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HIST2H2BD Gene(Pseudogene)

Histone Cluster 2 H2B Family Member D (Pseudogene)

GCID:
GC01P149850
GIFtS:
21
Genes Participants
UDN Logo

Aliases for HIST2H2BD Gene

Subcategory (RNA class) for HIST2H2BD Gene

lncRNA

Aliases for HIST2H2BD Gene

  • Histone Cluster 2 H2B Family Member D (Pseudogene) 2 3 5
  • Histone Cluster 2, H2bd (Pseudogene) 2 3
  • H2B Histone Family, Member O 2 3
  • Histone 2, H2bd 2 3
  • H2B/S 3
  • H2B/O 3
  • H2BFO 3

External Ids for HIST2H2BD Gene

ORGUL Members for HIST2H2BD Gene

Previous HGNC Symbols for HIST2H2BD Gene

  • H2BFO

Previous GeneCards Identifiers for HIST2H2BD Gene

  • GC01U900037
  • GC01P148081
  • GC01P149814
  • GC01M121204
  • GC01P149846
  • GC01P149847
  • GC01P149848
  • GC01P149849

Summaries for HIST2H2BD Gene

Entrez Gene Summary for HIST2H2BD Gene

  • Histones are basic nuclear proteins responsible for 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 found in a histone cluster on chromosome 1. [provided by RefSeq, Oct 2015]

GeneCards Summary for HIST2H2BD Gene

HIST2H2BD (Histone Cluster 2 H2B Family Member D (Pseudogene)) is a Pseudogene, and is affiliated with the lncRNA class. GO annotations related to this gene include protein heterodimerization activity.

UniProtKB/Swiss-Prot for HIST2H2BD 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.

fRNAdb sequence ontologies for HIST2H2BD Gene

  • nc_conserved_region: Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for HIST2H2BD

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for HIST2H2BD Gene

Genomics for HIST2H2BD Gene

Products:

  1. Regulatory Element

Regulatory Elements for HIST2H2BD Gene

Enhancers for HIST2H2BD 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
GH01G149157 2 FANTOM5 Ensembl ENCODE dbSUPER 11.7 -682.7 -682703 7.8 MLX ZFP64 DMAP1 YBX1 YY1 ZNF143 ZNF548 NFYC TBX21 PPARGC1A LOC647481 SF3B4 LOC101927468 HIST2H2BD HIST2H2BC ENSG00000261716 ENSG00000272824 HIST2H2AB SV2A PDE4DIP
GH01G148887 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11.7 -950.2 -950193 10.5 HDGF PKNOX1 FOXA2 WRNIP1 DMAP1 YY1 ZNF143 FOS DEK REST PDE4DIP HIST2H2BD HIST2H2BC ENSG00000261716 GC01M148879 RNU2-38P
GH01G148859 1 ENCODE dbSUPER 19.7 -983.4 -983379 0.2 ZNF777 ZSCAN18 ZBTB21 ZSCAN4 ZEB1 ZBTB48 ZNF169 ZNF350 FOS ZNF362 HIST2H2BD HIST2H2BC LOC647481 LOC101927468 ENSG00000261716 ENSG00000227700 RN7SKP88 GC01M148879
GH01G149941 1.4 ENCODE dbSUPER 12 +43.7 43664 5.9 MLX CREB3L1 AGO1 ZFP64 FEZF1 YY1 ZNF143 ZNF263 SP3 NFYC PRPF3 SV2A SF3B4 UBE2D3P3 ADAMTSL4 VPS45 HIST2H2BD GOLPH3L HIST2H2BC ENSG00000261716
GH01G150695 1.4 FANTOM5 ENCODE 11.7 +853.8 853827 2.5 HDGF PKNOX1 FOXA2 WRNIP1 SIN3A ARID4B DMAP1 ZBTB7B YY1 SLC30A9 HORMAD1 SETDB1 GABPB2 PRPF3 GOLPH3L HIST2H2BD HIST2H2BC ENSG00000261716 SF3B4 GC01P150630
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST2H2BD on UCSC Golden Path with GeneCards custom track

Promoters for HIST2H2BD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000013436 -539 4601 ATF1 FOXA2 CREB3L1 SIN3A ZNF2 ZNF121 ELK1 FOS SP3 YY2

Genomic Location for HIST2H2BD Gene

Chromosome:
1
Start:
149,843,039 bp from pter
End:
149,843,533 bp from pter
Size:
495 bases
Orientation:
Plus strand

