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HIST2H2BD Gene

pseudogene   GIFtS: 19
GCID: GC01P149814

Histone Cluster 2, H2bd (Pseudogene)

(Previous names: histone 2, H2bd, H2B histone family, member O)
(Previous symbol: H2BFO)
  Search for HIST2H2BD
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3.2

Aliases
Histone Cluster 2, H2bd (Pseudogene)1 2
H2BFO1 2
H2B Histone Family, Member O1
Histone 2, H2bd1
H2B/o2
H2B/s2

External Ids:    HGNC: 205171   Entrez Gene: 3378742   Ensembl: ENSG000002203237   UniProtKB: Q6DRA63   
ORGUL members:    fRNAdb10:FR083303      
RNAdb15:EVF18972    

Export aliases for HIST2H2BD gene to outside databases

Previous GC identifers: GC01U900037 GC01P148081 GC01M121204


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HIST2H2BD Gene:
HIST2H2BD (histone cluster 2, H2bd (pseudogene)) is a pseudogene, and is affiliated with the lncRNA class. GO annotations related to this gene include protein heterodimerization activity.

UniProtKB/Swiss-Prot: H2B2D_HUMAN, Q6DRA6
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



fRNAdb sequence ontology for HIST2H2BD:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for HIST2H2BD

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for HIST2H2BD
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HIST2H2BD


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q21.2   Ensembl cytogenetic band:  1q21.2   HGNC cytogenetic band: 1q21.2

HIST2H2BD Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HIST2H2BD gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P149814:  view genomic region     (about GC identifiers)

Start:
149,814,587 bp from pter      End:
149,815,100 bp from pter
Size:
514 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: H2B2D_HUMAN, Q6DRA6 (See protein sequence)
Recommended Name: Putative histone H2B type 2-D  
Size: 164 amino acids; 18018 Da
Subunit: 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
Caution: Could be the product of a pseudogene. In contrast to other H2B histones, it does not contain the
conserved residue in C-terminus that is the target of monoubiquitination

Explore the universe of human proteins at neXtProt for HIST2H2BD: NX_Q6DRA6

Post-translational modifications: 

  • 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 recombination1
  • 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 autosomes1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    HIST: Histones / Replication-dependent

    3 InterPro protein domains:
     IPR009072 Histone-fold
     IPR000558 Histone_H2B
     IPR007125 Histone_core_D

    Graphical View of Domain Structure for InterPro Entry Q6DRA6

    ProtoNet protein and cluster: Q6DRA6

    UniProtKB/Swiss-Prot: H2B2D_HUMAN, Q6DRA6
    Similarity: Belongs to the histone H2B family


    Find genes that share domains with HIST2H2BD           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: H2B2D_HUMAN, Q6DRA6
    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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0046982protein heterodimerization activity IEA--
         
    Find genes that share ontologies with HIST2H2BD           About GenesLikeMe


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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    H2B2D_HUMAN, Q6DRA6: Nucleus. Chromosome

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000786nucleosome IEA--
    GO:0005634nucleus IEA--

    Find genes that share ontologies with HIST2H2BD           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HIST2H2BD
    Interactions:

        Search GeneGlobe Interaction Network for HIST2H2BD

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006334nucleosome assembly IEA--

    Find genes that share ontologies with HIST2H2BD           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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      Browse compounds at ApexBio 

    Browse Tocris compounds for HIST2H2BD (H2B2D)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    1 fRNAdb Secondary structure:


    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000369385
    miRNA
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    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HIST2H2BD expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    HIST2H2BD Expression
    About this image

    HIST2H2BD Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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      --

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HIST2H2BD gene
    Selected SIMAP similar genes for HIST2H2BD using alignment to 1 protein entry:     H2B2D_HUMAN(see all similar genes):
    HIST2H2BC    HIST1H2BB    HIST1H2BC    HIST1H2BD    HIST1H2BE    HIST1H2BF
    HIST1H2BG    HIST1H2BH    HIST1H2BI    HIST1H2BJ    HIST1H2BK    HIST1H2BM
    HIST1H2BN    HIST1H2BO    HIST2H2BE    HIST3H2BB    H2BFS    HIST1H2BL

    Find genes that share paralogs with HIST2H2BD           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing HIST2H2BD
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HIST2H2BD gene integrated from 10 sources:
    (articles sorted by number of sources associating them with HIST2H2BD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Functional characterization of a human histone gene cluster duplication. (PubMed id 15527963)1, 2, 3 Braastad C.D....Stein G.S. (Gene 2004)
    2. The human and mouse replication-dependent histone genes. (PubMed id 12408966)1, 2, 3 Marzluff W.F.... Maltais L.J. (Genomics 2002)
    3. Inhibition of core histones acetylation by carcinogenic nickel(II). (PubMed id 16283522)1, 2 Golebiowski F. and Kasprzak K.S. (Mol. Cell. Biochem. 2005)
    4. Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase. (PubMed id 12757711)1, 2 Cheung W.L.... Allis C.D. (Cell 2003)
    5. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. (PubMed id 21925322)2 Tan M.... Zhao Y. (Cell 2011)
    6. Birth-and-death long-term evolution promotes histone H2B variant diversification in the male germinal cell line. (PubMed id 20194426)1 GonzA!lez-Romero R....EirA-n-LA^pez J.M. (Mol. Biol. Evol. 2010)
    7. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. (PubMed id 16916647)1 Kim S.C.... Zhao Y. (Mol. Cell 2006)
    8. Evidence for a human histone gene cluster containing H2B and H2A pseudogenes. (PubMed id 6326092)1 Marashi F....Stein G. (Proc. Natl. Acad. Sci. U.S.A. 1984)
    9. (PubMed id 16628248)10 
    10. (PubMed id 15608161)10 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 337874 HGNC: 20517 Ensembl:ENSG00000220323 euGenes: HUgn337874 ECgene: HIST2H2BD
    H-InvDB: HIST2H2BD

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for HIST2H2BD Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HIST2H2BD gene:
    Search GeneIP for patents involving HIST2H2BD

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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