Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an 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 histon... See more...

Aliases for H2BC18 Gene

Aliases for H2BC18 Gene

  • H2B Clustered Histone 18 2 3 5
  • Histone Cluster 2 H2B Family Member F 2 3
  • Histone Cluster 2, H2bf 2 3
  • Histone H2B Type 2-F 3 4
  • HIST2H2BF 3 4
  • H2B-Clustered Histone 18 4
  • Histone 2, H2bf 2
  • H2BC18 5

External Ids for H2BC18 Gene

Previous HGNC Symbols for H2BC18 Gene

  • HIST2H2BF

Previous GeneCards Identifiers for H2BC18 Gene

  • GC01M149871
  • GC01M149943
  • GC01M149955
  • GC01M149981

Summaries for H2BC18 Gene

Entrez Gene Summary for H2BC18 Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an 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 encodes a replication-dependent histone that is a member of the histone H2B family and is found in a histone cluster on chromosome 1. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BC18 Gene

H2BC18 (H2B Clustered Histone 18) is a Protein Coding gene. Diseases associated with H2BC18 include Fetal Akinesia Deformation Sequence 1. Among its related pathways are Chromatin organization and Deubiquitination. An important paralog of this gene is H2BC9.

UniProtKB/Swiss-Prot Summary for H2BC18 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 H2BC18 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC18 Gene

Genomics for H2BC18 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2BC18 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
GH01J149883 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.2 -74.3 -74328 6.2 BCLAF1 SP1 ZNF207 NCOR1 IKZF1 MYC ZNF600 ZNF580 ZNF592 ATF2 H2AC21 BOLA1 H2AC20 H2BC21 piR-45268-003 H2BC18 PRPF3 SF3B4 UBE2D3P3 H2BC19P
GH01J149810 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 0.0 -27 5.2 SP1 ZNF600 ZSCAN16 POLR2A SMAD5 ZNF639 IRF3 ZEB1 MNT ZNF217 HSALNG0006972 H2BC18 H3C13 piR-30912-003 lnc-HIST2H3D-2 PRPF3 SF3B4 H2BC19P SV2A H2BC20P
GH01J149792 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 0.4 +19.1 19140 2.3 ZIC2 NONO CTCF REST ZNF592 ELF1 CTBP1 CUX1 SMC3 DDX20 ENSG00000233030 HSALNG0006970 HSALNG0006971 lnc-FCGR1A-1 SV2A FCGR1A H2BC18 lnc-HIST2H3D-2
GH01J149787 Promoter/Enhancer 0.7 Ensembl ENCODE 0.4 +24.4 24372 0.8 IKZF1 KDM1A CBFA2T3 HSALNG0006968 FCGR1A ENSG00000233030 lnc-PPIAL4F-2-003 H2BC18 lnc-HIST2H3D-2
GH01J149782 Promoter 0.7 EPDnew Ensembl 0.3 +29.1 29072 1.8 FCGR1A HSALNG0006966 lnc-PPIAL4F-2-003 HSALNG0006968 H2BC18 lnc-HIST2H3D-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2BC18 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BC18

Genomic Locations for H2BC18 Gene

Latest Assembly
chr1:149,782,689-149,812,373
(GRCh38/hg38)
Size:
29,685 bases
Orientation:
Minus strand

Previous Assembly
chr1:149,754,245-149,783,925
(GRCh37/hg19 by Entrez Gene)
Size:
29,681 bases
Orientation:
Minus strand

chr1:149,754,245-149,783,928
(GRCh37/hg19 by Ensembl)
Size:
29,684 bases
Orientation:
Minus strand

Genomic View for H2BC18 Gene

Genes around H2BC18 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC18 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC18 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2BC18 Gene

Proteins for H2BC18 Gene

  • Protein details for H2BC18 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5QNW6-H2B2F_HUMAN
    Recommended name:
    Histone H2B type 2-F
    Protein Accession:
    Q5QNW6
    Secondary Accessions:
    • A8K0U9
    • B4DLA9

    Protein attributes for H2BC18 Gene

    Size:
    126 amino acids
    Molecular mass:
    13920 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 H2BC18 Gene

    Alternative splice isoforms for H2BC18 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for H2BC18 Gene

Post-translational modifications for H2BC18 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 H2BC18 Gene

No data available for DME Specific Peptides for H2BC18 Gene

Domains & Families for H2BC18 Gene

Gene Families for H2BC18 Gene

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

Protein Domains for H2BC18 Gene

Suggested Antigen Peptide Sequences for H2BC18 Gene

GenScript: Design optimal peptide antigens:
  • Histone H2B (B4DLA9_HUMAN)
  • Histone H2B (B4DR52_HUMAN)
  • Histone H2B type 2-F (H2B2F_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5QNW6

UniProtKB/Swiss-Prot:

H2B2F_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BC18: view

Function for H2BC18 Gene

Molecular function for H2BC18 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 H2BC18 Gene

