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Aliases for HIST1H2BD Gene

Aliases for HIST1H2BD Gene

  • Histone Cluster 1 H2B Family Member D 2 3 5
  • H2B Histone Family, Member B 2 3
  • HIRA-Interacting Protein 2 3 4
  • Histone Cluster 1, H2bd 2 3
  • Histone 1, H2bd 2 3
  • Histone H2B.1 B 3 4
  • Histone H2B.B 3 4
  • HIRIP2 3 4
  • H2BFB 3 4
  • H2B/B 3 4
  • Histone H2B Type 1-D 3
  • DJ221C16.6 3
  • H2B.1B 3

External Ids for HIST1H2BD Gene

Previous HGNC Symbols for HIST1H2BD Gene

  • H2BFB

Previous GeneCards Identifiers for HIST1H2BD Gene

  • GC06P026217
  • GC06P026266
  • GC06P026158
  • GC06P026102
  • GC06P026172
  • GC06P026177
  • GC06P026189
  • GC06P026370
  • GC06P026462

Summaries for HIST1H2BD Gene

Entrez Gene Summary for HIST1H2BD 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. Two transcripts that encode the same protein have been identified for this gene, which is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST1H2BD Gene

HIST1H2BD (Histone Cluster 1 H2B Family Member D) is a Protein Coding gene. Among its related pathways are DNA Double-Strand Break Repair 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 HIST1H2BE.

UniProtKB/Swiss-Prot for HIST1H2BD 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 HIST1H2BD Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H2BD Gene

Genomics for HIST1H2BD Gene

Regulatory Elements for HIST1H2BD Gene

Enhancers for HIST1H2BD 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
GH06G026294 1.6 Ensembl ENCODE dbSUPER 10.2 +138.6 138582 3.2 HDGF HNRNPUL1 FOXA2 PKNOX1 CREB3L1 MLX ARNT ARID4B SIN3A DMAP1 HMGN4 HIST1H3E HIST1H3G HIST1H2APS4 HIST1H2BH HIST1H2BD HIST1H1E HIST1H2BE HIST1H4G LARP1P1
GH06G026193 1.5 ENCODE dbSUPER 10.8 +42.9 42949 14.6 CREB3L1 MLX AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ABT1 BTN3A2 HIST1H3E HMGN4 HIST1H2AE HIST1H2BE LARP1P1 HIST1H2APS3 HIST1H1E HIST1H2BD
GH06G026065 1.5 Ensembl ENCODE dbSUPER 10.6 -91.8 -91767 1.1 HDGF HNRNPUL1 PKNOX1 ATF1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 ENSG00000272462 HIST1H4C HIST1H1E HIST1H2BD HIST1H1C GC06P026086
GH06G026170 1.4 ENCODE dbSUPER 9.6 +14.1 14139 5.3 HDGF PKNOX1 CREB3L1 ARNT AGO1 SIN3A YBX1 ZNF2 YY1 ZNF207 BTN3A2 TRIM38 HIST1H2BD ENSG00000272462 HIST1H2AE HIST1H3E LOC102724851 HIST1H2BE GC06P026894
GH06G026154 1.4 ENCODE dbSUPER 8.7 +0.0 23 5.8 CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC ABT1 HMGN4 BTN3A2 ZNF322 HIST1H3E HIST1H2BD ENSG00000272462 BTN3A1 GC06P026889
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST1H2BD on UCSC Golden Path with GeneCards custom track

Promoters for HIST1H2BD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000194991 -43 4401 CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC

Genomic Location for HIST1H2BD Gene

Chromosome:
6
Start:
26,157,843 bp from pter
End:
26,171,349 bp from pter
Size:
13,507 bases
Orientation:
Plus strand

Genomic View for HIST1H2BD Gene

Genes around HIST1H2BD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H2BD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H2BD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H2BD Gene

Proteins for HIST1H2BD Gene

  • Protein details for HIST1H2BD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P58876-H2B1D_HUMAN
    Recommended name:
    Histone H2B type 1-D
    Protein Accession:
    P58876

    Protein attributes for HIST1H2BD Gene

    Size:
    126 amino acids
    Molecular mass:
    13936 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.
    Miscellaneous:
    • The mouse orthologous protein seems not to exist.

neXtProt entry for HIST1H2BD Gene

Post-translational modifications for HIST1H2BD Gene

  • ADP-ribosylated on Ser-7 in response to DNA damage.
  • 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 isoforms=6 and posLast=121121
  • Glycosylation at posLast=113113
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H2BD Gene

No data available for DME Specific Peptides for HIST1H2BD Gene

Domains & Families for HIST1H2BD Gene

Gene Families for HIST1H2BD Gene

Protein Domains for HIST1H2BD Gene

Suggested Antigen Peptide Sequences for HIST1H2BD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P58876

