H2BC5 Gene (Protein Coding)

H2B Clustered Histone 5

GC06P052353
GIFtS:
29
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... See more...

Aliases for H2BC5 Gene

Aliases for H2BC5 Gene

  • H2B Clustered Histone 5 2 3 5
  • H2B/B 2 3 4
  • Histone Cluster 1 H2B Family Member D 2 3
  • H2B Histone Family, Member B 2 3
  • HIRA-Interacting Protein 2 3 4
  • Histone Cluster 1, H2bd 2 3
  • Histone H2B Type 1-D 3 4
  • Histone 1, H2bd 2 3
  • Histone H2B.1 B 3 4
  • Histone H2B.B 3 4
  • HIST1H2BD 3 4
  • HIRIP2 3 4
  • H2BFB 3 4
  • Histone H2B Type 1-C/E/F/G/I 3
  • H2B-Clustered Histone 5 4
  • Histone H2B.1 A 3
  • Histone H2B.A 3
  • Histone H2B.G 3
  • Histone H2B.H 3
  • Histone H2B.K 3
  • Histone H2B.L 3
  • DJ221C16.6 3
  • HIST1H2BC 3
  • HIST1H2BE 3
  • HIST1H2BF 3
  • HIST1H2BG 3
  • HIST1H2BI 3
  • H2B.1B 3
  • H2B/A 3
  • H2B/G 3
  • H2B/H 3
  • H2B/K 3
  • H2B/L 3
  • H2BFA 3
  • H2BFG 3
  • H2BFH 3
  • H2BFK 3
  • H2BFL 3
  • H2BC5 5

External Ids for H2BC5 Gene

Previous HGNC Symbols for H2BC5 Gene

  • H2BFB
  • HIST1H2BD

Previous GeneCards Identifiers for H2BC5 Gene

  • GC06P027653
  • GC06P028382
  • GC06P028898
  • GC06P049181

Summaries for H2BC5 Gene

Entrez Gene Summary for H2BC5 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 H2BC5 Gene

H2BC5 (H2B Clustered Histone 5) is a Protein Coding gene. Among its related pathways are DNA Double-Strand Break Repair and Cellular Senescence (REACTOME). An important paralog of this gene is H2BC4.

UniProtKB/Swiss-Prot Summary for H2BC5 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 H2BC5 Gene

Additional gene information for H2BC5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC5 Gene

Genomics for H2BC5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for H2BC5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2BC5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BC5

Genomic Locations for H2BC5 Gene

Latest Assembly
chr6:26,158,008-26,171,349
(GRCh38/hg38)
Size:
13,342 bases
Orientation:
Plus strand

Previous Assembly
chr6:26,158,349-26,171,577
(GRCh37/hg19 by Entrez Gene)
Size:
13,229 bases
Orientation:
Plus strand

chr6:26,158,349-26,171,577
(GRCh37/hg19 by Ensembl)
Size:
13,229 bases
Orientation:
Plus strand

Genomic View for H2BC5 Gene

Genes around H2BC5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC5 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for H2BC5 Gene

Proteins for H2BC5 Gene

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  • Protein details for H2BC5 Gene (UniProtKB/Swiss-Prot)

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

    Protein attributes for H2BC5 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 H2BC5 Gene

Post-translational modifications for H2BC5 Gene

  • 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.
  • GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).
  • 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.
  • ADP-ribosylated on Ser-7 in response to DNA damage.
  • Glycosylation at Ser113
  • Ubiquitination at Lys6
  • Modification sites at PhosphoSitePlus

Other Protein References for H2BC5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BC5 Gene

Domains & Families for H2BC5 Gene

Gene Families for H2BC5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for H2BC5 Gene

InterPro:

Suggested Antigen Peptide Sequences for H2BC5 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2B.b (H2B1D_HUMAN)

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 H2BC5: view

Function for H2BC5 Gene

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  6. Cell Lines for research

Molecular function for H2BC5 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.

Phenotypes From GWAS Catalog for H2BC5 Gene

Gene Ontology (GO) - Molecular Function for H2BC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA 21873635
GO:0005515 protein binding IPI 28514442
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2BC5: view
genes like me logo Genes that share phenotypes with H2BC5: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BC5 Gene

Localization for H2BC5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC5 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for H2BC5 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for H2BC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IEA,IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with H2BC5: view

