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    Hdac5 histone deacetylase 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84580, updated on 18-Apr-2019

    Summary

    Official Symbol
    Hdac5provided by RGD
    Official Full Name
    histone deacetylase 5provided by RGD
    Primary source
    RGD:619980
    See related
    Ensembl:ENSRNOG00000020905
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    mouse homolog is involved in mediating nuclear receptor repression [RGD, Feb 2006]
    Annotation information
    Annotation category: partial on reference assembly
    Expression
    Biased expression in Heart (RPKM 189.9), Brain (RPKM 149.1) and 9 other tissues See more
    Orthologs

    Genomic context

    See Hdac5 in Genome Data Viewer
    Location:
    10q32.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (90140183..90169853, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 10 NC_005109.3 (89927486..89956390, complement)

    Chromosome 10 - NC_005109.4Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene glucose 6 phosphatase catalytic subunit 3 Neighboring gene E2F1-inducible gene Neighboring gene ankyrin repeat and SOCS box-containing 16

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Alcoholism, organism-specific biosystem (from KEGG)
      Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
    • Alcoholism, conserved biosystem (from KEGG)
      Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
    • Apelin signaling pathway, organism-specific biosystem (from KEGG)
      Apelin signaling pathway, organism-specific biosystemApelin is an endogenous peptide capable of binding the apelin receptor (APJ), which was originally described as an orphan G-protein-coupled receptor. Apelin and APJ are widely expressed in various ti...
    • Cell cycle, organism-specific biosystem (from WikiPathways)
      Cell cycle, organism-specific biosystem(From http://en.wikipedia.org/wiki/Cell_cycle) The cell cycle is the series of events that takes place in a cell leading to its division and duplication (replication). Regulation of the cell cycle in...
    • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
      Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Epstein-Barr virus infection, conserved biosystem (from KEGG)
      Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Estrogen signaling, organism-specific biosystem (from WikiPathways)
      Estrogen signaling, organism-specific biosystemEstrogen receptor refers to a group of receptors which are activated by the hormone 17β-estradiol (estrogen). Two types of estrogen receptor exist: ER which is a member of the nuclear h...
    • Viral carcinogenesis, organism-specific biosystem (from KEGG)
      Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
    • Viral carcinogenesis, conserved biosystem (from KEGG)
      Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II proximal promoter sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II proximal promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    RNA polymerase II transcription corepressor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    RNA polymerase II transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    histone deacetylase activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    histone deacetylase binding IEA
    Inferred from Electronic Annotation
    more info
     
    histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein kinase C binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein kinase C binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    repressing transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    repressing transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    contributes_to transcription regulatory region DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular response to fluid shear stress ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    chromatin organization TAS
    Traceable Author Statement
    more info
    PubMed 
    heart development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    histone H3 deacetylation IEA
    Inferred from Electronic Annotation
    more info
     
    histone deacetylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    histone deacetylation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    multicellular organismal response to stress ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of cell migration involved in sprouting angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell migration involved in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of myotube differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of myotube differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of osteoblast differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    neuron differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    osteoblast development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of stem cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein deacetylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of gene expression, epigenetic IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of gene expression, epigenetic ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    NOT regulation of histone H3-K9 acetylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of myotube differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of protein binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of skeletal muscle fiber development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of striated muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    renal tubule morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to activity IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to cocaine IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to cocaine ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to drug IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    RNA polymerase II transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    histone deacetylase complex IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear body ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear speck ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone deacetylase 5
    NP_445902.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_053450.1NP_445902.1  histone deacetylase 5

      See identical proteins and their annotated locations for NP_445902.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      Related
      ENSRNOP00000052059.4, ENSRNOT00000055187.4
      Conserved Domains (2) summary
      cl17011
      Location:6701086
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl23765
      Location:68155
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005109.4 Reference Rnor_6.0 Primary Assembly

      Range
      90140183..90169853 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000078.1 Alternate Rn_Celera

      Range
      85868901..85904236 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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