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

Gene ID: 208727, updated on 13-Jan-2020

Summary

Official Symbol
Hdac4provided by MGI
Official Full Name
histone deacetylase 4provided by MGI
Primary source
MGI:MGI:3036234
See related
Ensembl:ENSMUSG00000026313
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
Expression
Ubiquitous expression in adrenal adult (RPKM 12.3), ovary adult (RPKM 10.9) and 28 other tissues See more
Orthologs

Genomic context

See Hdac4 in Genome Data Viewer
Location:
1; 1 D
Exon count:
34
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (91928779..92195702, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (93829311..94044970, complement)

Chromosome 1 - NC_000067.6Genomic 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 uncharacterized LOC108167659 Neighboring gene predicted gene, 35992 Neighboring gene DNA polymerase epsilon subunit 3 pseudogene

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)
  • Gene trapped (2) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

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
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
SUMO transferase activity ISO
Inferred from Sequence Orthology
more info
 
activating transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
potassium ion binding ISO
Inferred from Sequence Orthology
more info
 
promoter-specific chromatin binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
repressing transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription corepressor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling ISO
Inferred from Sequence Orthology
more info
 
histone H3 deacetylation ISO
Inferred from Sequence Orthology
more info
 
histone H4 deacetylation ISO
Inferred from Sequence Orthology
more info
 
histone deacetylation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of glycolytic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of myotube differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of pri-miRNA transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of pri-miRNA transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
osteoblast development IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine deacetylation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of lamellipodium assembly ISO
Inferred from Sequence Orthology
more info
 
positive regulation of male mating behavior ISO
Inferred from Sequence Orthology
more info
 
positive regulation of neuron apoptotic process ISO
Inferred from Sequence Orthology
more info
 
positive regulation of protein sumoylation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of reactive oxygen species biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
positive regulation of smooth muscle cell migration ISO
Inferred from Sequence Orthology
more info
 
positive regulation of smooth muscle cell proliferation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deacetylation ISO
Inferred from Sequence Orthology
more info
 
regulation of cardiac muscle contraction by calcium ion signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
regulation of protein binding ISO
Inferred from Sequence Orthology
more info
 
regulation of skeletal muscle fiber development IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of striated muscle cell differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
response to denervation involved in regulation of muscle adaptation IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to drug ISO
Inferred from Sequence Orthology
more info
 
response to interleukin-1 ISO
Inferred from Sequence Orthology
more info
 
skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
A band ISO
Inferred from Sequence Orthology
more info
 
Z disc ISO
Inferred from Sequence Orthology
more info
 
actomyosin IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol ISO
Inferred from Sequence Orthology
more info
 
histone deacetylase complex ISO
Inferred from Sequence Orthology
more info
 
neuromuscular junction IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
protein-containing complex ISO
Inferred from Sequence Orthology
more info
 
sarcomere ISO
Inferred from Sequence Orthology
more info
 
transcriptional 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

NCBI Reference Sequences (RefSeq)

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
    Q6NZM9
    Related
    ENSMUSP00000095249.3, ENSMUST00000097644.8
    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 108 details...Open this link in a new tab

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

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000067.6 Reference GRCm38.p6 C57BL/6J

    Range
    91928779..92195702 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017319488.2XP_017174977.1  histone deacetylase 4 isoform X6

    UniProtKB/Swiss-Prot
    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

  3. XM_017319487.2XP_017174976.1  histone deacetylase 4 isoform X3

  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_017319498.1XP_017174987.1  histone deacetylase 4 isoform X9

    Conserved Domains (1) summary
    cd10006
    Location:480888
    HDAC4; Histone deacetylase 4
  6. XM_030252550.1XP_030108410.1  histone deacetylase 4 isoform X8

  7. XM_030252529.1XP_030108389.1  histone deacetylase 4 isoform X1

  8. XM_030252549.1XP_030108409.1  histone deacetylase 4 isoform X7

  9. XM_030252541.1XP_030108401.1  histone deacetylase 4 isoform X6

  10. XM_030252531.1XP_030108391.1  histone deacetylase 4 isoform X2

  11. XM_017319482.2XP_017174971.1  histone deacetylase 4 isoform X3

  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

  14. XM_017319477.1XP_017174966.1  histone deacetylase 4 isoform X2

  15. XM_017319478.1XP_017174967.1  histone deacetylase 4 isoform X3

  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 X7

    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 X10

  19. XM_030252552.1XP_030108412.1  histone deacetylase 4 isoform X9

  20. XM_006529313.2XP_006529376.1  histone deacetylase 4 isoform X7

    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_006529314.4XP_006529377.1  histone deacetylase 4 isoform X7

    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
  22. 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
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