UniProtKB/Swiss-Prot:

H2B1D_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with HIST1H2BD: view

Function for HIST1H2BD Gene

Molecular function for HIST1H2BD 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 HIST1H2BD 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 HIST1H2BD: view
genes like me logo Genes that share phenotypes with HIST1H2BD: view

Animal Model Products

CRISPR Products

miRNA for HIST1H2BD Gene

miRTarBase miRNAs that target HIST1H2BD

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H2BD Gene

Localization for HIST1H2BD Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H2BD 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 HIST1H2BD gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for HIST1H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with HIST1H2BD: view

Pathways & Interactions for HIST1H2BD Gene

SuperPathways for HIST1H2BD 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 HIST1H2BD: view

Gene Ontology (GO) - Biological Process for HIST1H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA --
GO:0016567 protein ubiquitination TAS --
genes like me logo Genes that share ontologies with HIST1H2BD: view

No data available for SIGNOR curated interactions for HIST1H2BD Gene

Drugs & Compounds for HIST1H2BD Gene

No Compound Related Data Available

Transcripts for HIST1H2BD Gene

mRNA/cDNA for HIST1H2BD Gene

Unigene Clusters for HIST1H2BD Gene

Histone cluster 1, H2bd:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H2BD Gene

No ASD Table

Relevant External Links for HIST1H2BD Gene

GeneLoc Exon Structure for
HIST1H2BD
ECgene alternative splicing isoforms for
HIST1H2BD

Expression for HIST1H2BD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST1H2BD Gene

mRNA differential expression in normal tissues according to GTEx for HIST1H2BD Gene

This gene is overexpressed in Whole Blood (x4.3).

Protein differential expression in normal tissues from HIPED for HIST1H2BD Gene

This gene is overexpressed in Saliva (57.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HIST1H2BD Gene



Protein tissue co-expression partners for HIST1H2BD Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HIST1H2BD Gene:

HIST1H2BD

SOURCE GeneReport for Unigene cluster for HIST1H2BD Gene:

Hs.591797

Evidence on tissue expression from TISSUES for HIST1H2BD Gene

  • Blood(4.3)
  • Spleen(2.7)
  • Intestine(2.3)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with HIST1H2BD: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H2BD Gene

Orthologs for HIST1H2BD Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST1H2BD Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HIST1H2BI 35
  • 100 (a)
OneToOne
HIST1H2BD 34
  • 90.74 (n)
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BD 35
  • 100 (a)
OneToOne
LOC462491 34
  • 99.74 (n)
mouse
(Mus musculus)
Mammalia Hist1h2bm 35
  • 100 (a)
OneToOne
Hist3h2ba 16 34
  • 86.51 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 92 (a)
OneToMany
dog
(Canis familiaris)
Mammalia LOC611089 34
  • 91.53 (n)
-- 35
  • 71 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Hist3h2ba 34
  • 86.51 (n)
zebrafish
(Danio rerio)
Actinopterygii wufe11b02 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5545 34
Species where no ortholog for HIST1H2BD 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)
  • 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)
  • 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 HIST1H2BD Gene

ENSEMBL:
Gene Tree for HIST1H2BD (if available)
TreeFam:
Gene Tree for HIST1H2BD (if available)

Paralogs for HIST1H2BD Gene

Variants for HIST1H2BD Gene

Sequence variations from dbSNP and Humsavar for HIST1H2BD Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000015128 -- 26,157,852(+) AAAAA(A/G)GTCGG upstream-variant-2KB
rs1000066168 -- 26,158,087(+) AATAC(A/C/T)GCATC upstream-variant-2KB, utr-variant-5-prime
rs1000279080 -- 26,163,531(+) TTGAC(C/T)GTAGC intron-variant
rs1000406825 -- 26,164,790(+) GGCTC(-/T)TGGTG intron-variant
rs1000412746 -- 26,169,308(+) TATGG(C/T)GGTCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H2BD Gene

Variant ID Type Subtype PubMed ID
dgv375n21 CNV loss 19592680
dgv5926n100 CNV gain 25217958
esv3608394 CNV loss 21293372
esv3608395 CNV gain 21293372
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914
nsv970083 CNV duplication 23825009

Variation tolerance for HIST1H2BD Gene

Residual Variation Intolerance Score: 30.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.66; 31.76% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST1H2BD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H2BD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H2BD Gene

Disorders for HIST1H2BD Gene

Relevant External Links for HIST1H2BD

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H2BD

No disorders were found for HIST1H2BD Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H2BD Gene

Publications for HIST1H2BD 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. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 2 3 4 64
  3. 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
  4. 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
  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 HIST1H2BD Gene

Sources for HIST1H2BD Gene

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