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 H2BC1 Gene

Aliases for H2BC1 Gene

  • H2B Clustered Histone 1 2 3 5
  • TSH2B 2 3 4
  • H2B Histone Family, Member U, (Testis-Specific) 2 3
  • Histone Cluster 1 H2B Family Member A 2 3
  • Testis-Specific Histone H2B 3 4
  • Histone Cluster 1, H2ba 2 3
  • Histone H2B Type 1-A 3 4
  • Histone H2B, Testis 3 4
  • Histone 1, H2ba 2 3
  • BA317E16.3 2 3
  • HIST1H2BA 3 4
  • TSH2B.1 3 4
  • HTSH2B 3 4
  • H2BFU 2 3
  • STBP 2 3
  • H2BC1 5
  • TH2B 3

External Ids for H2BC1 Gene

Previous HGNC Symbols for H2BC1 Gene

  • HIST1H2BA

Previous GeneCards Identifiers for H2BC1 Gene

  • GC06P025827
  • GC06P025845
  • GC06P025855
  • GC06P025865

Summaries for H2BC1 Gene

Entrez Gene Summary for H2BC1 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 testis/sperm-specific member of the histone H2B family. Transcripts from this gene contain a palindromic termination element. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BC1 Gene

H2BC1 (H2B Clustered Histone 1) 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 H2BC3.

UniProtKB/Swiss-Prot Summary for H2BC1 Gene

  • Variant histone specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells (By similarity). Entirely replaces classical histone H2B prior nucleosome to protamine transition and probably acts as a nucleosome dissociating factor that creates a more dynamic chromatin, facilitating the large-scale exchange of histones (By similarity). Core component of nucleosome (By similarity). Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template (By similarity). Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability (By similarity). DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (By similarity). Also found in fat cells, its function and the presence of post-translational modifications specific to such cells are still unclear (PubMed:21249133).

Gene Wiki entry for H2BC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC1 Gene

Genomics for H2BC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2BC1 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 H2BC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BC1

Genomic Locations for H2BC1 Gene

Latest Assembly
chr6:25,726,777-25,727,345
(GRCh38/hg38)
Size:
569 bases
Orientation:
Plus strand

Previous Assembly
chr6:25,727,005-25,727,573
(GRCh37/hg19 by Entrez Gene)
Size:
569 bases
Orientation:
Plus strand

chr6:25,727,137-25,727,573
(GRCh37/hg19 by Ensembl)
Size:
437 bases
Orientation:
Plus strand

Genomic View for H2BC1 Gene

Genes around H2BC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2BC1 Gene

Proteins for H2BC1 Gene

  • Protein details for H2BC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96A08-H2B1A_HUMAN
    Recommended name:
    Histone H2B type 1-A
    Protein Accession:
    Q96A08
    Secondary Accessions:
    • B2R544
    • Q6NZ98
    • Q6NZA0
    • Q6NZA1

    Protein attributes for H2BC1 Gene

    Size:
    127 amino acids
    Molecular mass:
    14167 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.

    Three dimensional structures from OCA and Proteopedia for H2BC1 Gene

neXtProt entry for H2BC1 Gene

Post-translational modifications for H2BC1 Gene

  • Monoubiquitination at Lys-36 (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-122 (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.
  • 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.
  • Acetylated during spermatogenesis. Acetylated form is most abundant in spermatogonia compared to spermatocytes and round spermatids (By similarity).
  • Phosphorylated at Thr-117 in spermatogonia, spermatocytes and round spermatids.
  • Methylated at Lys-118 in spermatogonia, spermatocytes and round spermatids.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H2BC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BC1 Gene

Domains & Families for H2BC1 Gene

Gene Families for H2BC1 Gene

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

Protein Domains for H2BC1 Gene

Suggested Antigen Peptide Sequences for H2BC1 Gene

GenScript: Design optimal peptide antigens:
  • Testis-specific histone H2B (H2B1A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96A08

UniProtKB/Swiss-Prot:

H2B1A_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BC1: view

Function for H2BC1 Gene

Molecular function for H2BC1 Gene

UniProtKB/Swiss-Prot Function:
Variant histone specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells (By similarity). Entirely replaces classical histone H2B prior nucleosome to protamine transition and probably acts as a nucleosome dissociating factor that creates a more dynamic chromatin, facilitating the large-scale exchange of histones (By similarity). Core component of nucleosome (By similarity). Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template (By similarity). Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability (By similarity). DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (By similarity). Also found in fat cells, its function and the presence of post-translational modifications specific to such cells are still unclear (PubMed:21249133).

