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Aliases for HIST3H2BB Gene

Aliases for HIST3H2BB Gene

  • Histone Cluster 3 H2B Family Member B 2 3 5
  • Histone Cluster 3, H2bb 2 3
  • Histone 3, H2bb 2 3
  • H2B Type 12 3 4
  • Histone H2B Type 3-B 3
  • H2Bb 3

External Ids for HIST3H2BB Gene

Previous GeneCards Identifiers for HIST3H2BB Gene

  • GC01P224384
  • GC01P225031
  • GC01P225620
  • GC01P224952
  • GC01P226712
  • GC01P228645
  • GC01P199161

Summaries for HIST3H2BB Gene

Entrez Gene Summary for HIST3H2BB 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 HIST3H2BB Gene

HIST3H2BB (Histone Cluster 3 H2B Family Member B) is a Protein Coding gene. Among its related pathways are Mitotic Prophase and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST1H2BH.

UniProtKB/Swiss-Prot for HIST3H2BB 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 HIST3H2BB Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST3H2BB Gene

Genomics for HIST3H2BB Gene

Regulatory Elements for HIST3H2BB Gene

Enhancers for HIST3H2BB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F228500 1.5 FANTOM5 Ensembl ENCODE 11.9 +42.8 42794 1.8 WRNIP1 ARID4B SIN3A DMAP1 ZNF48 ZNF143 REST TBX21 KAT8 CREB3 HIST3H2A HIST3H2BB RPL23AP15 C1orf35 C1orf145 OBSCN RNF187 LOC105373124 ENSG00000279306
GH01F228130 1.3 Ensembl ENCODE 10.9 -326.5 -326496 2.0 ATF1 PKNOX1 ARID4B GLI4 YBX1 ZNF2 ZNF121 GLIS2 ZNF143 KLF7 CICP26 ENSG00000269890 C1orf35 HIST3H3 OBSCN C1orf145 RPL23AP15 HIST3H2A HIST3H2BB ENSG00000231563
GH01F228137 1.4 Ensembl ENCODE 10 -316.0 -316043 8.8 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF548 OBSCN CICP26 ENSG00000269890 C1orf145 C1orf35 FAM96AP2 MRPL55 DUSP5P1 ENSG00000231563 RPL23AP15
GH01F228377 1.2 Ensembl ENCODE 11.2 -79.4 -79406 1.8 SIN3A ZNF2 ZNF121 GLIS2 KLF7 SP3 TSHZ1 REST ZNF518A ZNF623 PRSS38 LOC100421842 ENSG00000233920 ENSG00000231563 MIR6742 TRIM11 RPL23AP15 HIST3H2A HIST3H2BB C1orf145
GH01F228268 1.2 Ensembl 10.4 -188.6 -188627 2.8 PKNOX1 ARNT CREB3L1 SIN3A FEZF1 ZNF2 ZNF766 ZNF302 CBX5 ZNF207 OBSCN CICP26 PRSS38 ENSG00000269890 HIST3H3 LOC100421842 ENSG00000233920 DUSP5P1 ENSG00000269934 C1orf145
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST3H2BB on UCSC Golden Path with GeneCards custom track

Promoters for HIST3H2BB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000083443 -307 4401 CREB3L1 DMAP1 FEZF1 YBX1 ZNF263 MCM3 SP3 ZFP41 ZNF610 GLIS1

Genomic Location for HIST3H2BB Gene

Chromosome:
1
Start:
228,458,107 bp from pter
End:
228,460,470 bp from pter
Size:
2,364 bases
Orientation:
Plus strand

Genomic View for HIST3H2BB Gene

Genes around HIST3H2BB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST3H2BB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST3H2BB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST3H2BB Gene

Proteins for HIST3H2BB Gene

  • Protein details for HIST3H2BB 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 HIST3H2BB 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.

neXtProt entry for HIST3H2BB Gene

Post-translational modifications for HIST3H2BB 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 121
  • Glycosylation at Ser 113
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST3H2BB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST3H2BB Gene

Domains & Families for HIST3H2BB Gene

Gene Families for HIST3H2BB Gene

Protein Domains for HIST3H2BB Gene

Suggested Antigen Peptide Sequences for HIST3H2BB Gene

GenScript: Design optimal peptide antigens:

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 HIST3H2BB: view

Function for HIST3H2BB Gene

Molecular function for HIST3H2BB 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 HIST3H2BB 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 HIST3H2BB: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST3H2BB Gene

Localization for HIST3H2BB Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST3H2BB 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 HIST3H2BB gene
Compartment Confidence
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for HIST3H2BB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000788 nuclear nucleosome IBA --
GO:0005634 nucleus IEA,IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with HIST3H2BB: view

Pathways & Interactions for HIST3H2BB Gene

SuperPathways for HIST3H2BB 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
4 Chromosome Maintenance
5 Cell Cycle, Mitotic
.60
genes like me logo Genes that share pathways with HIST3H2BB: view

