Hdac6 histone deacetylase 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Hdac6provided by RGD
Full Name: histone deacetylase 6provided by RGD
Primary source: RGD:619981
See related: Ensembl:ENSRNOG00000048738 AllianceGenome:RGD:619981
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 deacetylase activity. Involved in several processes, including generation of neurons; regulation of protein modification process; and response to glucocorticoid. Located in axon and centrosome. Used to study polycystic kidney disease and polycystic liver disease. Biomarker of hypertension and polycystic liver disease. Human ortholog(s) of this gene implicated in chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia. Orthologous to human HDAC6 (histone deacetylase 6). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: Xq12

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (17222538..17244373)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (14550645..14572445)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (15396185..15417486)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Selective HDAC6 inhibition protects against blood-brain barrier dysfunction after intracerebral hemorrhage.
Title: Selective HDAC6 inhibition protects against blood-brain barrier dysfunction after intracerebral hemorrhage.
Histone deacetylase 6 suppression of renal tubular epithelial cell promotes interstitial mineral deposition via alpha-tubulin acetylation.
Title: Histone deacetylase 6 suppression of renal tubular epithelial cell promotes interstitial mineral deposition via alpha-tubulin acetylation.
Knockdown of HDAC6 alleviates ventricular remodeling in experimental dilated cardiomyopathy via inhibition of NLRP3 inflammasome activation and promotion of cardiomyocyte autophagy.
Title: Knockdown of HDAC6 alleviates ventricular remodeling in experimental dilated cardiomyopathy via inhibition of NLRP3 inflammasome activation and promotion of cardiomyocyte autophagy.
Butyrate-containing structured lipids act on HDAC4, HDAC6, DNA damage and telomerase activity during promotion of experimental hepatocarcinogenesis.
Title: Butyrate-containing structured lipids act on HDAC4, HDAC6, DNA damage and telomerase activity during promotion of experimental hepatocarcinogenesis.
Overexpression of HDAC6, but not HDAC3 and HDAC4 in the penumbra after photothrombotic stroke in the rat cerebral cortex and the neuroprotective effects of alpha-phenyl tropolone, HPOB, and sodium valproate.
Title: Overexpression of HDAC6, but not HDAC3 and HDAC4 in the penumbra after photothrombotic stroke in the rat cerebral cortex and the neuroprotective effects of α-phenyl tropolone, HPOB, and sodium valproate.
Histone deacetylase-6 modulates amyloid beta-induced cognitive dysfunction rats by regulating PTK2B.
Title: Histone deacetylase-6 modulates amyloid beta-induced cognitive dysfunction rats by regulating PTK2B.
Cortactin deacetylation by HDAC6 and SIRT2 regulates neuronal migration and dendrite morphogenesis during cerebral cortex development.
Title: Cortactin deacetylation by HDAC6 and SIRT2 regulates neuronal migration and dendrite morphogenesis during cerebral cortex development.
Sepsis-induced muscle wasting may be regulated by glucocorticoid-dependent hyperacetylation caused by increased p300 and reduced HDAC6 expression and activity.
Title: Sepsis and glucocorticoids upregulate p300 and downregulate HDAC6 expression and activity in skeletal muscle.
catalytic activity of HDAC in cardiac tissue in hypertensive heart disease; HDAC6 was increased in stressed myocardium but not in a model of physiologic hypertrophy; activity induced by extracellular stimuli in cultured cardiomyocytes and fibroblasts
Title: Cardiac HDAC6 catalytic activity is induced in response to chronic hypertension.
We demonstrated that MeCP2 may negatively control the acetylation of alpha-tubulin through HDAC6 in cardiac fibroblast proliferation and fibrosis
Title: Epigenetic factors MeCP2 and HDAC6 control α-tubulin acetylation in cardiac fibroblast proliferation and fibrosis.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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 Hsp90 protein 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
NOT enables acetylspermidine deacetylase activity	ISO Inferred from Sequence Orthology more info
enables alpha-tubulin binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables beta-tubulin binding	ISO Inferred from Sequence Orthology more info
enables deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables dynein complex binding	ISO Inferred from Sequence Orthology 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 microtubule binding	ISO Inferred from Sequence Orthology more info
enables misfolded protein binding	ISO Inferred from Sequence Orthology more info
enables polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein lysine deacetylase activity	ISO Inferred from Sequence Orthology more info
enables tau protein binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info
enables tubulin deacetylase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within actin filament organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within aggresome assembly	ISO Inferred from Sequence Orthology more info
involved_in aggresome assembly	ISO Inferred from Sequence Orthology more info
involved_in axonal transport of mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonal transport of mitochondrion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to misfolded protein	ISO Inferred from Sequence Orthology more info
involved_in cellular response to parathyroid hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to topologically incorrect protein	ISO Inferred from Sequence Orthology more info
involved_in cilium disassembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collateral sprouting	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendritic spine morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within erythrocyte enucleation	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	ISO Inferred from Sequence Orthology more info
involved_in lysosome localization	ISO Inferred from Sequence Orthology more info
involved_in mitochondrion localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of aggrephagy	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of aggrephagy	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of axon extension involved in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of microtubule depolymerization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein acetylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein-containing complex disassembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of proteolysis	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization	ISO Inferred from Sequence Orthology more info
NOT involved_in polyamine deacetylation	ISO Inferred from Sequence Orthology more info
involved_in polyubiquitinated misfolded protein transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cellular response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cholangiocyte proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dendrite morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of epithelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mitophagy in response to mitochondrial depolarization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-serine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic transmission, glutamatergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of tubulin deacetylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein quality control for misfolded or incompletely synthesized proteins	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein-containing complex disassembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of establishment of protein localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in regulation of microtubule cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in response to amphetamine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to corticosterone	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to dexamethasone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to growth factor	ISO Inferred from Sequence Orthology more info
involved_in response to immobilization stress	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to misfolded protein	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
NOT involved_in spermidine deacetylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in caveola	ISO Inferred from Sequence Orthology more info
located_in cell leading edge	ISO Inferred from Sequence Orthology more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	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 dendrite	ISO Inferred from Sequence Orthology more info
part_of histone deacetylase complex	ISO Inferred from Sequence Orthology more info
located_in inclusion body	ISO Inferred from Sequence Orthology more info
located_in microtubule	ISO Inferred from Sequence Orthology more info
part_of microtubule associated complex	ISO Inferred from Sequence Orthology more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	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	ISO Inferred from Sequence Orthology more info
located_in perikaryon	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone deacetylase 6