Phenotypes From GWAS Catalog for H2BC1 Gene

Gene Ontology (GO) - Molecular Function for H2BC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA 21873635
GO:0042393 histone binding IEA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2BC1: view
genes like me logo Genes that share phenotypes with H2BC1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BC1 Gene

Localization for H2BC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC1 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 H2BC1 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for H2BC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region HDA 19135898
GO:0000786 nucleosome ISS --
GO:0005634 nucleus IEA,HDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2BC1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H2BC1 Gene

Pathways & Interactions for H2BC1 Gene

PathCards logo

SuperPathways for H2BC1 Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 DNA Double-Strand Break Repair
3 Cellular Senescence (REACTOME)
4 Chromosome Maintenance
5 Cell Cycle, Mitotic
.60
genes like me logo Genes that share pathways with H2BC1: view

Gene Ontology (GO) - Biological Process for H2BC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006323 DNA packaging IEA --
GO:0006325 chromatin organization IEA --
GO:0006334 nucleosome assembly IEA,ISS --
GO:0006337 nucleosome disassembly IEA,ISS --
GO:0006954 inflammatory response IEA --
genes like me logo Genes that share ontologies with H2BC1: view

No data available for SIGNOR curated interactions for H2BC1 Gene

Drugs & Compounds for H2BC1 Gene

No Compound Related Data Available

Transcripts for H2BC1 Gene

mRNA/cDNA for H2BC1 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 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 H2BC1

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC1 Gene

No ASD Table

Relevant External Links for H2BC1 Gene

GeneLoc Exon Structure for
H2BC1

Expression for H2BC1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BC1

SOURCE GeneReport for Unigene cluster for H2BC1 Gene:

Hs.591786

mRNA Expression by UniProt/SwissProt for H2BC1 Gene:

Q96A08-H2B1A_HUMAN
Tissue specificity: Mainly expressed in testis, and the corresponding protein is also present in mature sperm (at protein level). Also found in some fat cells.

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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2BC1 Gene

Orthologs for H2BC1 Gene

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

Orthologs for H2BC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BA 29 30
  • 97.9 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 30
  • 91 (a)
OneToMany
-- 30
  • 81 (a)
OneToMany
LOC488253 29
  • 79.79 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia HIST1H2BA 30
  • 88 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia HIST1H2BA 29 30
  • 80.58 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hist1h2ba 29 30
  • 80.31 (n)
OneToOne
H2bc1 16
Rat
(Rattus norvegicus)
Mammalia Hist1h2ba 29
  • 80.05 (n)
Chicken
(Gallus gallus)
Aves -- 30
  • 73 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii HIST1H2BA 30
  • 86 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta His2B:CG33900 30
  • 82 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea his-34 30
  • 80 (a)
ManyToMany
his-66 30
  • 80 (a)
ManyToMany
his-41 30
  • 80 (a)
ManyToMany
his-58 30
  • 80 (a)
ManyToMany
his-11 30
  • 80 (a)
ManyToMany
his-44 30
  • 80 (a)
ManyToMany
his-15 30
  • 80 (a)
ManyToMany
his-48 30
  • 80 (a)
ManyToMany
his-29 30
  • 80 (a)
ManyToMany
his-62 30
  • 80 (a)
ManyToMany
his-52 30
  • 79 (a)
ManyToMany
his-20 30
  • 79 (a)
ManyToMany
his-22 30
  • 79 (a)
ManyToMany
his-4 30
  • 79 (a)
ManyToMany
his-8 30
  • 79 (a)
ManyToMany
his-39 30
  • 76 (a)
ManyToMany
his-54 30
  • 69 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HTB1 30
  • 66 (a)
ManyToMany
HTB2 30
  • 66 (a)
ManyToMany
Species where no ortholog for H2BC1 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)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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)

Evolution for H2BC1 Gene

ENSEMBL:
Gene Tree for H2BC1 (if available)
TreeFam:
Gene Tree for H2BC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC1: view image
Alliance of Genome Resources:
Additional Orthologs for H2BC1

Paralogs for H2BC1 Gene

genes like me logo Genes that share paralogs with H2BC1: view

Variants for H2BC1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2BC1 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 H2BC1 Gene

Variant ID Type Subtype PubMed ID
esv3570813 CNV loss 25503493

Variation tolerance for H2BC1 Gene

Residual Variation Intolerance Score: 53.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.43; 9.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC1
Leiden Open Variation Database (LOVD)
H2BC1

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 H2BC1 Gene

Disorders for H2BC1 Gene

Additional Disease Information for H2BC1

No disorders were found for H2BC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2BC1 Gene

Publications for H2BC1 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. Human testis/sperm-specific histone H2B (hTSH2B). Molecular cloning and characterization. (PMID: 12213818) Zalensky AO … Bradbury EM (The Journal of biological chemistry 2002) 2 3 4
  3. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. (PMID: 16713563) Pavri R … Reinberg D (Cell 2006) 3 4
  4. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. (PMID: 16307923) Zhu B … Reinberg D (Molecular cell 2005) 3 4
  5. Inhibition of core histones acetylation by carcinogenic nickel(II). (PMID: 16283522) Golebiowski F … Kasprzak KS (Molecular and cellular biochemistry 2005) 3 4

Products for H2BC1 Gene

Sources for H2BC1 Gene