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

    Gene ID: 84580, updated on 9-Dec-2024

    Summary

    Official Symbol
    Hdac5provided by RGD
    Official Full Name
    histone deacetylase 5provided by RGD
    Primary source
    RGD:619980
    See related
    EnsemblRapid:ENSRNOG00000020905 AllianceGenome:RGD:619980
    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
    Enables chromatin binding activity. Involved in several processes, including cellular response to lipopolysaccharide; response to activity; and response to cocaine. Located in cytoplasm and nucleus. Part of protein-containing complex. Biomarker of acute kidney failure; depressive disorder; middle cerebral artery infarction; and pulmonary hypertension. Orthologous to human HDAC5 (histone deacetylase 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 189.9), Brain (RPKM 149.1) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Hdac5 in Genome Data Viewer
    Location:
    10q32.1
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (87653139..87688078, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (87152978..87187921, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (90140183..90169853, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene glucose 6 phosphatase catalytic subunit 3 Neighboring gene small nucleolar RNA, H/ACA box 33 Neighboring gene homologous recombination factor with OB-fold

    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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables chromatin binding PubMed 
    enables histone H3K14 deacetylase activity, hydrolytic mechanism  
    enables histone H3K4 deacetylase activity, hydrolytic mechanism  
    enables histone H3K9 deacetylase activity, hydrolytic mechanism  
    enables histone H4K12 deacetylase activity, hydrolytic mechanism  
    enables histone H4K16 deacetylase activity, hydrolytic mechanism  
    enables histone H4K5 deacetylase activity, hydrolytic mechanism  
    enables histone H4K8 deacetylase activity, hydrolytic mechanism  
    enables histone deacetylase activity  
    enables histone deacetylase activity  
    enables histone deacetylase binding  
    enables hydrolase activity  
    enables identical protein binding  
    enables metal ion binding  
    enables protein kinase C binding  
    enables protein kinase binding  
    enables protein lysine deacetylase activity  
    contributes_to transcription cis-regulatory region binding  
    enables transcription corepressor activity  
    enables transcription corepressor binding  
    Items 1 - 25 of 28
    Process Evidence Code Pubs
    involved_in cellular response to fluid shear stress  
    involved_in cellular response to lipopolysaccharide PubMed 
    involved_in chromatin organization  
    involved_in epigenetic regulation of gene expression  
    acts_upstream_of_or_within heart development  
    acts_upstream_of_or_within multicellular organismal response to stress  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription  
    involved_in negative regulation of cell migration involved in sprouting angiogenesis  
    acts_upstream_of_or_within negative regulation of gene expression  
    involved_in negative regulation of myotube differentiation  
    acts_upstream_of_or_within negative regulation of osteoblast differentiation  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in neuron differentiation PubMed 
    acts_upstream_of_or_within osteoblast development  
    acts_upstream_of osteoblast differentiation  
    involved_in positive regulation of DNA-binding transcription factor activity  
    involved_in positive regulation of neural precursor cell proliferation  
    involved_in positive regulation of stem cell proliferation  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in regulation of myotube differentiation  
    acts_upstream_of_or_within regulation of skeletal muscle fiber development  
    acts_upstream_of_or_within regulation of skeletal muscle fiber differentiation  
    involved_in renal tubule morphogenesis  
    involved_in response to activity PubMed 
    involved_in response to cocaine PubMed 
    acts_upstream_of_or_within response to cocaine  
    involved_in response to xenobiotic stimulus PubMed 
    Items 1 - 25 of 28
    Component Evidence Code Pubs
    located_in Golgi apparatus  
    located_in Golgi apparatus  
    part_of RNA polymerase II transcription repressor complex  
    located_in axonal growth cone  
    located_in chromatin  
    located_in cytoplasm PubMed 
    located_in cytoplasm  
    located_in cytosol  
    part_of histone deacetylase complex  
    located_in nuclear body  
    located_in nuclear speck  
    located_in nuclear speck  
    located_in nucleus PubMed 
    is_active_in nucleus  
    located_in nucleus  
    part_of protein-containing complex PubMed 

    General protein information

    Preferred Names
    histone deacetylase 5
    NP_445902.1
    XP_038942912.1
    XP_038942913.1
    XP_038942915.1
    XP_038942916.1
    XP_038942917.1
    XP_063126067.1
    XP_063126068.1
    XP_063126069.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      UniProtKB/TrEMBL
      A0A8I6AAJ0, A6HJH3
      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: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      87653139..87688078 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039086987.2XP_038942915.1  histone deacetylase 5 isoform X5

      UniProtKB/TrEMBL
      A0A8I5XW09, A0A8I6AAJ0
      Related
      ENSRNOP00000077322.2, ENSRNOT00000105575.2
      Conserved Domains (2) summary
      cl17011
      Location:6461062
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl25407
      Location:44131
      ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
    2. XM_039086988.2XP_038942916.1  histone deacetylase 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AAJ0
      Conserved Domains (2) summary
      cl17011
      Location:6291045
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl25407
      Location:27114
      ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
    3. XM_039086984.2XP_038942912.1  histone deacetylase 5 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AAJ0, A0A8I6G4R8
      Related
      ENSRNOP00000080604.1, ENSRNOT00000101600.2
      Conserved Domains (2) summary
      cl17011
      Location:6711087
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl25407
      Location:69156
      ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
    4. XM_039086985.2XP_038942913.1  histone deacetylase 5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AAJ0
      Conserved Domains (2) summary
      cl17011
      Location:6611077
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl25407
      Location:59146
      ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
    5. XM_063269997.1XP_063126067.1  histone deacetylase 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AAJ0
    6. XM_063269998.1XP_063126068.1  histone deacetylase 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AAJ0
      Related
      ENSRNOP00000052059.6, ENSRNOT00000055187.6
    7. XM_039086989.2XP_038942917.1  histone deacetylase 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AAJ0
      Conserved Domains (2) summary
      cl17011
      Location:6291045
      Arginase_HDAC; Arginase-like and histone-like hydrolases
      cl25407
      Location:27114
      ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
    8. XM_063269999.1XP_063126069.1  histone deacetylase 5 isoform X6

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