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HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

Gene ID: 10014, updated on 25-Dec-2022

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
110 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44076753..44123641, complement)
110 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 glucose-6-phosphatase catalytic subunit 3 Neighboring gene Sharpr-MPRA regulatory region 9416 Neighboring gene uncharacterized LOC105371789 Neighboring gene RNA, U6 small nuclear 131, pseudogene Neighboring gene homologous recombination factor with OB-fold

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

Homology

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 chromatin organization TAS
Traceable Author Statement
more info
PubMed 
involved_in chromatin remodeling TAS
Traceable Author Statement
more info
PubMed 
involved_in epigenetic regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heterochromatin formation TAS
Traceable Author Statement
more info
PubMed 
involved_in histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
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 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 protein deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in regulation of histone H3-K9 acetylation 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 
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

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

    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
    Q96DY4
    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
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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 X7

  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 X6

  10. XM_047435056.1XP_047291012.1  histone deacetylase 5 isoform X8

  11. XM_047435055.1XP_047291011.1  histone deacetylase 5 isoform X8

  12. XM_047435057.1XP_047291013.1  histone deacetylase 5 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

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

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.