Gene Ontology (GO) - Molecular Function for H2BC18 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 H2BC18: view
genes like me logo Genes that share phenotypes with H2BC18: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC18

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BC18 Gene

Localization for H2BC18 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC18 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 H2BC18 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for H2BC18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IEA,HDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with H2BC18: view

Pathways & Interactions for H2BC18 Gene

genes like me logo Genes that share pathways with H2BC18: view

Gene Ontology (GO) - Biological Process for H2BC18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA 21873635
genes like me logo Genes that share ontologies with H2BC18: view

No data available for SIGNOR curated interactions for H2BC18 Gene

Drugs & Compounds for H2BC18 Gene

No Compound Related Data Available

Transcripts for H2BC18 Gene

mRNA/cDNA for H2BC18 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 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 H2BC18

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC18 Gene

No ASD Table

Relevant External Links for H2BC18 Gene

GeneLoc Exon Structure for
H2BC18

Expression for H2BC18 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BC18

SOURCE GeneReport for Unigene cluster for H2BC18 Gene:

Hs.632451

Evidence on tissue expression from TISSUES for H2BC18 Gene

  • Nervous system(4.3)
  • Pancreas(4.2)
  • Heart(2.2)
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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for H2BC18 Gene

Orthologs for H2BC18 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2BC18 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LOC457260 29
  • 99.75 (n)
HIST2H2BF 30
  • 75 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 99 (a)
OneToMany
-- 30
  • 93 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia H2B 30
  • 99 (a)
ManyToMany
LOC505183 29
  • 89.68 (n)
Dog
(Canis familiaris)
Mammalia HIST2H2BF 30
  • 92 (a)
OneToOne
LOC608682 29
  • 89.22 (n)
Rat
(Rattus norvegicus)
Mammalia LOC100912338 29
  • 88.36 (n)
Mouse
(Mus musculus)
Mammalia Hist2h2bb 29 30
  • 88.36 (n)
OneToOne
H2bc18 16
Species where no ortholog for H2BC18 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)
  • 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)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for H2BC18 Gene

ENSEMBL:
Gene Tree for H2BC18 (if available)
TreeFam:
Gene Tree for H2BC18 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC18: view image
Alliance of Genome Resources:
Additional Orthologs for H2BC18

Paralogs for H2BC18 Gene

Pseudogenes.org Pseudogenes for H2BC18 Gene

genes like me logo Genes that share paralogs with H2BC18: view

Variants for H2BC18 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H2BC18 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs141598661 Likely Benign: not provided 149,782,764(-) G/A
NM_000566.3(FCGR1A):c.21G>A (p.Leu7=)
SYNONYMOUS_VARIANT,THREE_PRIME_UTR
rs587645491 Benign: not provided 149,791,461(-) AAAG/A
NM_001161334.1(H2BC18):c.378-8204_378-8202del
INFRAME_DELETION,INTRON
rs637882 Uncertain Significance: Peritoneal Gliomatosis 149,790,230(-) C/T
NM_000566.3(FCGR1A):c.736C>T (p.Gln246Ter)
NONSENSE,INTRON
rs74315310 Pathogenic: IGG receptor I, phagocytic, familial deficiency of 149,784,224(-) C/T
NM_001161334.1(H2BC18):c.378-964G>A
NONSENSE,INTRON
rs80039899 Likely Benign: not provided 149,784,064(-) C/T
NM_000566.3(FCGR1A):c.114C>T (p.Thr38=)
SYNONYMOUS_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H2BC18 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 H2BC18 Gene

Variant ID Type Subtype PubMed ID
dgv73n67 CNV gain 20364138
esv1007634 OTHER inversion 20482838
esv3587495 CNV loss 21293372
nsv469694 CNV loss 16826518
nsv7182 OTHER inversion 18451855
nsv824564 CNV gain 20364138
nsv831503 CNV gain 17160897
nsv831525 CNV gain 17160897
nsv946376 CNV duplication 23825009
nsv946377 CNV duplication 23825009
nsv952796 CNV duplication 24416366
nsv952802 CNV duplication 24416366

Variation tolerance for H2BC18 Gene

Residual Variation Intolerance Score: 68.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.01; 20.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BC18 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC18
Leiden Open Variation Database (LOVD)
H2BC18

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H2BC18 Gene

Disorders for H2BC18 Gene

MalaCards: The human disease database

(1) MalaCards diseases for H2BC18 Gene - From: COP

Disorder Aliases PubMed IDs
fetal akinesia deformation sequence 1
  • fads1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for H2BC18

genes like me logo Genes that share disorders with H2BC18: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H2BC18 Gene

Publications for H2BC18 Gene

  1. 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
  2. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. (PMID: 16713563) Pavri R … Reinberg D (Cell 2006) 3 4
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 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 H2BC18 Gene

Sources for H2BC18 Gene