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    Hdac4 histone deacetylase 4 [ Mus musculus (house mouse) ]

    Gene ID: 208727, updated on 21-Apr-2024

    Summary

    Official Symbol
    Hdac4provided by MGI
    Official Full Name
    histone deacetylase 4provided by MGI
    Primary source
    MGI:MGI:3036234
    See related
    Ensembl:ENSMUSG00000026313 AllianceGenome:MGI:3036234
    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
    HD4; 4932408F19Rik
    Summary
    Enables several functions, including chromatin binding activity; protein deacetylase activity; and transcription corepressor activity. Involved in regulation of nucleobase-containing compound metabolic process and response to denervation involved in regulation of muscle adaptation. Acts upstream of or within several processes, including negative regulation of osteoblast differentiation; osteoblast development; and regulation of cardiac muscle contraction by calcium ion signaling. Located in several cellular components, including actomyosin; cytosol; and neuromuscular junction. Is expressed in several structures, including alimentary system; early embryo; ganglia; hand; and telencephalon. Used to study eating disorder. Human ortholog(s) of this gene implicated in ataxia telangiectasia; chromosome 2q37 deletion syndrome; eating disorder; and retinal degeneration. Orthologous to human HDAC4 (histone deacetylase 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 12.3), ovary adult (RPKM 10.9) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    1 D; 1 46.24 cM
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (91856501..92123424, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (91928779..92195702, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene twist basic helix-loop-helix transcription factor 2 Neighboring gene predicted gene, 46117 Neighboring gene predicted gene, 46242 Neighboring gene VISTA enhancer mm901 Neighboring gene predicted gene, 50604 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:93955363-93955516 Neighboring gene STARR-seq mESC enhancer starr_01708 Neighboring gene STARR-seq mESC enhancer starr_01709 Neighboring gene STARR-positive B cell enhancer ABC_E1222 Neighboring gene STARR-seq mESC enhancer starr_01714 Neighboring gene STARR-seq mESC enhancer starr_01715 Neighboring gene predicted gene, 53573 Neighboring gene predicted gene, 53574

    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 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 ISO
    Inferred from Sequence Orthology
    more info
     
    enables SUMO transferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone deacetylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    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 molecular adaptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables potassium ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein lysine deacetylase activity IDA
    Inferred from Direct Assay
    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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression, epigenetic ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of glycolytic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of miRNA transcription IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in negative regulation of miRNA transcription 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 
    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 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription by competitive promoter binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 peptidyl-lysine deacetylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of lamellipodium assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of male mating behavior ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of protein sumoylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of reactive oxygen species biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of smooth muscle cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of smooth muscle cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II 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 protein deacetylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of cardiac muscle contraction by calcium ion signaling IMP
    Inferred from Mutant Phenotype
    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 response to denervation involved in regulation of muscle adaptation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to interleukin-1 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in type I interferon-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in A band ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Z disc ISO
    Inferred from Sequence Orthology
    more info
     
    located_in actomyosin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    located_in neuromuscular junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in sarcomere ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    histone deacetylase 4
    NP_997108.1
    XP_006529374.1
    XP_006529375.1
    XP_006529376.1
    XP_006529377.1
    XP_006529378.1
    XP_017174965.1
    XP_017174966.1
    XP_017174967.1
    XP_017174968.1
    XP_017174969.1
    XP_017174971.1
    XP_017174975.1
    XP_017174976.1
    XP_017174977.1
    XP_017174987.1
    XP_017174990.1
    XP_030108389.1
    XP_030108391.1
    XP_030108401.1
    XP_030108409.1
    XP_030108410.1
    XP_030108412.1
    XP_036019018.1
    XP_036019024.1

    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_207225.2NP_997108.1  histone deacetylase 4

      See identical proteins and their annotated locations for NP_997108.1

      Status: VALIDATED

      Source sequence(s)
      AC109197, AC163436, BC066052, BY265337
      Consensus CDS
      CCDS48324.1
      UniProtKB/Swiss-Prot
      Q3TRZ9, Q3U2J3, Q3V3Y4, Q6NZM9
      Related
      ENSMUSP00000095249.4, ENSMUST00000097644.9
      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461049
      HDAC4; Histone deacetylase 4

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      91856501..92123424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319488.2XP_017174977.1  histone deacetylase 4 isoform X7

      UniProtKB/Swiss-Prot
      Q3TRZ9, Q3U2J3, Q3V3Y4, Q6NZM9
      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461049
      HDAC4; Histone deacetylase 4
    2. XM_017319486.2XP_017174975.1  histone deacetylase 4 isoform X2

