Gene

  1. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 3 4
  2. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W. … Doenecke D. (Hum. Genet. 1997) 3 4
  5. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. (PMID: 16267050) Hake S.B. … Hunt D.F. (J. Biol. Chem. 2006) 3 4

Products for HIST1H3D Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate HIST1H3D
  • 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
  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H3D
  • Block miRNA regulation of HIST1H3D using miScript Target Protectors

Sources for HIST1H3D Gene

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