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Aliases for HIST1H4D Gene

Aliases for HIST1H4D Gene

  • Histone Cluster 1, H4d 2 3
  • H4 Histone Family, Member B 2 3
  • Histone 1, H4d 2 3
  • H4/B 3 4
  • H4FB 3 4
  • HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 4
  • DJ221C16.9 3
  • HIST2H4 4
  • H4/G 4
  • H4FG 4
  • H4/A 4
  • H4/C 4
  • H4/D 4
  • H4/E 4
  • H4/H 4
  • H4/I 4
  • H4/J 4
  • H4/K 4
  • H4/M 4
  • H4/N 4
  • H4/O 4
  • H4F2 4
  • H4FA 4
  • H4FC 4
  • H4FD 4
  • H4FE 4
  • H4FH 4
  • H4FI 4
  • H4FJ 4
  • H4FK 4
  • H4FM 4
  • H4FN 4
  • H4FO 4

External Ids for HIST1H4D Gene

Previous HGNC Symbols for HIST1H4D Gene

  • H4FB

Previous GeneCards Identifiers for HIST1H4D Gene

  • GC06M026246
  • GC06M026296
  • GC06M026131

Summaries for HIST1H4D Gene

Entrez Gene Summary for HIST1H4D 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 H4 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, Aug 2015]

GeneCards Summary for HIST1H4D Gene

HIST1H4D (Histone Cluster 1, H4d) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Apoptotic Pathways in Synovial Fibroblasts. GO annotations related to this gene include poly(A) RNA binding and histone binding.

UniProtKB/Swiss-Prot for HIST1H4D 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 HIST1H4D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H4D Gene

Genomics for HIST1H4D Gene

Regulatory Elements for HIST1H4D Gene

Genomic Location for HIST1H4D Gene

Chromosome:
6
Start:
26,188,710 bp from pter
End:
26,189,076 bp from pter
Size:
367 bases
Orientation:
Minus strand

Genomic View for HIST1H4D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H4D Gene

Proteins for HIST1H4D Gene

  • Protein details for HIST1H4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62805-H4_HUMAN
    Recommended name:
    Histone H4
    Protein Accession:
    P62805
    Secondary Accessions:
    • A2VCL0
    • P02304
    • P02305
    • Q6DRA9
    • Q6FGB8
    • Q6NWP7

    Protein attributes for HIST1H4D Gene

    Size:
    103 amino acids
    Molecular mass:
    11367 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    SequenceCaution:
    • Sequence=AAI28106.1; Type=Frameshift; Positions=3; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HIST1H4D Gene

neXtProt entry for HIST1H4D Gene

Proteomics data for HIST1H4D Gene at MOPED

Post-translational modifications for HIST1H4D Gene

  • Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.
  • Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.
  • 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.
  • Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by SUV420H1 and SUV420H2 and induces gene silencing
  • Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.
  • Phosphorylated by PAK2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4.
  • Sumoylated, which is associated with transcriptional repression.
  • 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. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me).
  • Ubiquitination at Lys 32, Lys 60, Lys 78, and Lys 80
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H4D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H4D Gene

Domains & Families for HIST1H4D Gene

Gene Families for HIST1H4D Gene

HGNC:

Protein Domains for HIST1H4D Gene

Graphical View of Domain Structure for InterPro Entry

P62805

UniProtKB/Swiss-Prot:

H4_HUMAN :
  • Belongs to the histone H4 family.
Family:
  • Belongs to the histone H4 family.
genes like me logo Genes that share domains with HIST1H4D: view

No data available for Suggested Antigen Peptide Sequences for HIST1H4D Gene

Function for HIST1H4D Gene

Molecular function for HIST1H4D 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 HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 3035717
GO:0005515 protein binding IPI 9540062
GO:0035575 histone demethylase activity (H4-K20 specific) TAS --
GO:0042393 histone binding IPI 20498094
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with HIST1H4D: view

Phenotypes for HIST1H4D Gene

GenomeRNAi human phenotypes for HIST1H4D:
genes like me logo Genes that share phenotypes with HIST1H4D: view

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H4D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H4D Gene

Localization for HIST1H4D Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HIST1H4D Gene COMPARTMENTS Subcellular localization image for HIST1H4D gene
Compartment Confidence
extracellular 5
nucleus 5
cytoskeleton 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000784 nuclear chromosome, telomeric region IDA 19135898
GO:0000786 nucleosome TAS 3035717
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA 14585971
genes like me logo Genes that share ontologies with HIST1H4D: view

Pathways & Interactions for HIST1H4D Gene

SuperPathways for HIST1H4D Gene

Superpath Contained pathways
1 RNA Polymerase I Promoter Opening
2 RNA Polymerase I Transcription
3 G2/M DNA damage checkpoint
4 DNA Double-Strand Break Repair
5 Cellular Senescence
genes like me logo Genes that share pathways with HIST1H4D: view

