H2BC9 Gene (Protein Coding)

H2B Clustered Histone 9

GC06P052356
GIFtS:
30
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 H2BC9 Gene

Aliases for H2BC9 Gene

  • H2B Clustered Histone 9 2 3 5
  • H2B/J 2 3 4
  • Histone Cluster 1 H2B Family Member H 2 3
  • H2B Histone Family, Member J 2 3
  • Histone Cluster 1, H2bh 2 3
  • Histone H2B Type 1-H 3 4
  • Histone 1, H2bh 2 3
  • Histone H2B.J 3 4
  • HIST1H2BH 3 4
  • H2BFJ 3 4
  • H2B-Clustered Histone 9 4
  • H2BC9 5

External Ids for H2BC9 Gene

Previous HGNC Symbols for H2BC9 Gene

  • H2BFJ
  • HIST1H2BH

Previous GeneCards Identifiers for H2BC9 Gene

  • GC06P027671
  • GC06P028386
  • GC06P028901
  • GC06P049184

Summaries for H2BC9 Gene

Entrez Gene Summary for H2BC9 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 large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BC9 Gene

H2BC9 (H2B Clustered Histone 9) is a Protein Coding gene. Diseases associated with H2BC9 include Brachydactyly, Type C and Potocki-Shaffer Syndrome. 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 H2BC9 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 H2BC9 Gene

Additional gene information for H2BC9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC9 Gene

Genomics for H2BC9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for H2BC9 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
GH06J026120 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 1.6 -127.2 -127170 8.7 BCLAF1 SP1 ZNF207 NCOR1 IKZF1 MYC ZNF600 SSRP1 ZNF580 ZNF592 H2AC6 H2BC4 piR-31751 piR-40096 piR-50446 ABT1 BTN2A2 BTN2A1 BTN2A3P HMGN4
GH06J026248 Promoter/Enhancer 2.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.7 +3.7 3698 13 BCLAF1 SP1 ZNF207 NCOR1 IKZF1 ZNF592 POLR2A CEBPA CHD4 YY1 LOC105374986 ABT1 ZNF322 GUSBP2 H2AC9P H4C8 LARP1P1 BTN2A2 H4C3 ENSG00000272462
GH06J026264 Enhancer 0.2 Ensembl 0.4 +13.2 13187 0.8 H4C8 BTN3A2 H3C8 lnc-HIST1H2BH-1 H2BC9
GH06J026266 Enhancer 0.2 FANTOM5 0.4 +15.0 15024 0.2 H3C8 lnc-HIST1H2BH-1 H2BC9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2BC9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BC9

Genomic Locations for H2BC9 Gene

Latest Assembly
chr6:26,251,614-26,253,710
(GRCh38/hg38)
Size:
2,097 bases
Orientation:
Plus strand

Previous Assembly
chr6:26,251,842-26,252,303
(GRCh37/hg19 by Entrez Gene)
Size:
462 bases
Orientation:
Plus strand

Genomic View for H2BC9 Gene

Genes around H2BC9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC9 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for H2BC9 Gene

Proteins for H2BC9 Gene

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  • Protein details for H2BC9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q93079-H2B1H_HUMAN
    Recommended name:
    Histone H2B type 1-H
    Protein Accession:
    Q93079
    Secondary Accessions:
    • B2R541
    • Q4VB74

    Protein attributes for H2BC9 Gene

    Size:
    126 amino acids
    Molecular mass:
    13892 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 (Probable). The octamer wraps approximately 147 bp of DNA (Probable). Found in a complex with PPAR9; DTX3L AND STAT1; the interaction is likely to induce DTX3L-mediated ubiquitination of H2BC9/H2BJ (PubMed:26479788).

neXtProt entry for H2BC9 Gene

Post-translational modifications for H2BC9 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 (PubMed:16627869). Monoubiquitinated by DTX3L upon encephalomyocarditis virus (EMCV)-mediated infection (PubMed:26479788).
  • 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 H2BC9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BC9 Gene

Domains & Families for H2BC9 Gene

Gene Families for H2BC9 Gene

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

Protein Domains for H2BC9 Gene

InterPro:

Suggested Antigen Peptide Sequences for H2BC9 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2B.j (H2B1H_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q93079

UniProtKB/Swiss-Prot:

