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HDAC4 histone deacetylase 4 [ Homo sapiens (human) ]

Gene ID: 9759, updated on 13-Feb-2020

Summary

Official Symbol
HDAC4provided by HGNC
Official Full Name
histone deacetylase 4provided by HGNC
Primary source
HGNC:HGNC:14063
See related
Ensembl:ENSG00000068024 MIM:605314
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
HD4; AHO3; BDMR; HDACA; HA6116; HDAC-4; HDAC-A
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 class II of the histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. This protein does not bind DNA directly, but through transcription factors MEF2C and MEF2D. It seems to interact in a multiprotein complex with RbAp48 and HDAC3. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 2.4), testis (RPKM 1.6) and 24 other tissues See more
Orthologs

Genomic context

See HDAC4 in Genome Data Viewer
Location:
2q37.3
Exon count:
37
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (239048168..239401647, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (239969864..240323346, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8511 Neighboring gene twist family bHLH transcription factor 2 Neighboring gene long intergenic non-protein coding RNA 1940 Neighboring gene microRNA 4440 Neighboring gene microRNA 4441 Neighboring gene uncharacterized LOC85009 Neighboring gene microRNA 4269 Neighboring gene microRNA 2467 Neighboring gene HDAC4 antisense RNA 1 Neighboring gene uncharacterized LOC401040 Neighboring gene uncharacterized LOC105373966

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

Associated conditions

Description Tests
Chromosome 2q37 deletion syndrome
MedGen: C2931817 GeneReviews: 2q37 Microdeletion Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2011-11-07)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2011-11-07)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
NHGRI GWA Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
NHGRI GWA Catalog
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
NHGRI GWA Catalog
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
reverse transcriptase gag-pol Amino acid starvation-dependent HDAC4 downregulation leads to HIV-1 transcriptional activation and RT activity production in T-lymphocytes PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0288

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
SUMO transferase activity EXP
Inferred from Experiment
more info
PubMed 
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
potassium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
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 TAS
Traceable Author Statement
more info
 
protein kinase binding IEA
Inferred from Electronic Annotation
more info
 
repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
B cell activation TAS
Traceable Author Statement
more info
PubMed 
B cell differentiation TAS
Traceable Author Statement
more info
PubMed 
cardiac muscle hypertrophy in response to stress TAS
Traceable Author Statement
more info
PubMed 
cellular response to mechanical stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to parathyroid hormone stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to tumor necrosis factor IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
histone H3 deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H4 deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
inflammatory response TAS
Traceable Author Statement
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of glycolytic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of myotube differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of pri-miRNA transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
osteoblast development IEA
Inferred from Electronic Annotation
more info
 
peptidyl-lysine deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of lamellipodium assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of male mating behavior IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein sumoylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of reactive oxygen species biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of smooth muscle cell migration IEA
Inferred from Electronic Annotation
more info
 
positive regulation of smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
protein sumoylation IEA
Inferred from Electronic Annotation
more info
 
regulation of cardiac muscle contraction by calcium ion signaling IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of skeletal muscle fiber development IEA
Inferred from Electronic Annotation
more info
 
response to denervation involved in regulation of muscle adaptation ISS
Inferred from Sequence or Structural Similarity
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to interleukin-1 IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal system development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
A band IEA
Inferred from Electronic Annotation
more info
 
Z disc IEA
Inferred from Electronic Annotation
more info
 
actomyosin IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 4
Names
histone deacetylase A
NP_006028.2
XP_006712940.1
XP_006712941.1
XP_006712942.1
XP_006712943.1
XP_011510519.1
XP_011510520.1
XP_011510521.1
XP_011510522.1
XP_011510523.1
XP_011510524.1
XP_011510525.1
XP_011510526.1
XP_011510527.1
XP_011510528.1
XP_011510529.1
XP_011510532.1
XP_016860883.1
XP_016860884.1
XP_024309025.1

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.

