Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and ... See more...

Aliases for H2BC11 Gene

Aliases for H2BC11 Gene

  • H2B Clustered Histone 11 2 3
  • Histone Cluster 1 H2B Family Member J 2 3 5
  • H2B Histone Family, Member R 2 3
  • Histone Cluster 1, H2bj 2 3
  • Histone H2B Type 1-J 3 4
  • Histone 1, H2bj 2 3
  • Histone H2B.1 3 4
  • Histone H2B.R 3 4
  • HIST1H2BJ 3 5
  • H2BFR 3 4
  • H2B/R 3 4
  • H2BJ 3

External Ids for H2BC11 Gene

Previous HGNC Symbols for H2BC11 Gene

  • H2BFR
  • HIST1H2BJ

Summaries for H2BC11 Gene

Entrez Gene Summary for H2BC11 Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the histone microcluster on chromosome 6p21.33. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BC11 Gene

H2BC11 (H2B Clustered Histone 11) 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 H2BC12.

UniProtKB/Swiss-Prot Summary for H2BC11 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.
  • Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

Gene Wiki entry for H2BC11 Gene

Additional gene information for H2BC11 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC11 Gene

Genomics for H2BC11 Gene

GeneHancer (GH) Regulatory Elements for H2BC11 Gene

Promoters and enhancers for H2BC11 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J027126 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.4 -5.2 -5226 23 PPP1R10 FOXK2 E2F8 ZNF785 SP1 ZBTB40 CTCF SREBF1 ZBTB6 LCORL H4C9 H2BC11 ZKSCAN8 ABT1 BTN2A3P HMGN4 ZNF322 ZNF391 BTN2A1 BTN2A2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2BC11 on UCSC Golden Path with GeneCards custom track

Genomic Locations for H2BC11 Gene

Genomic Locations for H2BC11 Gene
chr6:27,125,897-27,132,796
(GRCh38/hg38)
Size:
6,900 bases
Orientation:
Minus strand
chr6:27,093,676-27,100,575
(GRCh37/hg19)
Size:
6,900 bases
Orientation:
Minus strand

Genomic View for H2BC11 Gene

Genes around H2BC11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2BC11 Gene

Proteins for H2BC11 Gene

  • Protein details for H2BC11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P06899-H2B1J_HUMAN
    Recommended name:
    Histone H2B type 1-J
    Protein Accession:
    P06899
    Secondary Accessions:
    • B2R4J4
    • O60816

    Protein attributes for H2BC11 Gene

    Size:
    126 amino acids
    Molecular mass:
    13904 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. Heterodimer HIST1H2BJ and H2AFZ interacts with VPS72 (via N-terminal domain) (PubMed:26974126).

    Three dimensional structures from OCA and Proteopedia for H2BC11 Gene

neXtProt entry for H2BC11 Gene

Post-translational modifications for H2BC11 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 H2BC11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BC11 Gene

Domains & Families for H2BC11 Gene

Gene Families for H2BC11 Gene

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

Protein Domains for H2BC11 Gene

Suggested Antigen Peptide Sequences for H2BC11 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2B.r (H2B1J_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P06899

UniProtKB/Swiss-Prot:

H2B1J_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BC11: view

Function for H2BC11 Gene

Molecular function for H2BC11 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.
UniProtKB/Swiss-Prot Function:
Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

Phenotypes From GWAS Catalog for H2BC11 Gene

Gene Ontology (GO) - Molecular Function for H2BC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001530 lipopolysaccharide binding IDA 11859126
GO:0003677 DNA binding NAS,IBA 6647026
GO:0005515 protein binding IPI 20498094
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2BC11: view
genes like me logo Genes that share phenotypes with H2BC11: view

Animal Models for H2BC11 Gene

MGI Knock Outs for H2BC11:

Animal Model Products

CRISPR Products

miRNA for H2BC11 Gene

miRTarBase miRNAs that target H2BC11

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for H2BC11 Gene

Localization for H2BC11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC11 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 H2BC11 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for H2BC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome NAS 6647026
GO:0005615 extracellular space IDA 11859126
GO:0005634 nucleus IDA,IEA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2BC11: view

Pathways & Interactions for H2BC11 Gene

PathCards logo

SuperPathways for H2BC11 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 H2BC11: view

Gene Ontology (GO) - Biological Process for H2BC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002227 innate immune response in mucosa IDA 12860195
GO:0006334 nucleosome assembly NAS,IBA 6647026
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway IDA 11859126
GO:0016567 protein ubiquitination TAS --
GO:0019731 antibacterial humoral response IDA 12860195
genes like me logo Genes that share ontologies with H2BC11: view