H2B1H_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BC9: view

Function for H2BC9 Gene

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Molecular function for H2BC9 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 H2BC9 Gene

Gene Ontology (GO) - Molecular Function for H2BC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,NAS 9119399
GO:0005515 protein binding IPI 26479788
GO:0019899 enzyme binding IPI 26479788
GO:0044389 ubiquitin-like protein ligase binding IPI 26479788
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with H2BC9: view
genes like me logo Genes that share phenotypes with H2BC9: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BC9 Gene

Localization for H2BC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC9 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 H2BC9 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4
plasma membrane 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for H2BC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome NAS 9119399
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 H2BC9: view

Pathways & Interactions for H2BC9 Gene

PathCards logo

SuperPathways for H2BC9 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 H2BC9: view

Gene Ontology (GO) - Biological Process for H2BC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA,NAS 9119399
GO:0016567 protein ubiquitination TAS --
genes like me logo Genes that share ontologies with H2BC9: view

No data available for SIGNOR curated interactions for H2BC9 Gene

Drugs & Compounds for H2BC9 Gene

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No Compound Related Data Available

Transcripts for H2BC9 Gene

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mRNA/cDNA for H2BC9 Gene

1 REFSEQ mRNAs :
5 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 H2BC9

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC9 Gene

No ASD Table

Relevant External Links for H2BC9 Gene

GeneLoc Exon Structure for
H2BC9

Expression for H2BC9 Gene

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  1. Primer products for research

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BC9

SOURCE GeneReport for Unigene cluster for H2BC9 Gene:

Hs.247815

Evidence on tissue expression from TISSUES for H2BC9 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with H2BC9: view

Primer products for research

No data available for mRNA expression in normal human tissues , 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 H2BC9 Gene

Orthologs for H2BC9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for H2BC9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LOC463172 29
  • 98.94 (n)
Mouse
(Mus musculus)
 Mammalia Hist1h2bq 29
  • 91.2 (n)
H2bc23 16
H2bc24 16
Dog
(Canis familiaris)
 Mammalia LOC483164 29
  • 90.21 (n)
Rat
(Rattus norvegicus)
 Mammalia LOC100359692 29
  • 89.15 (n)
Cow
(Bos Taurus)
 Mammalia HIST2H2BF 29
  • 84.8 (n)
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AGR183C 29
  • 69.97 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes HTB2 29
  • 64.43 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F13310g 29
  • 61.43 (n)
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT3G53650 29
  • 65.83 (n)
Rice
(Oryza sativa)
 Liliopsida Os01g0153100 29
  • 74.84 (n)
Bread mold
(Neurospora crassa)
 Ascomycetes NCU02435 29
  • 69.42 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes htb1 29
  • 65.84 (n)
Species where no ortholog for H2BC9 was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for H2BC9 Gene

ENSEMBL:
Gene Tree for H2BC9 (if available)
TreeFam:
Gene Tree for H2BC9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC9: view image
Alliance of Genome Resources:
Additional Orthologs for H2BC9

Paralogs for H2BC9 Gene

Paralogs for H2BC9 Gene

genes like me logo Genes that share paralogs with H2BC9: view

Variants for H2BC9 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2BC9 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 H2BC9 Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914
nsv601173 CNV loss 21841781
nsv981112 CNV duplication 23825009

Variation tolerance for H2BC9 Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.30; 6.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BC9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC9
Leiden Open Variation Database (LOVD)
H2BC9

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 H2BC9 Gene

Disorders for H2BC9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for H2BC9 Gene - From: COP

Disorder Aliases PubMed IDs
brachydactyly, type c
  • bdc
potocki-shaffer syndrome
  • pss
- elite association - COSMIC cancer census association via MalaCards
Search H2BC9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H2BC9

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with H2BC9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H2BC9 Gene

Publications for H2BC9 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W … Doenecke D (Genomics 1997) 2 3 4
  3. PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection. (PMID: 26479788) Zhang Y … Holtzman MJ (Nature immunology 2015) 3 4
  4. Gene-specific characterization of human histone H2B by electron capture dissociation. (PMID: 16457587) Siuti N … Pesavento JJ (Journal of proteome research 2006) 3 4
  5. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck HC … Jensen ON (Molecular & cellular proteomics : MCP 2006) 3 4

ExternalLinks

View latest publications for H2BC9 gene in Mastermind

Products for H2BC9 Gene

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