Hdac5 histone deacetylase 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hdac5provided by RGD
Official Full Name: histone deacetylase 5provided by RGD
Primary source: RGD:619980
See related: EnsemblRapid:ENSRNOG00000020905 AllianceGenome:RGD:619980
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables chromatin binding activity. Involved in several processes, including cellular response to lipopolysaccharide; response to activity; and response to cocaine. Located in cytoplasm and nucleus. Part of protein-containing complex. Biomarker of acute kidney failure; depressive disorder; middle cerebral artery infarction; and pulmonary hypertension. Orthologous to human HDAC5 (histone deacetylase 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 189.9), Brain (RPKM 149.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.1

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (87653139..87688078, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (87152978..87187921, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (90140183..90169853, complement)

Chromosome 10 - NC_086028.1 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

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

Histone deacetylase 5-induced deficiency of signal transducer and activator of transcription-3 acetylation contributes to spinal astrocytes degeneration in painful diabetic neuropathy.
Title: Histone deacetylase 5-induced deficiency of signal transducer and activator of transcription-3 acetylation contributes to spinal astrocytes degeneration in painful diabetic neuropathy.
Protein phosphatase 1 regulates reactive oxygen species-dependent degradation of histone deacetylase 5 by intermittent hypoxia.
Title: Protein phosphatase 1 regulates reactive oxygen species-dependent degradation of histone deacetylase 5 by intermittent hypoxia.
Overexpressing Histone Deacetylase 5 in Rat Dorsal Striatum Alters Reward-Guided Decision-Making and Associated Neural Encoding.
Title: Overexpressing Histone Deacetylase 5 in Rat Dorsal Striatum Alters Reward-Guided Decision-Making and Associated Neural Encoding.
Cyclic AMP represses pathological MEF2 activation by myocyte-specific hypo-phosphorylation of HDAC5.
Title: Cyclic AMP represses pathological MEF2 activation by myocyte-specific hypo-phosphorylation of HDAC5.
HDAC4 and HDAC5 form a complex with DREAM that epigenetically down-regulates NCX3 gene and its pharmacological inhibition reduces neuronal stroke damage.
Title: HDAC4 and HDAC5 form a complex with DREAM that epigenetically down-regulates NCX3 gene and its pharmacological inhibition reduces neuronal stroke damage.
Differences in the Role of HDACs 4 and 5 in the Modulation of Processes Regulating MAFbx and MuRF1 Expression during Muscle Unloading.
Title: Differences in the Role of HDACs 4 and 5 in the Modulation of Processes Regulating MAFbx and MuRF1 Expression during Muscle Unloading.
HDAC5 was increased in RSC96 Schwann cells stimulated with high glucose. HDAC5 inhibition by shRNA did not affect LC3-II/LC3-I levels under these conditions.
Title: STAT3 phosphorylation mediates high glucose-impaired cell autophagy in an HDAC1-dependent and -independent manner in Schwann cells of diabetic peripheral neuropathy.
Overall increased lactate decreased the nuclear content of HDAC5 at 6 h.
Title: A physiological drop in pH decreases mitochondrial respiration, and HDAC and Akt signaling, in L6 myocytes.
These findings establish a role of the catalytic domain of HDAC5 in the control of cardiomyocyte redox homeostasis and define TMP195 and TMP269 as a novel class of NRF2 activators that function by suppressing the enzymatic activity of an epigenetic regulator.
Title: HDAC5 catalytic activity suppresses cardiomyocyte oxidative stress and NRF2 target gene expression.
HDAC5 overexpression in dorsal striatum increased methamphetamine seeking on withdrawal day 30 but not day 2. In contrast, HDAC5 knockdown in the dorsal striatum decreased meth seeking on withdrawal day 30 but not on day 2; this manipulation also altered other HDACs (Hdac1 and Hdac4) and potential HDAC5 targets (Gnb4 and Suv39h1).
Title: Role of Dorsal Striatum Histone Deacetylase 5 in Incubation of Methamphetamine Craving.

Submit: New GeneRIF Correction See all GeneRIFs (30)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH130527 (e-PCR)
- UniSTS:213811

MARC_2891-2892:991933643:1 (e-PCR)
- UniSTS:230971

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	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
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein kinase C binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein lysine deacetylase activity	ISO Inferred from Sequence Orthology more info
contributes_to transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organismal response to stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell migration involved in sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
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 neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within osteoblast development	ISO Inferred from Sequence Orthology more info
acts_upstream_of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of skeletal muscle fiber development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of skeletal muscle fiber differentiation	ISO Inferred from Sequence Orthology more info
involved_in renal tubule morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in response to activity	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to cocaine	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to cocaine	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of RNA polymerase II transcription repressor complex	ISO Inferred from Sequence Orthology more info
located_in axonal growth cone	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone deacetylase 5

NP_445902.1

EC 3.5.1.98

XP_038942912.1

EC 3.5.1.98

XP_038942913.1

EC 3.5.1.98

XP_038942915.1

EC 3.5.1.98

XP_038942916.1

EC 3.5.1.98

XP_038942917.1

EC 3.5.1.98

XP_063126067.1

EC 3.5.1.98

XP_063126068.1

EC 3.5.1.98

XP_063126069.1

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_053450.1 → NP_445902.1 histone deacetylase 5

See identical proteins and their annotated locations for NP_445902.1

Status: PROVISIONAL

Source sequence(s)

CH473948

UniProtKB/TrEMBL

A0A8I6AAJ0, A6HJH3

Conserved Domains (2) summary

cl17011
Location:670 → 1086

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl23765
Location:68 → 155

iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

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_086028.1 Reference GRCr8

Range

87653139..87688078 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086987.2 → XP_038942915.1 histone deacetylase 5 isoform X5

UniProtKB/TrEMBL

A0A8I5XW09, A0A8I6AAJ0

Related

ENSRNOP00000077322.2, ENSRNOT00000105575.2

Conserved Domains (2) summary

cl17011
Location:646 → 1062

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl25407
Location:44 → 131

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
XM_039086988.2 → XP_038942916.1 histone deacetylase 5 isoform X4

UniProtKB/TrEMBL

A0A8I6AAJ0

Conserved Domains (2) summary

cl17011
Location:629 → 1045

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl25407
Location:27 → 114

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
XM_039086984.2 → XP_038942912.1 histone deacetylase 5 isoform X2

UniProtKB/TrEMBL

A0A8I6AAJ0, A0A8I6G4R8

Related

ENSRNOP00000080604.1, ENSRNOT00000101600.2

Conserved Domains (2) summary

cl17011
Location:671 → 1087

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl25407
Location:69 → 156

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
XM_039086985.2 → XP_038942913.1 histone deacetylase 5 isoform X3

UniProtKB/TrEMBL

A0A8I6AAJ0

Conserved Domains (2) summary

cl17011
Location:661 → 1077

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl25407
Location:59 → 146

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
XM_063269997.1 → XP_063126067.1 histone deacetylase 5 isoform X1
XM_063269998.1 → XP_063126068.1 histone deacetylase 5 isoform X4

Related

ENSRNOP00000052059.6, ENSRNOT00000055187.6
XM_039086989.2 → XP_038942917.1 histone deacetylase 5 isoform X4

UniProtKB/TrEMBL

A0A8I6AAJ0

Conserved Domains (2) summary

cl17011
Location:629 → 1045

Arginase_HDAC; Arginase-like and histone-like hydrolases

cl25407
Location:27 → 114

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)
XM_063269999.1 → XP_063126069.1 histone deacetylase 5 isoform X6