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 H2BC12 Gene

Aliases for H2BC12 Gene

  • H2B Clustered Histone 12 2 3 5
  • Histone Cluster 1 H2B Family Member K 2 3
  • H2B Histone Family, Member T 2 3
  • HIRA-Interacting Protein 1 3 4
  • Histone Cluster 1, H2bk 2 3
  • Histone H2B Type 1-K 3 4
  • Histone 1, H2bk 2 3
  • HIST1H2BK 3 4
  • H2BFAiii 2 3
  • H2BFT 3 4
  • H2B K 3 4
  • Histone Family Member 3
  • H2BC12 5
  • HIRIP1 4
  • H2B/S 3
  • H2BK 3

External Ids for H2BC12 Gene

Previous HGNC Symbols for H2BC12 Gene

  • H2BFT
  • HIST1H2BK

Previous GeneCards Identifiers for H2BC12 Gene

  • GC06M027139
  • GC06M027150

Summaries for H2BC12 Gene

Entrez Gene Summary for H2BC12 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 encodes a replication-dependent histone that is a member of the histone H2B family. The protein encoded is an antimicrobial protein with antibacterial and antifungal activity. Two transcripts that encode the same protein have been identified for this gene, which is found in the histone microcluster on chromosome 6p21.33. [provided by RefSeq, Aug 2015]

GeneCards Summary for H2BC12 Gene

H2BC12 (H2B Clustered Histone 12) is a Protein Coding gene. Among its related pathways are Chromatin organization and Signaling by GPCR. An important paralog of this gene is H2BC7.

UniProtKB/Swiss-Prot Summary for H2BC12 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 H2BC12 Gene

Additional gene information for H2BC12 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H2BC12 Gene

Genomics for H2BC12 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for H2BC12 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
GH06J027176 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas 13.1 -30.7 -30738 3.1 ZNF221 RNF2 HNRNPL CREB1 CTCF PRDM10 ZNF629 ZNF512 IKZF1 NFKBIZ TRI-AAT5-2 piR-36037-008 piR-33415-004 BTN3A2 ZKSCAN8 BTN2A2 ABT1 BTN2A1 ZNF204P HMGN4
GH06J027114 Enhancer 0.9 ENCODE 10.7 +31.8 31778 0.9 LEF1 JUND PKNOX1 REST NR2C1 BRD9 ZNF24 DPF2 SOX6 ZNF184 Z46261-002 H2BC12 ABT1 ENSG00000272468 lnc-HIST1H2BJ-5 H2BC11 lnc-HIST1H2AG-4 ZNF322
GH06J027120 Enhancer 0.6 Ensembl 11.5 +25.8 25758 1 JUND POLR2A FOSL1 MAFG IRF2 JUNB TFDP1 ZNF592 BATF SUPT5H ENSG00000261584 H2BC12 H3C12 ZNF391 ENSG00000272468 Z46261-002 lnc-HIST1H2BJ-5 H2BC11 lnc-HIST1H2AG-4 ZNF322
GH06J027785 Enhancer 0.6 Ensembl 10.1 -638.9 -638942 0.8 ZNF300 SOX6 HMBOX1 ZBTB48 NCOR1 FOSL1 TAL1 NR2F6 HDAC2 CEBPB piR-41944 ZSCAN12 ZKSCAN8 GUSBP2 ZSCAN9 H2BC13 ZKSCAN3 H3C12 H2BC12 POM121L2
GH06J027851 Enhancer 0.3 Ensembl 8.9 -704.5 -704543 0.4 ZBTB12 ZNF603P H4C11 H3C12 H2BC13 H2BC12 lnc-HIST1H2AL-1 H2AC15 H2AC16 H2BC15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H2BC12 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H2BC12

Genomic Locations for H2BC12 Gene

Genomic Locations for H2BC12 Gene
chr6:27,138,293-27,146,858
(GRCh38/hg38)
Size:
8,566 bases
Orientation:
Minus strand
chr6:27,106,072-27,114,637
(GRCh37/hg19)
Size:
8,566 bases
Orientation:
Minus strand

Genomic View for H2BC12 Gene

Genes around H2BC12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H2BC12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H2BC12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H2BC12 Gene

Proteins for H2BC12 Gene

  • Protein details for H2BC12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60814-H2B1K_HUMAN
    Recommended name:
    Histone H2B type 1-K
    Protein Accession:
    O60814
    Secondary Accessions:
    • A8K7P7
    • Q2VPI7

