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 H2BU1 Gene

Aliases for H2BU1 Gene

  • H2B.U Histone 1 2 3 4 5
  • Histone Cluster 3 H2B Family Member B 2 3
  • Histone Cluster 3, H2bb 2 3
  • Histone H2B Type 3-B 3 4
  • Histone 3, H2bb 2 3
  • H2B Type 12 3 4
  • HIST3H2BB 3 4
  • H2BU1 5
  • H2Bb 3

External Ids for H2BU1 Gene

Previous HGNC Symbols for H2BU1 Gene

  • HIST3H2BB

Summaries for H2BU1 Gene

Entrez Gene Summary for H2BU1 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. Transcripts from this gene contain a palindromic termination element. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BU1 Gene

H2BU1 (H2B.U 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 H2BU1 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 H2BU1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BU1 Gene

Genomics for H2BU1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2BU1 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 H2BU1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BU1

Genomic Locations for H2BU1 Gene

Latest Assembly
chr1:228,458,103-228,460,470
(GRCh38/hg38)
Size:
2,368 bases
Orientation:
Plus strand

Previous Assembly
chr1:228,645,804-228,646,259
(GRCh37/hg19 by Entrez Gene)
Size:
456 bases
Orientation:
Plus strand

chr1:228,645,808-228,646,259
(GRCh37/hg19 by Ensembl)
Size:
452 bases
Orientation:
Plus strand

Alternative Locations (GRCh38/hg38)

  • chr1(PATCHES):49,302-49,757 (+)

Genomic View for H2BU1 Gene

Genes around H2BU1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BU1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BU1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2BU1 Gene

Proteins for H2BU1 Gene

  • Protein details for H2BU1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N257-H2B3B_HUMAN
    Recommended name:
    Histone H2B type 3-B
    Protein Accession:
    Q8N257
    Secondary Accessions:
    • A4FU05
    • Q3ZCP6
    • Q5TA30

    Protein attributes for H2BU1 Gene

    Size:
    126 amino acids
    Molecular mass:
    13908 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.

    Three dimensional structures from OCA and Proteopedia for H2BU1 Gene

neXtProt entry for H2BU1 Gene

Post-translational modifications for H2BU1 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.
  • Glycosylation at Ser113
  • Modification sites at PhosphoSitePlus

Other Protein References for H2BU1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BU1 Gene

Domains & Families for H2BU1 Gene

Gene Families for H2BU1 Gene

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

Protein Domains for H2BU1 Gene

Suggested Antigen Peptide Sequences for H2BU1 Gene

GenScript: Design optimal peptide antigens:
  • H2B type 12 (H2B3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N257

UniProtKB/Swiss-Prot:

H2B3B_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BU1: view

Function for H2BU1 Gene

Molecular function for H2BU1 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 H2BU1 Gene

Gene Ontology (GO) - Molecular Function for H2BU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IBA 21873635
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2BU1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BU1

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BU1 Gene

Localization for H2BU1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BU1 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 H2BU1 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 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 H2BU1 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 H2BU1: view

Pathways & Interactions for H2BU1 Gene

PathCards logo

SuperPathways for H2BU1 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 H2BU1: view

Gene Ontology (GO) - Biological Process for H2BU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA 21873635
genes like me logo Genes that share ontologies with H2BU1: view

No data available for SIGNOR curated interactions for H2BU1 Gene

Drugs & Compounds for H2BU1 Gene

No Compound Related Data Available

Transcripts for H2BU1 Gene

mRNA/cDNA for H2BU1 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 H2BU1

Alternative Splicing Database (ASD) splice patterns (SP) for H2BU1 Gene

No ASD Table

Relevant External Links for H2BU1 Gene

GeneLoc Exon Structure for
H2BU1

Expression for H2BU1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BU1

SOURCE GeneReport for Unigene cluster for H2BU1 Gene:

Hs.376691
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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2BU1 Gene

Orthologs for H2BU1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H2BU1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HIST3H2BB 30
  • 100 (a)
OneToOne
LOC469701 29
  • 99.21 (n)
Mouse
(Mus musculus)
Mammalia Hist3h2ba 30
  • 97 (a)
OneToOne
Hist3h2bb-ps 29
  • 91.27 (n)
H2bu1-ps 16
Dog
(Canis familiaris)
Mammalia -- 30
  • 97 (a)
OneToMany
LOC482202 29
  • 93.65 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 96 (a)
ManyToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 96 (a)
ManyToMany
Rat
(Rattus norvegicus)
Mammalia Hist3h2bb 29
  • 91.01 (n)
Cow
(Bos Taurus)
Mammalia HIST3H2BB 29 30
  • 84.92 (n)
OneToOne
Chicken
(Gallus gallus)
Aves H2B-V 30
  • 92 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 91 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii zgc:112234 30 30 30 30 30
  • 91 (a)
ManyToMany
zgc:194989 30
  • 90 (a)
ManyToMany
wu:fe11b02 30 30 30 30 30 30 30 30
  • 86 (a)
ManyToMany
ano9a 30 30
  • 85 (a)
ManyToMany
zgc:173587 30
  • 84 (a)
ManyToMany
si:dkey-261m9.6 30
  • 84 (a)
ManyToMany
si:dkey-261m9.19 30
  • 84 (a)
ManyToMany
CABZ01086354.1 30
  • 83 (a)
ManyToMany
zgc:171759 30 30 30 30 30 30 30 30 30 30
  • 45 (a)
ManyToMany
Species where no ortholog for H2BU1 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)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for H2BU1 Gene

ENSEMBL:
Gene Tree for H2BU1 (if available)
TreeFam:
Gene Tree for H2BU1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BU1: view image
Alliance of Genome Resources:
Additional Orthologs for H2BU1

Paralogs for H2BU1 Gene

Pseudogenes.org Pseudogenes for H2BU1 Gene

genes like me logo Genes that share paralogs with H2BU1: view

Variants for H2BU1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2BU1 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 H2BU1 Gene

Variant ID Type Subtype PubMed ID
esv32853 CNV gain 17666407
nsv1013500 CNV gain 25217958
nsv517545 CNV loss 19592680
nsv523935 CNV loss 19592680
nsv549296 CNV gain 21841781
nsv826908 CNV gain 20364138
nsv827019 CNV loss 20364138
nsv945354 CNV duplication 23825009

Variation tolerance for H2BU1 Gene

Residual Variation Intolerance Score: 23.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.32; 7.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BU1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BU1
Leiden Open Variation Database (LOVD)
H2BU1

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 H2BU1 Gene

Disorders for H2BU1 Gene

Additional Disease Information for H2BU1

No disorders were found for H2BU1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2BU1 Gene

Publications for H2BU1 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. 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
  3. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck HC … Jensen ON (Molecular & cellular proteomics : MCP 2006) 3 4
  4. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. (PMID: 16713563) Pavri R … Reinberg D (Cell 2006) 3 4
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4

Products for H2BU1 Gene

Sources for H2BU1 Gene