Hdac4 histone deacetylase 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hdac4provided by RGD
Official Full Name: histone deacetylase 4provided by RGD
Primary source: RGD:619979
See related: Ensembl:ENSRNOG00000020372 AllianceGenome:RGD:619979
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 promoter-specific chromatin binding activity. Involved in several processes, including cellular response to mechanical stimulus; cellular response to parathyroid hormone stimulus; and positive regulation of lamellipodium assembly. Located in cytosol; nucleus; and sarcomere. Part of protein-containing complex. Biomarker of middle cerebral artery infarction. Human ortholog(s) of this gene implicated in ataxia telangiectasia; chromosome 2q37 deletion syndrome; eating disorder; and retinal degeneration. Orthologous to human HDAC4 (histone deacetylase 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 60.6), Thymus (RPKM 53.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q36

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (99950972..100200994, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (92503467..92750164, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (99052945..99299715, complement)

Chromosome 9 - NC_086027.1 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
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?

Urine-derived stem cells-extracellular vesicles ameliorate diabetic osteoporosis through HDAC4/HIF-1alpha/VEGFA axis by delivering microRNA-26a-5p.
Title: Urine-derived stem cells-extracellular vesicles ameliorate diabetic osteoporosis through HDAC4/HIF-1α/VEGFA axis by delivering microRNA-26a-5p.
Role of Glucocorticoid Signaling and HDAC4 Activation in Diaphragm and Gastrocnemius Proteolytic Activity in Septic Rats.
Title: Role of Glucocorticoid Signaling and HDAC4 Activation in Diaphragm and Gastrocnemius Proteolytic Activity in Septic Rats.
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.
HDAC4 induces the development of asthma by increasing Slug-upregulated CXCL12 expression through KLF5 deacetylation.
Title: HDAC4 induces the development of asthma by increasing Slug-upregulated CXCL12 expression through KLF5 deacetylation.
Beneficial Effects of a Mixture of Algae and Extra Virgin Olive Oils on the Age-Induced Alterations of Rodent Skeletal Muscle: Role of HDAC-4.
Title: Beneficial Effects of a Mixture of Algae and Extra Virgin Olive Oils on the Age-Induced Alterations of Rodent Skeletal Muscle: Role of HDAC-4.
Leucine Supplementation Decreases HDAC4 Expression and Nuclear Localization in Skeletal Muscle Fiber of Rats Submitted to Hindlimb Immobilization.
Title: Leucine Supplementation Decreases HDAC4 Expression and Nuclear Localization in Skeletal Muscle Fiber of Rats Submitted to Hindlimb Immobilization.
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.
miR-873-3p targets HDAC4 to stimulate matrix metalloproteinase-13 expression upon parathyroid hormone exposure in rat osteoblasts.
Title: miR-873-3p targets HDAC4 to stimulate matrix metalloproteinase-13 expression upon parathyroid hormone exposure in rat osteoblasts.
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.
The data indicated that a single bout of preconditioning exercise prior to hindlimb unloading may exert a protective effect in disuse muscle atrophy in old rats and that these effects may be partially mediated by the HDAC4/Gadd45alpha axis.
Title: Exercise preconditioning attenuates hind limb unloading-induced gastrocnemius muscle atrophy possibly via the HDAC4/Gadd45 axis in old rats.

Submit: New GeneRIF Correction See all GeneRIFs (37)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BG377748 (e-PCR)
- UniSTS:244522

UniSTS:234174 (e-PCR)
- UniSTS:234174

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor 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
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables SUMO transferase activity	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
contributes_to histone binding	ISO Inferred from Sequence Orthology more info
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 identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables potassium ion binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell population proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology 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 cellular response to tumor necrosis factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	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 population proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of glycolytic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of glycolytic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of miRNA transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of miRNA transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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 negative regulation of transcription by competitive promoter binding	ISO Inferred from Sequence Orthology more info
involved_in osteoblast development	IEA Inferred from Electronic Annotation more info
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-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lamellipodium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of male mating behavior	IMP Inferred from Mutant Phenotype 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 sumoylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of reactive oxygen species biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of cardiac muscle contraction by calcium ion signaling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cardiac muscle contraction by calcium ion signaling	ISO Inferred from Sequence Orthology more info
involved_in regulation of skeletal muscle fiber development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of skeletal muscle fiber development	ISO Inferred from Sequence Orthology more info
involved_in regulation of skeletal muscle fiber differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of skeletal muscle fiber differentiation	ISO Inferred from Sequence Orthology more info
involved_in response to alcohol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to denervation involved in regulation of muscle adaptation	IEA Inferred from Electronic Annotation more info
involved_in response to denervation involved in regulation of muscle adaptation	ISO Inferred from Sequence Orthology more info
involved_in response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in skeletal system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info
involved_in type I interferon-mediated signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in A band	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
located_in actomyosin	IEA Inferred from Electronic Annotation more info
located_in actomyosin	ISO Inferred from Sequence Orthology more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of histone deacetylase complex	IEA Inferred from Electronic Annotation more info
part_of histone deacetylase complex	ISO Inferred from Sequence Orthology more info
located_in neuromuscular junction	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	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 nucleoplasm	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
located_in sarcomere	IDA Inferred from Direct Assay more info	PubMed
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone deacetylase 4