Pathways & Interactions for H2BC5 Gene

PathCards logo

SuperPathways for H2BC5 Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
DNA methylation
.88
RNA Polymerase I Promoter Opening
.88
B-WICH complex positively regulates rRNA expression
.86
Positive epigenetic regulation of rRNA expression
.86
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
.86
SIRT1 negatively regulates rRNA Expression
.84
NoRC negatively regulates rRNA expression
.83
RNA Polymerase I Chain Elongation
.83
PRC2 methylates histones and DNA
.83
RNA Polymerase I Transcription
.81
Negative epigenetic regulation of rRNA expression
.81
RNA Polymerase I Promoter Clearance
.81
Condensation of Prophase Chromosomes
.78
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
.76
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
.75
Epigenetic regulation of gene expression
.73
RHO GTPases activate PKNs
.72
Formation of the beta-catenin-TCF transactivating complex
.64
HDACs deacetylate histones
.60
Amyloid fiber formation
.55
Activation of anterior HOX genes in hindbrain development during early embryogenesis
.50
Activation of HOX genes during differentiation
.50
Systemic lupus erythematosus
.43
Neutrophil extracellular trap formation
.38
Alcoholism
.35
2 DNA Double-Strand Break Repair
DNA Double-Strand Break Repair
.83
Homology Directed Repair
.83
HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
.79
Processing of DNA double-strand break ends
.74
G2/M DNA damage checkpoint
.74
DNA Repair
.53
3 Cellular Senescence (REACTOME)
Cellular Senescence
.64
Oxidative Stress Induced Senescence
.64
Senescence-Associated Secretory Phenotype (SASP)
.56
Cellular responses to stress
.44
4 Chromosome Maintenance
Chromosome Maintenance
.75
Telomere Maintenance
.75
Deposition of new CENPA-containing nucleosomes at the centromere
.66
Nucleosome assembly
.66
5 Cell Cycle, Mitotic
Cell Cycle
.83
Cell Cycle, Mitotic
.83
M Phase
.60
genes like me logo Genes that share pathways with H2BC5: view

Gene Ontology (GO) - Biological Process for H2BC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA 21873635
GO:0016567 protein ubiquitination TAS --
genes like me logo Genes that share ontologies with H2BC5: view

No data available for SIGNOR curated interactions for H2BC5 Gene

Drugs & Compounds for H2BC5 Gene

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No Compound Related Data Available

Transcripts for H2BC5 Gene

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mRNA/cDNA for H2BC5 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC5

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC5 Gene

No ASD Table

Relevant External Links for H2BC5 Gene

GeneLoc Exon Structure for
H2BC5

Expression for H2BC5 Gene

Products:

  1. Primer products for research

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BC5

SOURCE GeneReport for Unigene cluster for H2BC5 Gene:

Hs.591797

Evidence on tissue expression from TISSUES for H2BC5 Gene

  • Blood(4.4)
  • Spleen(2.9)
  • Intestine(2.7)
  • Kidney(2.4)
  • Nervous system(2.4)
  • Liver(2.3)
  • Lung(2.2)
  • Bone marrow(2.1)
  • Heart(2.1)
No Expression Related Data Available

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2BC5 Gene

Orthologs for H2BC5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H2BC5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia HIST1H2BD 30
  • 100 (a)
 OneToOne
LOC462491 29
  • 99.74 (n)
Cow
(Bos Taurus)
 Mammalia HIST1H2BI 30
  • 100 (a)
 OneToOne
HIST1H2BD 29
  • 90.74 (n)
Mouse
(Mus musculus)
 Mammalia Hist1h2bm 30
  • 100 (a)
 OneToOne
Hist3h2ba 29
  • 86.51 (n)
H2bu2 16
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 92 (a)
 OneToMany
Dog
(Canis familiaris)
 Mammalia LOC611089 29
  • 91.53 (n)
-- 30
  • 71 (a)
 ManyToMany
Rat
(Rattus norvegicus)
 Mammalia Hist3h2ba 29
  • 86.51 (n)
Zebrafish
(Danio rerio)
 Actinopterygii wufe11b02 29
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.5545 29
Species where no ortholog for H2BC5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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 H2BC5 Gene

ENSEMBL:
Gene Tree for H2BC5 (if available)
TreeFam:
Gene Tree for H2BC5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC5: view image
Alliance of Genome Resources:
Additional Orthologs for H2BC5

Paralogs for H2BC5 Gene

Paralogs for H2BC5 Gene

Pseudogenes.org Pseudogenes for H2BC5 Gene

genes like me logo Genes that share paralogs with H2BC5: view

Variants for H2BC5 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2BC5 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for H2BC5 Gene

Variant ID Type Subtype PubMed ID
dgv375n21 CNV loss 19592680
dgv5926n100 CNV gain 25217958
esv3608394 CNV loss 21293372
esv3608395 CNV gain 21293372
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914
nsv970083 CNV duplication 23825009

Variation tolerance for H2BC5 Gene

Residual Variation Intolerance Score: 30.3% 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)

Additional Variant Information for H2BC5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC5
Leiden Open Variation Database (LOVD)
H2BC5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H2BC5 Gene

Disorders for H2BC5 Gene

Additional Disease Information for H2BC5

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for H2BC5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2BC5 Gene

Publications for H2BC5 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  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 3 4
  3. Gene-specific characterization of human histone H2B by electron capture dissociation. (PMID: 16457587) Siuti N … Pesavento JJ (Journal of proteome research 2006) 3 4
  4. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck HC … Jensen ON (Molecular & cellular proteomics : MCP 2006) 3 4
  5. Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. (PMID: 16319397) Bonenfant D … van Oostrum J (Molecular & cellular proteomics : MCP 2006) 3 4

ExternalLinks

View latest publications for H2BC5 gene in Mastermind

Products for H2BC5 Gene

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