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

Gene ID: 208727, updated on 22-Jan-2023

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
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Genomic context

See Hdac4 in Genome Data Viewer
Location:
1; 1 D
Exon count:
35
Annotation release Status Assembly Chr Location
109 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 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

Homology

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 
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 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 sequence-specific DNA binding 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 organization IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
 
involved_in epigenetic regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3 deacetylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H4 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H4 deacetylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone deacetylation 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 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
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 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
 
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 
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 
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)

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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_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
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    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
    Q3V3Y4
    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