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    HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

    Gene ID: 10014, updated on 7-Jul-2024

    Summary

    Official Symbol
    HDAC5provided by HGNC
    Official Full Name
    histone deacetylase 5provided by HGNC
    Primary source
    HGNC:HGNC:14068
    See related
    Ensembl:ENSG00000108840 MIM:605315; AllianceGenome:HGNC:14068
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HD5; NY-CO-9
    Summary
    Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to the class II histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. It coimmunoprecipitates only with HDAC3 family member and might form multicomplex proteins. It also interacts with myocyte enhancer factor-2 (MEF2) proteins, resulting in repression of MEF2-dependent genes. This gene is thought to be associated with colon cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 14.0), ovary (RPKM 13.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HDAC5 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44076753..44123641, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44929260..44976146, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42154121..42201009, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42146518-42147445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42147446-42148372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12251 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42149300-42150225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42152642-42153376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42154394-42154933 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:42159496-42160695 Neighboring gene glucose-6-phosphatase catalytic subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42169749-42170254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42172728-42173488 Neighboring gene Sharpr-MPRA regulatory region 9416 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42176231-42176442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42182651-42183302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42189382-42189882 Neighboring gene uncharacterized LOC105371789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42202517-42203016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42215327-42215850 Neighboring gene RNA, U6 small nuclear 131, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8576 Neighboring gene Sharpr-MPRA regulatory region 5 Neighboring gene homologous recombination factor with OB-fold Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12254

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ90614

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in B cell activation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in B cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to insulin stimulus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inflammatory response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of cell migration involved in sprouting angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression, epigenetic NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of myotube differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of myotube differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to activity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to cocaine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    part_of histone deacetylase complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone deacetylase 5
    Names
    antigen NY-CO-9
    NP_001015053.1
    NP_001369322.1
    NP_005465.2
    XP_011522451.1
    XP_047291003.1
    XP_047291004.1
    XP_047291005.1
    XP_047291006.1
    XP_047291007.1
    XP_047291008.1
    XP_047291009.1
    XP_047291010.1
    XP_047291011.1
    XP_047291012.1
    XP_047291013.1
    XP_054170588.1
    XP_054170589.1
    XP_054170590.1
    XP_054170591.1
    XP_054170592.1
    XP_054170593.1
    XP_054170594.1
    XP_054170595.1
    XP_054170596.1
    XP_054170597.1
    XP_054170598.1

    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_001015053.2NP_001015053.1  histone deacetylase 5 isoform 3

      See identical proteins and their annotated locations for NP_001015053.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
      Source sequence(s)
      AB011172, AC023855, BC051824, CN290533
      Consensus CDS
      CCDS32663.1
      UniProtKB/Swiss-Prot
      Q9UQL6
      Related
      ENSP00000225983.5, ENST00000225983.10
      Conserved Domains (2) summary
      cd10164
      Location:69165
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:6801096
      HDAC5; Histone deacetylase 5
    2. NM_001382393.1NP_001369322.1  histone deacetylase 5 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AB011172, AC023855, BC051824
      Consensus CDS
      CCDS45696.1
      UniProtKB/Swiss-Prot
      C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
      Related
      ENSP00000468004.1, ENST00000586802.5
      Conserved Domains (2) summary
      cd10164
      Location:68164
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:6791095
      HDAC5; Histone deacetylase 5
    3. NM_005474.5NP_005465.2  histone deacetylase 5 isoform 1

      See identical proteins and their annotated locations for NP_005465.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is 1 aa shorter compared to isoform 3.
      Source sequence(s)
      AB011172, AC023855, BC051824, BM564861
      Consensus CDS
      CCDS45696.1
      UniProtKB/Swiss-Prot
      C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
      Related
      ENSP00000507606.1, ENST00000682912.1
      Conserved Domains (2) summary
      cd10164
      Location:68164
      ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
      cd10007
      Location:6791095
      HDAC5; Histone deacetylase 5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44076753..44123641 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435054.1XP_047291010.1  histone deacetylase 5 isoform X6

    2. XM_047435052.1XP_047291008.1  histone deacetylase 5 isoform X5

    3. XM_047435050.1XP_047291006.1  histone deacetylase 5 isoform X3

    4. XM_011524149.3XP_011522451.1  histone deacetylase 5 isoform X4

      Conserved Domains (2) summary
      cd10007
      Location:6711087
      HDAC5; Histone deacetylase 5
      cl23765
      Location:69156
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
    5. XM_047435048.1XP_047291004.1  histone deacetylase 5 isoform X2

    6. XM_047435051.1XP_047291007.1  histone deacetylase 5 isoform X3

    7. XM_047435049.1XP_047291005.1  histone deacetylase 5 isoform X2

    8. XM_047435047.1XP_047291003.1  histone deacetylase 5 isoform X1

    9. XM_047435053.1XP_047291009.1  histone deacetylase 5 isoform X9

    10. XM_047435056.1XP_047291012.1  histone deacetylase 5 isoform X7

    11. XM_047435055.1XP_047291011.1  histone deacetylase 5 isoform X7

    12. XM_047435057.1XP_047291013.1  histone deacetylase 5 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      44929260..44976146 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314620.1XP_054170595.1  histone deacetylase 5 isoform X6

    2. XM_054314619.1XP_054170594.1  histone deacetylase 5 isoform X5

    3. XM_054314616.1XP_054170591.1  histone deacetylase 5 isoform X3

    4. XM_054314618.1XP_054170593.1  histone deacetylase 5 isoform X4

    5. XM_054314614.1XP_054170589.1  histone deacetylase 5 isoform X2

    6. XM_054314617.1XP_054170592.1  histone deacetylase 5 isoform X3

    7. XM_054314615.1XP_054170590.1  histone deacetylase 5 isoform X2

    8. XM_054314613.1XP_054170588.1  histone deacetylase 5 isoform X1

    9. XM_054314622.1XP_054170597.1  histone deacetylase 5 isoform X7

    10. XM_054314621.1XP_054170596.1  histone deacetylase 5 isoform X7

    11. XM_054314623.1XP_054170598.1  histone deacetylase 5 isoform X8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_139205.1: Suppressed sequence

      Description
      NM_139205.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.