No data available for SIGNOR curated interactions for H2BC11 Gene

Drugs & Compounds for H2BC11 Gene

No Compound Related Data Available

Transcripts for H2BC11 Gene

mRNA/cDNA for H2BC11 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(253) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC11 Gene

No ASD Table

Relevant External Links for H2BC11 Gene

GeneLoc Exon Structure for
H2BC11
ECgene alternative splicing isoforms for
H2BC11

Expression for H2BC11 Gene

NURSA nuclear receptor signaling pathways regulating expression of H2BC11 Gene:

H2BC11

SOURCE GeneReport for Unigene cluster for H2BC11 Gene:

Hs.656567

Evidence on tissue expression from TISSUES for H2BC11 Gene

  • Nervous system(4.2)
No Expression Related Data Available

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 H2BC11 Gene

Orthologs for H2BC11 Gene

This gene was present in the common ancestor of animals.

Orthologs for H2BC11 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia HIST1H2BJ 33
  • 100 (a)
OneToOne
LOC488288 32
  • 92.59 (n)
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BJ 33
  • 100 (a)
OneToOne
HIST1H2BK 32
  • 98.94 (n)
cow
(Bos Taurus)
Mammalia HIST1H2BJ 33
  • 99 (a)
OneToOne
LOC522960 32
  • 91.01 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 99 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 33
  • 99 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hist2h2be 33 32
  • 86.51 (n)
OneToOne
H2bc21 17
rat
(Rattus norvegicus)
Mammalia Hist2h2be 32
  • 85.45 (n)
chicken
(Gallus gallus)
Aves -- 33
  • 82 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 93 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487485 32
  • 85.98 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:112234 33 33 33 33 33
  • 94 (a)
ManyToMany
ano9a 33 33
  • 94 (a)
ManyToMany
wu:fe11b02 33 33 33 33 33 33 33 33
  • 94 (a)
ManyToMany
zgc:194989 33
  • 93 (a)
ManyToMany
zgc:171759 33 33 33 33 33 33 33 33 33 33
  • 93 (a)
ManyToMany
si:dkey-261m9.19 33
  • 86 (a)
ManyToMany
si:dkey-261m9.6 33
  • 86 (a)
ManyToMany
zgc:173587 33
  • 86 (a)
ManyToMany
CABZ01086354.1 33
  • 86 (a)
ManyToMany
African malaria mosquito
(Anopheles gambiae)
Insecta H2B_ANOGA_c 32
  • 76.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta His2B:CG33892 32
  • 76.11 (n)
worm
(Caenorhabditis elegans)
Secernentea his-54 32
  • 69.59 (n)
Species where no ortholog for H2BC11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for H2BC11 Gene

ENSEMBL:
Gene Tree for H2BC11 (if available)
TreeFam:
Gene Tree for H2BC11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC11: view image

Paralogs for H2BC11 Gene

Pseudogenes.org Pseudogenes for H2BC11 Gene

genes like me logo Genes that share paralogs with H2BC11: view

Variants for H2BC11 Gene

Sequence variations from dbSNP and Humsavar for H2BC11 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000107163 -- 27,131,958(-) G/A downstream_transcript_variant
rs1001283944 -- 27,133,597(-) C/T upstream_transcript_variant
rs1001313399 -- 27,133,468(-) T/C upstream_transcript_variant
rs1002289581 -- 27,134,532(-) T/C upstream_transcript_variant
rs1002319247 -- 27,134,237(-) A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for H2BC11 Gene

Variant ID Type Subtype PubMed ID
nsv1029124 CNV loss 25217958
nsv965698 CNV duplication 23825009

Variation tolerance for H2BC11 Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.87; 18.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BC11 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC11

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H2BC11 Gene

Disorders for H2BC11 Gene

Additional Disease Information for H2BC11

No disorders were found for H2BC11 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2BC11 Gene

Publications for H2BC11 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 56
  2. The primary structure and expression of four cloned human histone genes. (PMID: 6647026) Zhong R … Heintz N (Nucleic acids research 1983) 2 3 4 56
  3. Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1. (PMID: 26974126) Latrick CM … Hamiche A (Nature structural & molecular biology 2016) 3 4 56
  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 56
  5. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck HC … Jensen ON (Molecular & cellular proteomics : MCP 2006) 3 4 56

Products for H2BC11 Gene

Sources for H2BC11 Gene