Genomic

  1. NG_009235.1 RefSeqGene

    Range
    5001..357780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001378414.1NP_001365343.1  histone deacetylase 4 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC017028, AC062017
  2. NM_001378415.1NP_001365344.1  histone deacetylase 4 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC017028, AC062017
  3. NM_001378416.1NP_001365345.1  histone deacetylase 4 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC017028, AC062017
  4. NM_001378417.1NP_001365346.1  histone deacetylase 4 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC017028, AC062017
  5. NM_006037.4NP_006028.2  histone deacetylase 4 isoform 2

    See identical proteins and their annotated locations for NP_006028.2

    Status: REVIEWED

    Source sequence(s)
    AC017028, AC062017
    Consensus CDS
    CCDS2529.1
    UniProtKB/Swiss-Prot
    P56524
    Related
    ENSP00000264606.3, ENST00000345617.7
    Conserved Domains (2) summary
    cd10162
    Location:91152
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6491057
    HDAC4; Histone deacetylase 4

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    239048168..239401647 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512221.1XP_011510523.1  histone deacetylase 4 isoform X6

    Conserved Domains (2) summary
    cd10162
    Location:91152
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6541062
    HDAC4; Histone deacetylase 4
  2. XM_011512226.2XP_011510528.1  histone deacetylase 4 isoform X10

    Conserved Domains (2) summary
    cd10162
    Location:67128
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6301038
    HDAC4; Histone deacetylase 4
  3. XM_006712878.3XP_006712941.1  histone deacetylase 4 isoform X6

    Conserved Domains (2) summary
    cd10162
    Location:91152
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6541062
    HDAC4; Histone deacetylase 4
  4. XM_011512223.2XP_011510525.1  histone deacetylase 4 isoform X6

    See identical proteins and their annotated locations for XP_011510525.1

    Conserved Domains (2) summary
    cd10162
    Location:91152
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6541062
    HDAC4; Histone deacetylase 4
  5. XM_011512222.3XP_011510524.1  histone deacetylase 4 isoform X6

    See identical proteins and their annotated locations for XP_011510524.1

    Related
    ENSP00000440481.2, ENST00000543185.5
    Conserved Domains (2) summary
    cd10162
    Location:91152
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6541062
    HDAC4; Histone deacetylase 4
  6. XM_017005394.1XP_016860883.1  histone deacetylase 4 isoform X9

  7. XM_011512219.2XP_011510521.1  histone deacetylase 4 isoform X4

    Conserved Domains (2) summary
    cd10162
    Location:115176
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6731076
    HDAC4; Histone deacetylase 4
  8. XM_006712877.3XP_006712940.1  histone deacetylase 4 isoform X2

    Conserved Domains (2) summary
    cd10162
    Location:115176
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6731081
    HDAC4; Histone deacetylase 4
  9. XM_011512218.2XP_011510520.1  histone deacetylase 4 isoform X3

    Conserved Domains (2) summary
    cd10162
    Location:115176
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6781081
    HDAC4; Histone deacetylase 4
  10. XM_011512217.2XP_011510519.1  histone deacetylase 4 isoform X1

    Conserved Domains (2) summary
    cd10162
    Location:115176
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6781086
    HDAC4; Histone deacetylase 4
  11. XM_006712879.3XP_006712942.1  histone deacetylase 4 isoform X11

    See identical proteins and their annotated locations for XP_006712942.1

    Conserved Domains (2) summary
    cd10162
    Location:64125
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6271035
    HDAC4; Histone deacetylase 4
  12. XM_006712880.3XP_006712943.1  histone deacetylase 4 isoform X11

    See identical proteins and their annotated locations for XP_006712943.1

    Conserved Domains (2) summary
    cd10162
    Location:64125
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6271035
    HDAC4; Histone deacetylase 4
  13. XM_011512220.2XP_011510522.1  histone deacetylase 4 isoform X5

    Conserved Domains (2) summary
    cd10162
    Location:92153
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6551063
    HDAC4; Histone deacetylase 4
  14. XM_011512225.2XP_011510527.1  histone deacetylase 4 isoform X8

    Conserved Domains (2) summary
    cd10162
    Location:86147
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6441052
    HDAC4; Histone deacetylase 4
  15. XM_011512224.2XP_011510526.1  histone deacetylase 4 isoform X7

    Conserved Domains (2) summary
    cd10162
    Location:86147
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6491057
    HDAC4; Histone deacetylase 4
  16. XM_024453257.1XP_024309025.1  histone deacetylase 4 isoform X11

    Conserved Domains (2) summary
    cd10162
    Location:64125
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6271035
    HDAC4; Histone deacetylase 4
  17. XM_011512227.2XP_011510529.1  histone deacetylase 4 isoform X12

    Conserved Domains (2) summary
    cd10162
    Location:43104
    ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase
    cd10006
    Location:6061014
    HDAC4; Histone deacetylase 4
  18. XM_017005395.1XP_016860884.1  histone deacetylase 4 isoform X13

  19. XM_011512230.1XP_011510532.1  histone deacetylase 4 isoform X14

    Conserved Domains (1) summary
    cd10006
    Location:238646
    HDAC4; Histone deacetylase 4
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