Genomic View for HIST2H2BD Gene

Genes around HIST2H2BD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST2H2BD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST2H2BD Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HIST2H2BD Gene

ORGUL Member Location for HIST2H2BD Gene

ORGUL Member Location for HIST2H2BD gene

Proteins for HIST2H2BD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HIST2H2BD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6DRA6-H2B2D_HUMAN
    Recommended name:
    Putative histone H2B type 2-D
    Protein Accession:
    Q6DRA6

    Protein attributes for HIST2H2BD Gene

    Size:
    164 amino acids
    Molecular mass:
    18018 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 HIST2H2BD Gene

Post-translational modifications for HIST2H2BD Gene

  • 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.
  • 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.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HIST2H2BD Gene

Domains & Families for HIST2H2BD Gene

Gene Families for HIST2H2BD Gene

HGNC:

Protein Domains for HIST2H2BD Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HIST2H2BD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6DRA6

UniProtKB/Swiss-Prot:

H2B2D_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with HIST2H2BD: view

Function for HIST2H2BD Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HIST2H2BD 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 HIST2H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST2H2BD: view

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HIST2H2BD Gene

Localization for HIST2H2BD Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST2H2BD Gene

Nucleus. Chromosome.

Gene Ontology (GO) - Cellular Components for HIST2H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IEA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with HIST2H2BD: view

No data available for Subcellular locations from COMPARTMENTS for HIST2H2BD Gene

Pathways & Interactions for HIST2H2BD Gene

SuperPathways for HIST2H2BD Gene

PathCards logo More details on SuperPathways for HIST2H2BD
No Data Available

Interacting Proteins for HIST2H2BD Gene

Selected Interacting proteins: Q6DRA6-H2B2D_HUMAN for HIST2H2BD Gene via IID

Symbol External ID(s) Details
CBX5

Gene Ontology (GO) - Biological Process for HIST2H2BD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA --
genes like me logo Genes that share ontologies with HIST2H2BD: view

No data available for Pathways by source and SIGNOR curated interactions for HIST2H2BD Gene

Drugs & Compounds for HIST2H2BD Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HIST2H2BD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

fRNAdb Secondary structures for HIST2H2BD Gene

  • FR083303

mRNA/cDNA for HIST2H2BD Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST2H2BD Gene

No ASD Table

Relevant External Links for HIST2H2BD Gene

GeneLoc Exon Structure for
HIST2H2BD
ECgene alternative splicing isoforms for
HIST2H2BD

Expression for HIST2H2BD Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST2H2BD Gene

mRNA expression in normal human tissues for HIST2H2BD Gene
mRNA expression by GTEx for HIST2H2BD Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST2H2BD Gene:

HIST2H2BD
genes like me logo Genes that share expression patterns with HIST2H2BD: view

No data available for 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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST2H2BD Gene

Orthologs for HIST2H2BD Gene

Evolution for HIST2H2BD Gene

ENSEMBL:
Gene Tree for HIST2H2BD (if available)
TreeFam:
Gene Tree for HIST2H2BD (if available)

No data available for Orthologs for HIST2H2BD Gene

Paralogs for HIST2H2BD Gene

(20) SIMAP similar genes for HIST2H2BD Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST2H2BD: view

No data available for Paralogs for HIST2H2BD Gene

Variants for HIST2H2BD Gene

Relevant External Links for HIST2H2BD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST2H2BD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations from dbSNP and Humsavar , Structural Variations from Database of Genomic Variants (DGV) and Variation tolerance for HIST2H2BD Gene

Disorders for HIST2H2BD Gene

Relevant External Links for HIST2H2BD

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST2H2BD

No disorders were found for HIST2H2BD Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST2H2BD Gene

Publications for HIST2H2BD Gene

  1. Functional characterization of a human histone gene cluster duplication. (PMID: 15527963) Braastad C.D. … Stein G.S. (Gene 2004) 2 3 4 64
  2. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
  3. Inhibition of core histones acetylation by carcinogenic nickel(II). (PMID: 16283522) Golebiowski F. … Kasprzak K.S. (Mol. Cell. Biochem. 2005) 3 4 64
  4. Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase. (PMID: 12757711) Cheung W.L. … Allis C.D. (Cell 2003) 3 4 64
  5. Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage. (PMID: 25963833) Drissi R. … Boisvert F.M. (Mol. Cell Proteomics 2015) 3 64

Products for HIST2H2BD Gene

Sources for HIST2H2BD Gene

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