NP_001413957.1

EC 3.5.1.98

NP_001413958.1

EC 3.5.1.98

XP_006256821.1

EC 3.5.1.98

XP_038956396.1

EC 3.5.1.98

XP_063135794.1

EC 3.5.1.98

XP_063135796.1

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_001427028.1 → NP_001413957.1 histone deacetylase 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021
NM_001427029.1 → NP_001413958.1 histone deacetylase 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

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_086039.1 Reference GRCr8

Range

17222538..17244373

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039100468.2 → XP_038956396.1 histone deacetylase 6 isoform X1

UniProtKB/TrEMBL

A0A1L5YJQ7

Conserved Domains (3) summary

cd10003
Location:484 → 834

HDAC6-dom2; Histone deacetylase 6, domain 2

pfam02148
Location:1070 → 1132

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

cl17011
Location:98 → 434

Arginase_HDAC; Arginase-like and histone-like hydrolases
XM_006256759.5 → XP_006256821.1 histone deacetylase 6 isoform X1

See identical proteins and their annotated locations for XP_006256821.1

UniProtKB/TrEMBL

A0A1L5YJQ7

Related

ENSRNOP00000063689.3

Conserved Domains (3) summary

cd10003
Location:484 → 834

HDAC6-dom2; Histone deacetylase 6, domain 2

pfam02148
Location:1070 → 1132

zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

cl17011
Location:98 → 434

Arginase_HDAC; Arginase-like and histone-like hydrolases
XM_063279726.1 → XP_063135796.1 histone deacetylase 6 isoform X2
XM_063279724.1 → XP_063135794.1 histone deacetylase 6 isoform X1