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Aliases for HIST1H2BD Gene

Aliases for HIST1H2BD Gene

  • Histone Cluster 1, H2bd 2 3
  • 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
  • H2BFB 3 4
  • H2B/B 3 4
  • 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
  • GC06P026172

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 replication-dependent histone that is 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, Aug 2015]

GeneCards Summary for HIST1H2BD Gene

HIST1H2BD (Histone Cluster 1, H2bd) 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 sequence-specific DNA binding and 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

Chromosome:
6
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

    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 Lys 6 and Lys 121
  • Glycosylation at Ser 113
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H2BD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H2BD Gene

Domains & Families for HIST1H2BD Gene

Gene Families for HIST1H2BD Gene

HGNC:

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 :
  • Belongs to the histone H2B family.
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:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H2BD: view

Phenotypes for HIST1H2BD Gene

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

miRNA for HIST1H2BD Gene

miRTarBase miRNAs that target HIST1H2BD

miRNA Products

Inhibitory RNA Products

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

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets 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
extracellular 5
nucleus 5
cytoskeleton 1
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:0005634 nucleus IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0070062 extracellular exosome IDA 20458337
genes like me logo Genes that share ontologies with HIST1H2BD: view

Pathways & Interactions for HIST1H2BD Gene

SuperPathways for HIST1H2BD 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 HIST1H2BD: view

Pathways by source 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

No data available for SIGNOR curated interactions for HIST1H2BD Gene

Drugs & Compounds for HIST1H2BD Gene

No Compound Related Data Available

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

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 differential expression in normal tissues according to GTEx for HIST1H2BD Gene

This gene is overexpressed in Whole Blood (x4.3).

Protein differential expression in normal tissues from HIPED for HIST1H2BD Gene

This gene is overexpressed in Saliva (57.3).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with HIST1H2BD: view

Protein tissue co-expression partners for HIST1H2BD 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 mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and 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
cow
(Bos Taurus)
Mammalia HIST1H2BD 35
  • 90.74 (n)
  • 100 (a)
HIST1H2BI 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LOC611089 35
  • 91.53 (n)
  • 97.62 (a)
-- 36
  • 71 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hist3h2ba 35
  • 86.51 (n)
  • 93.65 (a)
Hist1h2bm 36
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LOC462491 35
  • 99.74 (n)
  • 100 (a)
HIST1H2BD 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hist3h2ba 35
  • 86.51 (n)
  • 93.65 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 92 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii wufe11b02 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5545 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

Variation tolerance for HIST1H2BD Gene

Residual Variation Intolerance Score: 30.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.66; 31.76% of all genes are more intolerant (likely to be disease-causing)

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

Relevant External Links for HIST1H2BD

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H2BD
genes like me logo Genes that share disorders with HIST1H2BD: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H2BD Gene

Publications for HIST1H2BD Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 67
  2. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 2 67
  3. Luzp4 defines a new mRNA export pathway in cancer cells. (PMID: 25662211) Viphakone N. … Wilson S.A. (Nucleic Acids Res. 2015) 67
  4. The central role of EED in the orchestration of polycomb group complexes. (PMID: 24457600) Cao Q. … Chinnaiyan A.M. (Nat Commun 2014) 67
  5. The intracellular interactome of tetraspanin-enriched microdomains reveals their function as sorting machineries toward exosomes. (PMID: 23463506) Perez-Hernandez D. … YA!A+ez-MA^ M. (J. Biol. Chem. 2013) 67

Products for HIST1H2BD Gene

Sources for HIST1H2BD Gene

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