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HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

Gene ID: 10014, updated on 4-Jan-2025

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
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Genomic context

See HDAC5 in Genome Data Viewer
Location:
17q21.31
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44076753..44123641, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44929260..44976146, complement)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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

General gene information

Clone Names

  • FLJ90614

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding PubMed 
enables chromatin binding  
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 PubMed 
enables histone deacetylase binding PubMed 
enables identical protein binding PubMed 
enables metal ion binding  
enables protein binding PubMed 
enables protein kinase C binding PubMed 
enables protein lysine deacetylase activity PubMed 
contributes_to transcription cis-regulatory region binding PubMed 
enables transcription corepressor binding PubMed 
Process Evidence Code Pubs
involved_in B cell activation PubMed 
involved_in B cell differentiation PubMed 
involved_in cellular response to insulin stimulus PubMed 
involved_in cellular response to lipopolysaccharide  
involved_in epigenetic regulation of gene expression  
involved_in inflammatory response PubMed 
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of cell migration involved in sprouting angiogenesis PubMed 
involved_in negative regulation of gene expression, epigenetic PubMed 
involved_in negative regulation of myotube differentiation PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in neuron differentiation  
involved_in positive regulation of DNA-binding transcription factor activity PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in regulation of myotube differentiation  
involved_in regulation of protein binding PubMed 
involved_in response to activity  
involved_in response to cocaine  
involved_in response to xenobiotic stimulus  
Component Evidence Code Pubs
located_in Golgi apparatus  
located_in cytoplasm PubMed 
located_in cytosol  
part_of histone deacetylase complex  
part_of histone deacetylase complex PubMed 
located_in nuclear speck  
located_in nucleoplasm  
located_in nucleus 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)

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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

    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

    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_2024_08

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

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