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461054
      HDAC4; Histone deacetylase 4
    3. XM_017319487.2XP_017174976.1  histone deacetylase 4 isoform X3

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511054
      HDAC4; Histone deacetylase 4
    4. XM_017319480.2XP_017174969.1  histone deacetylase 4 isoform X1

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511059
      HDAC4; Histone deacetylase 4
    5. XM_017319498.2XP_017174987.1  histone deacetylase 4 isoform X10

      Conserved Domains (1) summary
      cd10006
      Location:480888
      HDAC4; Histone deacetylase 4
    6. XM_030252529.1XP_030108389.1  histone deacetylase 4 isoform X1

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511059
      HDAC4; Histone deacetylase 4
    7. XM_030252549.1XP_030108409.1  histone deacetylase 4 isoform X8

      Conserved Domains (2) summary
      cd10162
      Location:63124
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6241032
      HDAC4; Histone deacetylase 4
    8. XM_030252550.2XP_030108410.1  histone deacetylase 4 isoform X9

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6021010
      HDAC4; Histone deacetylase 4
    9. XM_030252541.1XP_030108401.1  histone deacetylase 4 isoform X7

      UniProtKB/Swiss-Prot
      Q3TRZ9, Q3U2J3, Q3V3Y4, Q6NZM9
      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461049
      HDAC4; Histone deacetylase 4
    10. XM_030252531.1XP_030108391.1  histone deacetylase 4 isoform X2

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461054
      HDAC4; Histone deacetylase 4
    11. XM_017319482.2XP_017174971.1  histone deacetylase 4 isoform X3

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511054
      HDAC4; Histone deacetylase 4
    12. XM_006529315.3XP_006529378.1  histone deacetylase 4 isoform X1

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511059
      HDAC4; Histone deacetylase 4
    13. XM_017319479.1XP_017174968.1  histone deacetylase 4 isoform X4

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6071015
      HDAC4; Histone deacetylase 4
    14. XM_017319477.1XP_017174966.1  histone deacetylase 4 isoform X2

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6461054
      HDAC4; Histone deacetylase 4
    15. XM_017319478.1XP_017174967.1  histone deacetylase 4 isoform X3

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511054
      HDAC4; Histone deacetylase 4
    16. XM_017319476.1XP_017174965.1  histone deacetylase 4 isoform X1

      Conserved Domains (2) summary
      cd10162
      Location:90151
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6511059
      HDAC4; Histone deacetylase 4
    17. XM_006529312.2XP_006529375.1  histone deacetylase 4 isoform X8

      See identical proteins and their annotated locations for XP_006529375.1

      Conserved Domains (2) summary
      cd10162
      Location:63124
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6241032
      HDAC4; Histone deacetylase 4
    18. XM_017319501.2XP_017174990.1  histone deacetylase 4 isoform X11

      Conserved Domains (1) summary
      cd10006
      Location:480883
      HDAC4; Histone deacetylase 4
    19. XM_030252552.1XP_030108412.1  histone deacetylase 4 isoform X10

      Conserved Domains (1) summary
      cd10006
      Location:480888
      HDAC4; Histone deacetylase 4
    20. XM_006529313.2XP_006529376.1  histone deacetylase 4 isoform X8

      See identical proteins and their annotated locations for XP_006529376.1

      Conserved Domains (2) summary
      cd10162
      Location:63124
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6241032
      HDAC4; Histone deacetylase 4
    21. XM_036163125.1XP_036019018.1  histone deacetylase 4 isoform X6

      Conserved Domains (2) summary
      cd10162
      Location:99160
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6601068
      HDAC4; Histone deacetylase 4
    22. XM_006529314.4XP_006529377.1  histone deacetylase 4 isoform X8

      See identical proteins and their annotated locations for XP_006529377.1

      Conserved Domains (2) summary
      cd10162
      Location:63124
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6241032
      HDAC4; Histone deacetylase 4
    23. XM_036163131.1XP_036019024.1  histone deacetylase 4 isoform X8

      Conserved Domains (2) summary
      cd10162
      Location:63124
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6241032
      HDAC4; Histone deacetylase 4
    24. XM_006529311.4XP_006529374.1  histone deacetylase 4 isoform X5

      Conserved Domains (2) summary
      cd10162
      Location:104165
      ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
      cd10006
      Location:6651073
      HDAC4; Histone deacetylase 4