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HDAC3 histone deacetylase 3 [ Homo sapiens (human) ]

Gene ID: 8841, updated on 1-Jun-2020

Summary

Official Symbol
HDAC3provided by HGNC
Official Full Name
histone deacetylase 3provided by HGNC
Primary source
HGNC:HGNC:4854
See related
Ensembl:ENSG00000171720 MIM:605166
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
HD3; RPD3; KDAC3; RPD3-2
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 the histone deacetylase/acuc/apha family. It has histone deacetylase activity and represses transcription when tethered to a promoter. It may participate in the regulation of transcription through its binding with the zinc-finger transcription factor YY1. This protein can also down-regulate p53 function and thus modulate cell growth and apoptosis. This gene is regarded as a potential tumor suppressor gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 21.1), adrenal (RPKM 20.9) and 25 other tissues See more
Orthologs

Genomic context

See HDAC3 in Genome Data Viewer
Location:
5q31.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (141620876..141636856, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141000443..141016423, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene diaphanous related formin 1 Neighboring gene DIAPH1 antisense RNA 1 Neighboring gene RPS27A pseudogene 10 Neighboring gene RELT like 2 Neighboring gene FCH and double SH3 domains 1 Neighboring gene ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 promoter transcription is restricted by HDAC3 in 2D10 cells as shown through shRNA knockdown or an HDAC3 specific inhibitor (BRD3308) PubMed

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif is identified to have a physical interaction with histone deacetylase 3 (HDAC3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Vpr vpr HIV-1 Vpr depletes HDAC3 in HIV-1 latently infected J-Lat cells by targeting HDAC3 for proteasomal degradation; HDAC3 was degraded on HIV-1 LTR and resulting in recruitment of active transcription markers to the viral promoter and provirus activation PubMed
vpr HIV-1 Vpr binds and depletes chromatin-associated HDAC3 and HDAC1 through a VprBP-dependent mechanism resulting in hyperacetylation of histones on the HIV-1 LTR resulting in reactivation of HIV-1 promoter leading to acute infection PubMed
vpr HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
cyclin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cellular response to fluid shear stress IDA
Inferred from Direct Assay
more info
PubMed 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian rhythm TAS
Traceable Author Statement
more info
 
histone H3 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H4 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of JNK cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
NOT negative regulation of myotube differentiation 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of protein import into nucleus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
protein deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
regulation of protein stability IDA
Inferred from Direct Assay
more info
PubMed 
spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
mitotic spindle IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus TAS
Traceable Author Statement
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 3
Names
SMAP45
NP_001341968.1
NP_001341969.1
NP_001341970.1
NP_003874.2

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_029678.2 RefSeqGene

    Range
    5008..20976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001355039.2NP_001341968.1  histone deacetylase 3 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC008781, KC877130
    Conserved Domains (1) summary
    cd10005
    Location:3383
    HDAC3; Histone deacetylase 3 (HDAC3)
  2. NM_001355040.1NP_001341969.1  histone deacetylase 3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
    Conserved Domains (1) summary
    cl17011
    Location:5230
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  3. NM_001355041.1NP_001341970.1  histone deacetylase 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
    Conserved Domains (1) summary
    cl17011
    Location:1196
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  4. NM_003883.4NP_003874.2  histone deacetylase 3 isoform 2

    See identical proteins and their annotated locations for NP_003874.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC000614, BM461585, DB456387
    Consensus CDS
    CCDS4264.1
    UniProtKB/Swiss-Prot
    O15379
    Related
    ENSP00000302967.3, ENST00000305264.8
    Conserved Domains (1) summary
    cd10005
    Location:3383
    HDAC3; Histone deacetylase 3 (HDAC3)

RNA

  1. NR_149164.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
  2. NR_149165.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
  3. NR_149166.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
  4. NR_149167.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
  5. NR_149168.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130
  6. NR_149169.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008781, KC877130

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    141620876..141636856 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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