Hdac3 histone deacetylase 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hdac3provided by RGD
Official Full Name: histone deacetylase 3provided by RGD
Primary source: RGD:619977
See related: EnsemblRapid:ENSRNOG00000019618 AllianceGenome:RGD:619977
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including chromatin binding activity; enzyme binding activity; and transcription corepressor binding activity. Contributes to histone deacetylase activity. Involved in several processes, including cellular response to mechanical stimulus; negative regulation of cytokine production; and positive regulation of apoptotic process. Located in chromatin and nucleus. Biomarker of acute kidney failure and impotence. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human HDAC3 (histone deacetylase 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 182.1), Lung (RPKM 168.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18p11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (30021847..30041061, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (29770637..29789850, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (31073057..31094347, complement)

Chromosome 18 - NC_086036.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HDAC3 Impairs Cardiac Function in Chronic Heart Failure Rats via Mediating MicroRNA-26b-3p to Target High Mobility Group AT-Hook 2.
Title: HDAC3 Impairs Cardiac Function in Chronic Heart Failure Rats via Mediating MicroRNA-26b-3p to Target High Mobility Group AT-Hook 2.
Depleted HDAC3 attenuates hyperuricemia-induced renal interstitial fibrosis via miR-19b-3p/SF3B3 axis.
Title: Depleted HDAC3 attenuates hyperuricemia-induced renal interstitial fibrosis via miR-19b-3p/SF3B3 axis.
Depleted histone deacetylase 3 or restored microRNA-19b-1-5p facilitates recovery of spinal cord injury via inactivating JAK2/STAT3 signaling pathway.
Title: Depleted histone deacetylase 3 or restored microRNA-19b-1-5p facilitates recovery of spinal cord injury via inactivating JAK2/STAT3 signaling pathway.
Histone deacetylase 3 suppresses the expression of SHP-1 via deacetylation of DNMT1 to promote heart failure.
Title: Histone deacetylase 3 suppresses the expression of SHP-1 via deacetylation of DNMT1 to promote heart failure.
Inhibited histone deacetylase 3 ameliorates myocardial ischemia-reperfusion injury in a rat model by elevating microRNA-19a-3p and reducing cyclin-dependent kinase 2.
Title: Inhibited histone deacetylase 3 ameliorates myocardial ischemia-reperfusion injury in a rat model by elevating microRNA-19a-3p and reducing cyclin-dependent kinase 2.
miR-27a promotion resulting from silencing of HDAC3 facilitates the recovery of spinal cord injury by inhibiting PAK6 expression in rats.
Title: miR-27a promotion resulting from silencing of HDAC3 facilitates the recovery of spinal cord injury by inhibiting PAK6 expression in rats.
we show that Nr4a2 is regulated by histone deacetylase HDAC3 in the aged mouse hippocampus.
Title: HDAC3-Mediated Repression of the Nr4a Family Contributes to Age-Related Impairments in Long-Term Memory.
In healthy cerebellar granule neurons HDAC3 associates weakly with the Npas4 promoter, however, this association is robustly increased in neurons primed to die. Study found that HDAC3 also associates differentially with the Bdnfr gene promoter, with higher association in dying neurons. Overexpression of HDAC3 leads to a suppression of Npas4 and Bdnf expression in cortical neurons.
Title: The Bdnf and Npas4 genes are targets of HDAC3-mediated transcriptional repression.
findings suggest that HDAC3, and its cross talk function with GSK-3beta, may be a promising target for myocardium I/R injury.
Title: HDAC3 Mediates Cardioprotection of Remifentanil Postconditioning by Targeting GSK-3β in H9c2 Cardiomyocytes in Hypoxia/Reoxygenation Injury.
Study shows that habits are negatively regulated by histone deacetylase 3 in the dorsal striatum.
Title: Habits Are Negatively Regulated by Histone Deacetylase 3 in the Dorsal Striatum.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables GTPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables NF-kappaB binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables cyclin binding	ISO Inferred from Sequence Orthology more info
enables deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables histone H3K14 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K4 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K9 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K12 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K16 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K5 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K8 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
contributes_to histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IEA Inferred from Electronic Annotation 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 histone decrotonylase activity	ISO Inferred from Sequence Orthology more info
enables histone decrotonylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein de-2-hydroxyisobutyrylase activity	ISO Inferred from Sequence Orthology more info
enables protein de-2-hydroxyisobutyrylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein decrotonylase activity	IEA Inferred from Electronic Annotation more info
enables protein decrotonylase activity	ISO Inferred from Sequence Orthology more info
enables protein decrotonylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein lysine deacetylase activity	ISO Inferred from Sequence Orthology more info
enables protein lysine delactylase activity	ISO Inferred from Sequence Orthology more info
enables protein lysine delactylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info
enables tubulin deacetylase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-specific protease binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fluid shear stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to parathyroid hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in cornified envelope assembly	ISO Inferred from Sequence Orthology more info
involved_in epidermis development	ISO Inferred from Sequence Orthology more info
involved_in epigenetic regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of mitotic spindle orientation	ISO Inferred from Sequence Orthology more info
involved_in establishment of skin barrier	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of JNK cascade	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-1 production	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in negative regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein export from nucleus	IMP Inferred from Mutant Phenotype 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 RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of TOR signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of TOR signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein import into nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of type B pancreatic cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein deacetylation	ISO Inferred from Sequence Orthology more info
involved_in protein modification process	IDA Inferred from Direct Assay more info	PubMed
involved_in random inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein stability	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to dexamethasone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in spindle assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
is_active_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
part_of histone deacetylase complex	ISO Inferred from Sequence Orthology more info
located_in mitotic spindle	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	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: histone deacetylase 3

Names: HD3; protein deacetylase HDAC3; protein deacylase HDAC3

NP_445900.2

EC 3.5.1.98

XP_063133703.1

EC 3.5.1.98

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)

NM_053448.2 → NP_445900.2 histone deacetylase 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000018

UniProtKB/Swiss-Prot

Q6P6W3, Q99PA0

UniProtKB/TrEMBL

A0A0G2K1C8, A6J3D3

Related

ENSRNOP00000071791.3, ENSRNOT00000078667.3

Conserved Domains (1) summary

cd10005
Location:3 → 383

HDAC3; Histone deacetylase 3 (HDAC3)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086036.1 Reference GRCr8

Range

30021847..30041061 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063277633.1 → XP_063133703.1 histone deacetylase 3 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001393765.1: Suppressed sequence

Description

NM_001393765.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.