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Aliases for HIST1H2BD Gene

Aliases for HIST1H2BD Gene

  • Histone Cluster 1, H2bd 2 3
  • H2BFB 3 4 6
  • H2B Histone Family, Member B 2 3
  • HIRA-Interacting Protein 2 3 4
  • Histone 1, H2bd 2 3
  • Histone H2B.1 B 3 4
  • Histone H2B.B 3 4
  • HIRIP2 3 4
  • H2B/B 3 4
  • Histone H2B Type 1-D 3
  • DJ221C16.6 3
  • H2B.1B 3

External Ids for HIST1H2BD Gene

Previous HGNC Symbols for HIST1H2BD Gene

  • H2BFB

Previous GeneCards Identifiers for HIST1H2BD Gene

  • GC06P026217
  • GC06P026266
  • GC06P026158
  • GC06P026102

Summaries for HIST1H2BD Gene

Entrez Gene Summary for HIST1H2BD 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 is intronless and encodes a member of the histone H2B family. Two transcripts that encode the same protein have been identified for this gene, which is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Jul 2008]

GeneCards Summary for HIST1H2BD Gene

HIST1H2BD (Histone Cluster 1, H2bd) is a Protein Coding gene. Among its related pathways are Disease and Cell Cycle, Mitotic. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is HIST1H2BN.

UniProtKB/Swiss-Prot for HIST1H2BD 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 HIST1H2BD Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H2BD Gene

Genomics for HIST1H2BD Gene

Regulatory Elements for HIST1H2BD Gene

Epigenetics Products

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

Genomic Location for HIST1H2BD Gene

Start:
26,157,843 bp from pter
End:
26,171,349 bp from pter
Size:
13,507 bases
Orientation:
Plus strand

Genomic View for HIST1H2BD Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HIST1H2BD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H2BD Gene

Proteins for HIST1H2BD Gene

  • Protein details for HIST1H2BD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P58876-H2B1D_HUMAN
    Recommended name:
    Histone H2B type 1-D
    Protein Accession:
    P58876
    Secondary Accessions:

    Protein attributes for HIST1H2BD Gene

    Size:
    126 amino acids
    Molecular mass:
    13936 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:
    • The mouse orthologous protein seems not to exist

neXtProt entry for HIST1H2BD Gene

Proteomics data for HIST1H2BD Gene at MOPED

Post-translational modifications for HIST1H2BD Gene

  • 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.
  • GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).
  • Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 Lys-4 (H3K4me) and Lys-79 (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 Lys-4 and Lys-79 methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons.
  • Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription (By similarity). Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination.
  • Ubiquitination at Lys6, Lys44, Lys47, Lys58, Lys109, Lys117, and Lys121
  • Glycosylation at Ser113
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H2BD Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for HIST1H2BD Gene

Domains for HIST1H2BD Gene

Gene Families for HIST1H2BD Gene

HGNC:
  • HIST :Histones / Replication-dependent

Protein Domains for HIST1H2BD Gene

Suggested Antigen Peptide Sequences for HIST1H2BD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P58876

UniProtKB/Swiss-Prot:

H2B1D_HUMAN :
  • P58876
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with HIST1H2BD: view

Function for HIST1H2BD Gene

Molecular function for HIST1H2BD 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 HIST1H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA --
GO:0043565 sequence-specific DNA binding --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H2BD: view

Phenotypes for HIST1H2BD Gene

GenomeRNAi human phenotypes for HIST1H2BD:
genes like me logo Genes that share phenotypes with HIST1H2BD: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for HIST1H2BD Gene

Localization for HIST1H2BD Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H2BD Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HIST1H2BD Gene COMPARTMENTS Subcellular localization image for HIST1H2BD gene
Compartment Confidence
nucleus 5
cytosol 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for HIST1H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome --
GO:0000788 nuclear nucleosome IBA --
GO:0005622 intracellular --
GO:0005634 nucleus IDA 16319397
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with HIST1H2BD: view