Names: HD4

NP_445901.1

EC 3.5.1.98

XP_006245500.2

EC 3.5.1.98

XP_006245505.1

EC 3.5.1.98

XP_008765501.1

EC 3.5.1.98

XP_017452030.3

EC 3.5.1.98

XP_038939859.1

EC 3.5.1.98

XP_063123529.1

EC 3.5.1.98

XP_063123530.1

EC 3.5.1.98

XP_063123531.1

EC 3.5.1.98

XP_063123532.1

EC 3.5.1.98

XP_063123533.1

EC 3.5.1.98

XP_063123534.1

EC 3.5.1.98

XP_063123535.1

EC 3.5.1.98

XP_063123536.1

EC 3.5.1.98

XP_063123538.1

EC 3.5.1.98

XP_063123539.1

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_053449.1 → NP_445901.1 histone deacetylase 4

See identical proteins and their annotated locations for NP_445901.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q99P99

UniProtKB/TrEMBL

A0A8I5ZP14

Related

ENSRNOP00000079742.1, ENSRNOT00000107908.1

Conserved Domains (2) summary

cd10162
Location:90 → 151

ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase

cd10006
Location:647 → 1050

HDAC4; Histone deacetylase 4

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_086027.1 Reference GRCr8

Range

99950972..100200994 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063267463.1 → XP_063123533.1 histone deacetylase 4 isoform X6

UniProtKB/TrEMBL

A0A8L2UKG8
XM_063267465.1 → XP_063123535.1 histone deacetylase 4 isoform X8
XM_006245443.4 → XP_006245505.1 histone deacetylase 4 isoform X6

UniProtKB/TrEMBL

A0A8I5ZP14, A0A8L2UKG8

Related

ENSRNOP00000027622.6

Conserved Domains (2) summary

cd10162
Location:90 → 151

ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase

cd10006
Location:652 → 1060

HDAC4; Histone deacetylase 4
XM_063267466.1 → XP_063123536.1 histone deacetylase 4 isoform X8
XM_006245438.2 → XP_006245500.2 histone deacetylase 4 isoform X6

UniProtKB/TrEMBL

A0A8I5ZP14, A0A8L2UKG8

Conserved Domains (2) summary

cd10162
Location:90 → 151

ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase

cd10006
Location:652 → 1060

HDAC4; Histone deacetylase 4
XM_063267468.1 → XP_063123538.1 histone deacetylase 4 isoform X9

UniProtKB/Swiss-Prot

Q99P99
XM_063267464.1 → XP_063123534.1 histone deacetylase 4 isoform X7
XM_063267469.1 → XP_063123539.1 histone deacetylase 4 isoform X10
XM_008767279.4 → XP_008765501.1 histone deacetylase 4 isoform X11

UniProtKB/TrEMBL

A6JQT7

Conserved Domains (2) summary

cd10162
Location:63 → 124

ClassIIa_HDAC4_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase

cd10006
Location:625 → 1033

HDAC4; Histone deacetylase 4
XM_063267459.1 → XP_063123529.1 histone deacetylase 4 isoform X2
XM_063267461.1 → XP_063123531.1 histone deacetylase 4 isoform X4
XM_017596541.3 → XP_017452030.3 histone deacetylase 4 isoform X1
XM_063267462.1 → XP_063123532.1 histone deacetylase 4 isoform X5
XM_063267460.1 → XP_063123530.1 histone deacetylase 4 isoform X3
XM_039083931.2 → XP_038939859.1 histone deacetylase 4 isoform X12

UniProtKB/TrEMBL

A6JQT9

Conserved Domains (1) summary

cd10006
Location:481 → 889

HDAC4; Histone deacetylase 4