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Hdac5 histone deacetylase 5 [ Mus musculus (house mouse) ]

Gene ID: 15184, updated on 6-Jun-2024

Summary

Official Symbol
Hdac5provided by MGI
Official Full Name
histone deacetylase 5provided by MGI
Primary source
MGI:MGI:1333784
See related
Ensembl:ENSMUSG00000008855 AllianceGenome:MGI:1333784
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
HD5; Hdac4; mHDA1; mKIAA0600
Summary
Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; transcription corepressor activity; and transcription corepressor binding activity. Involved in several processes, including cellular response to fluid shear stress; positive regulation of cell population proliferation; and regulation of myotube differentiation. Acts upstream of or within several processes, including negative regulation of macromolecule metabolic process; negative regulation of osteoblast differentiation; and osteoblast development. Located in several cellular components, including axonal growth cone; chromatin; and nuclear body. Part of RNA polymerase II transcription repressor complex. Is expressed in several structures, including central nervous system; early embryo; head bone; sensory organ; and upper arm. Orthologous to human HDAC5 (histone deacetylase 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lung adult (RPKM 20.5), adrenal adult (RPKM 19.0) and 28 other tissues See more
Orthologs
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Genomic context

See Hdac5 in Genome Data Viewer
Location:
11 D; 11 65.82 cM
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (102085244..102120968, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (102195747..102230172, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene STARR-positive B cell enhancer ABC_E10715 Neighboring gene glucose 6 phosphatase, catalytic, 3 Neighboring gene STARR-positive B cell enhancer ABC_E378 Neighboring gene microRNA 8101 Neighboring gene STARR-positive B cell enhancer ABC_E911 Neighboring gene homologous recombination factor with OB-fold Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:102128926-102129035 Neighboring gene ankyrin repeat and SOCS box-containing 16

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
 
enables histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
enables histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase C binding ISO
Inferred from Sequence Orthology
more info
 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein lysine deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
contributes_to transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription corepressor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription corepressor binding ISO
Inferred from Sequence Orthology
more info
 
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 fluid shear stress IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chromatin organization TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within heart development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in inflammatory response TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within multicellular organismal response to stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of myotube differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of striated muscle tissue development TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in nervous system development TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within osteoblast development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of neural precursor cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of stem cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of myotube differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of protein binding ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of skeletal muscle fiber development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within regulation of skeletal muscle fiber differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in renal tubule morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to cocaine IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within response to cocaine IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to xenobiotic stimulus ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
part_of RNA polymerase II transcription repressor complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in axonal growth cone IDA
Inferred from Direct Assay
more info
PubMed 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm TAS
Traceable Author Statement
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
part_of histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
histone deacetylase 5
Names
histone deacetylase 4
histone deacetylase mHDA1
NP_001071164.1
NP_001271177.1
NP_001271178.1
NP_001271179.1
NP_001348525.1
NP_001392161.1
NP_001392162.1
NP_001392163.1
NP_001392164.1
NP_001392165.1
NP_001392166.1
NP_001392167.1
NP_001392168.1
NP_001392169.1
NP_001392170.1
NP_001392171.1
NP_001392173.1
NP_034542.3

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_001077696.2NP_001071164.1  histone deacetylase 5 isoform 1

    See identical proteins and their annotated locations for NP_001071164.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36341.1
    UniProtKB/TrEMBL
    Q3U2E0, Q3UJF1
    Related
    ENSMUSP00000102770.3, ENSMUST00000107152.9
    Conserved Domains (2) summary
    cd10007
    Location:6721091
    HDAC5; Histone deacetylase 5
    cl25407
    Location:69156
    ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
  2. NM_001284248.2NP_001271177.1  histone deacetylase 5 isoform 3

    See identical proteins and their annotated locations for NP_001271177.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS70320.1
    UniProtKB/TrEMBL
    B7ZDF5, Q3U2E0
    Related
    ENSMUSP00000008999.6, ENSMUST00000008999.12
    Conserved Domains (2) summary
    cd10007
    Location:6901109
    HDAC5; Histone deacetylase 5
    cl25407
    Location:87174
    ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
  3. NM_001284249.2NP_001271178.1  histone deacetylase 5 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
    Conserved Domains (2) summary
    cd10007
    Location:6301049
    HDAC5; Histone deacetylase 5
    cl25407
    Location:27114
    ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
  4. NM_001284250.2NP_001271179.1  histone deacetylase 5 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS70321.1
    UniProtKB/TrEMBL
    B7ZDF7, Q3U2E0
    Related
    ENSMUSP00000102768.2, ENSMUST00000107150.8
    Conserved Domains (2) summary
    cd10007
    Location:6711090
    HDAC5; Histone deacetylase 5
    cl23765
    Location:68155
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
  5. NM_001361596.2NP_001348525.1  histone deacetylase 5 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
    Conserved Domains (2) summary
    cd10007
    Location:6301049
    HDAC5; Histone deacetylase 5
    cl25407
    Location:27114
    ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
  6. NM_001405232.1NP_001392161.1  histone deacetylase 5 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  7. NM_001405233.1NP_001392162.1  histone deacetylase 5 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  8. NM_001405234.1NP_001392163.1  histone deacetylase 5 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  9. NM_001405235.1NP_001392164.1  histone deacetylase 5 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  10. NM_001405236.1NP_001392165.1  histone deacetylase 5 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  11. NM_001405237.1NP_001392166.1  histone deacetylase 5 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  12. NM_001405238.1NP_001392167.1  histone deacetylase 5 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  13. NM_001405239.1NP_001392168.1  histone deacetylase 5 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  14. NM_001405240.1NP_001392169.1  histone deacetylase 5 isoform 12

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  15. NM_001405241.1NP_001392170.1  histone deacetylase 5 isoform 13

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/Swiss-Prot
    Q9JL73, Q9Z2V6
  16. NM_001405242.1NP_001392171.1  histone deacetylase 5 isoform 13

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/Swiss-Prot
    Q9JL73, Q9Z2V6
  17. NM_001405244.1NP_001392173.1  histone deacetylase 5 isoform 14

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0
  18. NM_010412.4NP_034542.3  histone deacetylase 5 isoform 2

    See identical proteins and their annotated locations for NP_034542.3

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    Q3U2E0, Q6P9T4
    Conserved Domains (2) summary
    cd10007
    Location:6711090
    HDAC5; Histone deacetylase 5
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    102085244..102120968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)