Pathways for HIST1H2BD Gene

genes like me logo Genes that share pathways with HIST1H2BD: view

Pathways by source for HIST1H2BD Gene

29 Reactome pathways for HIST1H2BD Gene
3 KEGG pathways for HIST1H2BD Gene
1 GeneGo (Thomson Reuters) pathway for HIST1H2BD Gene

Gene Ontology (GO) - Biological Process for HIST1H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IBA --
genes like me logo Genes that share ontologies with HIST1H2BD: view

Transcripts for HIST1H2BD Gene

mRNA/cDNA for HIST1H2BD Gene

Unigene Clusters for HIST1H2BD Gene

Histone cluster 1, H2bd:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H2BD

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for HIST1H2BD
  • 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 HIST1H2BD Gene

No ASD Table

Relevant External Links for HIST1H2BD Gene

GeneLoc Exon Structure for
HIST1H2BD
ECgene alternative splicing isoforms for
HIST1H2BD

Expression for HIST1H2BD Gene

mRNA expression in normal human tissues for HIST1H2BD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H2BD Gene

This gene is overexpressed in Whole Blood (4.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HIST1H2BD Gene

SOURCE GeneReport for Unigene cluster for HIST1H2BD Gene Hs.591797

genes like me logo Genes that share expressions with HIST1H2BD: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for HIST1H2BD Gene

Orthologs for HIST1H2BD Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST1H2BD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BD 36
  • 100 (a)
OneToOne
LOC462491 35
  • 99.74 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia HIST1H2BD 35
  • 90.74 (n)
  • 100 (a)
HIST1H2BI 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 71 (a)
ManyToMany
LOC611089 35
  • 91.53 (n)
  • 97.62 (a)
mouse
(Mus musculus)
Mammalia Hist1h2bm 36
  • 100 (a)
OneToOne
Hist3h2ba 35
  • 86.51 (n)
  • 93.65 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 92 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Hist3h2ba 35
  • 86.51 (n)
  • 93.65 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5545 35
zebrafish
(Danio rerio)
Actinopterygii wufe11b02 35
Species with no ortholog for HIST1H2BD:
  • 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIST1H2BD Gene

ENSEMBL:
Gene Tree for HIST1H2BD (if available)
TreeFam:
Gene Tree for HIST1H2BD (if available)

Paralogs for HIST1H2BD Gene

genes like me logo Genes that share paralogs with HIST1H2BD: view

Variants for HIST1H2BD Gene

Sequence variations from dbSNP and Humsavar for HIST1H2BD Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs806966 -- 26,159,267(+) ttttt(G/T)ttttt intron-variant, downstream-variant-500B
rs806967 -- 26,165,204(+) AGTGG(C/G)AATCC intron-variant
rs1009181 -- 26,158,765(-) TACGT(A/G)CCCAT downstream-variant-500B, intron-variant
rs1059490 -- 26,171,022(+) ACTGA(C/T)AATAT utr-variant-3-prime
rs1417998 -- 26,161,791(+) ATAAA(A/T)GAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H2BD Gene

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

Relevant External Links for HIST1H2BD Gene

HapMap Linkage Disequilibrium report
HIST1H2BD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H2BD Gene

Disorders for HIST1H2BD Gene

No disorders were found for HIST1H2BD Gene.

No data available for UniProtKB/Swiss-Prot for HIST1H2BD Gene

Publications for HIST1H2BD Gene

  1. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 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. Core histones and HIRIP3, a novel histone-binding protein, directly interact with WD repeat protein HIRA. (PMID: 9710638) Lorain S. … Lipinski M. (Mol. Cell. Biol. 1998) 3 4
  4. Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase. (PMID: 12757711) Cheung W.L. … Allis C.D. (Cell 2003) 3 4
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall A.J. … Beck S. (Nature 2003) 3 4

Products for HIST1H2BD Gene

Sources for HIST1H2BD Gene

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