SIGNOR curated interactions for HIST1H4D Gene

Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for HIST1H4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0000278 mitotic cell cycle TAS --
GO:0000723 telomere maintenance TAS --
GO:0000724 double-strand break repair via homologous recombination TAS --
GO:0006281 DNA repair TAS --
genes like me logo Genes that share ontologies with HIST1H4D: view

Drugs & Compounds for HIST1H4D Gene

No Compound Related Data Available

Transcripts for HIST1H4D Gene

mRNA/cDNA for HIST1H4D Gene

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

Unigene Clusters for HIST1H4D Gene

Histone cluster 1, H4d:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H4D

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H4D Gene

No ASD Table

Relevant External Links for HIST1H4D Gene

GeneLoc Exon Structure for
HIST1H4D
ECgene alternative splicing isoforms for
HIST1H4D

Expression for HIST1H4D Gene

mRNA expression in normal human tissues for HIST1H4D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H4D Gene

This gene is overexpressed in Whole Blood (x18.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for HIST1H4D Gene



SOURCE GeneReport for Unigene cluster for HIST1H4D Gene Hs.248179

genes like me logo Genes that share expression patterns with HIST1H4D: view

Protein tissue co-expression partners for HIST1H4D Gene

- Elite partner

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

In Situ Assay Products

No data available for Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HIST1H4D Gene

Orthologs for HIST1H4D Gene

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

Orthologs for HIST1H4D Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC100337407 35
  • 77.67 (n)
  • 99.03 (a)
dog
(Canis familiaris)
Mammalia LOC100856225 35
  • 84.79 (n)
  • 100 (a)
mouse
(Mus musculus)
Mammalia Hist1h4m 35
  • 82.85 (n)
  • 100 (a)
Hist1h4d 16
chimpanzee
(Pan troglodytes)
Mammalia LOC748513 35
  • 80.26 (n)
  • 100 (a)
rat
(Rattus norvegicus)
Mammalia Hist2h4a 35
  • 85.11 (n)
  • 100 (a)
chicken
(Gallus gallus)
Aves HIST1H46L2 35
  • 84.47 (n)
  • 100 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495739 35
  • 82.52 (n)
  • 100 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100002181 35
  • 77.67 (n)
  • 100 (a)
fruit fly
(Drosophila melanogaster)
Insecta His4:CG33891 35
  • 79.94 (n)
  • 99.03 (a)
worm
(Caenorhabditis elegans)
Secernentea his-60 35
  • 76.7 (n)
  • 99.03 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER012C 35
  • 80.26 (n)
  • 92.23 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E08647g 35
  • 69.9 (n)
  • 93.2 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHF1 35
  • 69.58 (n)
  • 92.23 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU01634 35
  • 77.78 (n)
  • 92.47 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes hhf3 35
  • 76.05 (n)
  • 91.26 (a)
Species with no ortholog for HIST1H4D:
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)

Evolution for HIST1H4D Gene

ENSEMBL:
Gene Tree for HIST1H4D (if available)
TreeFam:
Gene Tree for HIST1H4D (if available)

Paralogs for HIST1H4D Gene

(3) SIMAP similar genes for HIST1H4D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H4D: view

No data available for Paralogs for HIST1H4D Gene

Variants for HIST1H4D Gene

Sequence variations from dbSNP and Humsavar for HIST1H4D Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs806977 -- 26,189,387(+) TGACA(A/G)TTGTC upstream-variant-2KB
rs7738063 -- 26,189,443(+) CAGGG(G/T)GCttt upstream-variant-2KB
rs11753837 -- 26,190,519(+) CTTGT(A/G)AGAAG upstream-variant-2KB
rs11756143 -- 26,189,761(+) TAAGG(G/T)GCTTT upstream-variant-2KB
rs13204572 -- 26,189,128(+) GCCAC(A/C/G)CAGCA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST1H4D Gene

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

Variation tolerance for HIST1H4D Gene

Residual Variation Intolerance Score: 29.45% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.79; 16.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST1H4D Gene

HapMap Linkage Disequilibrium report
HIST1H4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H4D Gene

Disorders for HIST1H4D Gene

UniProtKB/Swiss-Prot

H4_HUMAN
  • Note=Chromosomal aberrations involving HISTONE H4 is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;6)(q27;p21), with BCL6.

Relevant External Links for HIST1H4D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H4D
genes like me logo Genes that share disorders with HIST1H4D: view

No data available for MalaCards and Genatlas for HIST1H4D Gene

Publications for HIST1H4D Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 67
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W. … Doenecke D. (Genomics 1997) 2 67
  3. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome A.S. … Carapito C. (Proteomics 2015) 67
  4. Human tNASP promotes in vitro nucleosome assembly with histone H3.3. (PMID: 25615412) Kato D. … Kurumizaka H. (Biochemistry 2015) 67
  5. Uncovering global SUMOylation signaling networks in a site-specific manner. (PMID: 25218447) Hendriks I.A. … Vertegaal A.C. (Nat. Struct. Mol. Biol. 2014) 67

Products for HIST1H4D Gene

Sources for HIST1H4D Gene

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