    Protein attributes for H2BC12 Gene

    Size:
    126 amino acids
    Molecular mass:
    13890 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 H2BC12 Gene

neXtProt entry for H2BC12 Gene

Post-translational modifications for H2BC12 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 H2BC12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H2BC12 Gene

Domains & Families for H2BC12 Gene

Gene Families for H2BC12 Gene

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

Protein Domains for H2BC12 Gene

Suggested Antigen Peptide Sequences for H2BC12 Gene

GenScript: Design optimal peptide antigens:
  • HIRA-interacting protein 1 (H2B1K_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O60814

UniProtKB/Swiss-Prot:

H2B1K_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with H2BC12: view

Function for H2BC12 Gene

Molecular function for H2BC12 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 H2BC12 Gene

Gene Ontology (GO) - Molecular Function for H2BC12 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 H2BC12: view
genes like me logo Genes that share phenotypes with H2BC12: view

Animal Model Products

CRISPR Products

miRNA for H2BC12 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC12

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H2BC12 Gene

Localization for H2BC12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H2BC12 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 H2BC12 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for H2BC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005615 extracellular space IDA 12860195
GO:0005634 nucleus IEA,IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with H2BC12: view

Pathways & Interactions for H2BC12 Gene

PathCards logo

SuperPathways for H2BC12 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 H2BC12: view

Gene Ontology (GO) - Biological Process for H2BC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002227 innate immune response in mucosa IDA 12860195
GO:0006334 nucleosome assembly IBA 21873635
GO:0016567 protein ubiquitination TAS --
GO:0019731 antibacterial humoral response IDA 12860195
GO:0031640 killing of cells of other organism IDA 15019208
genes like me logo Genes that share ontologies with H2BC12: view

No data available for SIGNOR curated interactions for H2BC12 Gene

Drugs & Compounds for H2BC12 Gene

No Compound Related Data Available

Transcripts for H2BC12 Gene

mRNA/cDNA for H2BC12 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H2BC12

Alternative Splicing Database (ASD) splice patterns (SP) for H2BC12 Gene

No ASD Table

Relevant External Links for H2BC12 Gene

GeneLoc Exon Structure for
H2BC12

Expression for H2BC12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H2BC12

SOURCE GeneReport for Unigene cluster for H2BC12 Gene:

Hs.437275

Evidence on tissue expression from TISSUES for H2BC12 Gene

  • Stomach(4.3)
  • Pancreas(4.2)
  • Nervous system(2.6)
  • Intestine(2.4)
  • Blood(2.2)
  • Liver(2)
genes like me logo Genes that share expression patterns with H2BC12: view

Primer Products

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 H2BC12 Gene

Orthologs for H2BC12 Gene

This gene was present in the common ancestor of mammals.

Orthologs for H2BC12 Gene

Organism Taxonomy Gene Similarity Type Details
Dog
(Canis familiaris)
Mammalia HIST1H2BK 31
  • 100 (a)
OneToOne
LOC488303 30
  • 92.86 (n)
Cow
(Bos Taurus)
Mammalia HIST1H2BK 31
  • 100 (a)
OneToOne
HIST1H2BM 30
  • 90.74 (n)
Chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BK 30 31
  • 99.47 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hist1h2bk 30 31
  • 92.06 (n)
OneToOne
H2bc12 17
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 91 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Hist1h2bk 30
  • 90.74 (n)
Species where no ortholog for H2BC12 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 H2BC12 Gene

ENSEMBL:
Gene Tree for H2BC12 (if available)
TreeFam:
Gene Tree for H2BC12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H2BC12: view image

Paralogs for H2BC12 Gene

genes like me logo Genes that share paralogs with H2BC12: view

Variants for H2BC12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H2BC12 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
780599 Benign: not provided 27,139,614(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for H2BC12 Gene

Structural Variations from Database of Genomic Variants (DGV) for H2BC12 Gene

Variant ID Type Subtype PubMed ID
nsv1029124 CNV loss 25217958
nsv970091 CNV duplication 23825009

Variation tolerance for H2BC12 Gene

Residual Variation Intolerance Score: 51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H2BC12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H2BC12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H2BC12 Gene

Disorders for H2BC12 Gene

No disorders were found for H2BC12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H2BC12 Gene

Publications for H2BC12 Gene

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

Products for H2BC12 Gene

  • Signalway Proteins for H2BC12

Sources for H2BC12 Gene