Interacting Proteins for HIST3H2BB Gene

Selected Interacting proteins: Q8N257-H2B3B_HUMAN for HIST3H2BB Gene via IID

Gene Ontology (GO) - Biological Process for HIST3H2BB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA --
genes like me logo Genes that share ontologies with HIST3H2BB: view

No data available for SIGNOR curated interactions for HIST3H2BB Gene

Transcripts for HIST3H2BB Gene

mRNA/cDNA for HIST3H2BB Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HIST3H2BB Gene

Histone cluster 3, H2bb:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST3H2BB Gene

No ASD Table

Relevant External Links for HIST3H2BB Gene

GeneLoc Exon Structure for
HIST3H2BB
ECgene alternative splicing isoforms for
HIST3H2BB

Expression for HIST3H2BB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HIST3H2BB Gene

mRNA differential expression in normal tissues according to GTEx for HIST3H2BB Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.9), Cervix - Ectocervix (x6.0), Brain - Spinal cord (cervical c-1) (x4.2), and Brain - Cerebellum (x4.1).

Protein differential expression in normal tissues from HIPED for HIST3H2BB Gene

This gene is overexpressed in CD8 Tcells (16.8), Pancreas (14.6), NK cells (8.8), Testis (8.1), Ovary (7.9), and Fetal gut (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HIST3H2BB Gene



Protein tissue co-expression partners for HIST3H2BB Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST3H2BB Gene:

HIST3H2BB

SOURCE GeneReport for Unigene cluster for HIST3H2BB Gene:

Hs.376691
genes like me logo Genes that share expression patterns with HIST3H2BB: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for HIST3H2BB Gene

Orthologs for HIST3H2BB Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST3H2BB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HIST3H2BB 35
  • 100 (a)
OneToOne
LOC469701 34
  • 99.21 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 97 (a)
OneToMany
LOC482202 34
  • 93.65 (n)
mouse
(Mus musculus)
Mammalia Hist3h2ba 35
  • 97 (a)
OneToOne
Hist3h2bb-ps 34 16
  • 91.27 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 96 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 96 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Hist3h2bb 34
  • 91.01 (n)
cow
(Bos Taurus)
Mammalia HIST3H2BB 34 35
  • 84.92 (n)
chicken
(Gallus gallus)
Aves H2B-V 35
  • 92 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 91 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii zgc:194989 35
  • 90 (a)
ManyToMany
wu:fe11b02 35 35 35 35 35 35 35 35
  • 86 (a)
ManyToMany
ano9a 35 35
  • 85 (a)
ManyToMany
zgc:171759 35 35 35 35 35 35 35 35 35 35
  • 85 (a)
ManyToMany
si:dkey-261m9.19 35
  • 84 (a)
ManyToMany
si:dkey-261m9.6 35
  • 84 (a)
ManyToMany
zgc:112234 35 35 35 35 35
  • 84 (a)
ManyToMany
zgc:173587 35
  • 84 (a)
ManyToMany
CABZ01086354.1 35
  • 83 (a)
ManyToMany
Species where no ortholog for HIST3H2BB was found in the sources mined by GeneCards:
  • 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)
  • 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 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 HIST3H2BB Gene

ENSEMBL:
Gene Tree for HIST3H2BB (if available)
TreeFam:
Gene Tree for HIST3H2BB (if available)

Paralogs for HIST3H2BB Gene

Pseudogenes.org Pseudogenes for HIST3H2BB Gene

genes like me logo Genes that share paralogs with HIST3H2BB: view

Variants for HIST3H2BB Gene

Sequence variations from dbSNP and Humsavar for HIST3H2BB Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs10916317 -- 228,457,362(-) CCTAC(C/T)ATCTC downstream-variant-500B, upstream-variant-2KB
rs111618582 -- 228,458,841(+) ATTTC(-/T)TTTTT downstream-variant-500B, upstream-variant-2KB
rs112284883 -- 228,458,672(+) GTGTG(-/TGTG)TGTGT downstream-variant-500B, upstream-variant-2KB
rs113534981 -- 228,458,627(+) CCTAG(C/T)GGTTG downstream-variant-500B, upstream-variant-2KB
rs115202565 -- 228,456,356(+) AAAAC(C/T)GTACA upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST3H2BB 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 HIST3H2BB 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)

Relevant External Links for HIST3H2BB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST3H2BB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST3H2BB Gene

Disorders for HIST3H2BB Gene

Relevant External Links for HIST3H2BB

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST3H2BB

No disorders were found for HIST3H2BB Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST3H2BB Gene

Publications for HIST3H2BB Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
  2. Characterization of histones H2A and H2B variants and their post- translational modifications by mass spectrometry. (PMID: 16319397) Bonenfant D. … van Oostrum J. (Mol. Cell. Proteomics 2006) 3 4 64
  3. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck H.C. … Jensen O.N. (Mol. Cell. Proteomics 2006) 3 4 64
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  5. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. (PMID: 16713563) Pavri R. … Reinberg D. (Cell 2006) 3 4 64

Products for HIST3H2BB Gene

Sources for HIST3H2BB Gene

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