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

Gene ID: 84580, updated on 3-Jan-2019

Summary

Official Symbol
Hdac5provided by RGD
Official Full Name
histone deacetylase 5provided by RGD
Primary source
RGD:619980
See related
Ensembl:ENSRNOG00000020905
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
mouse homolog is involved in mediating nuclear receptor repression [RGD, Feb 2006]
Annotation information
Annotation category: partial on reference assembly
Expression
Biased expression in Heart (RPKM 189.9), Brain (RPKM 149.1) and 9 other tissues See more
Orthologs

Genomic context

See Hdac5 in Genome Data Viewer
Location:
10q32.1
Exon count:
24
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (90140183..90169853, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 10 NC_005109.3 (89927486..89956390, complement)

Chromosome 10 - NC_005109.4Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene glucose 6 phosphatase catalytic subunit 3 Neighboring gene E2F1-inducible gene Neighboring gene ankyrin repeat and SOCS box-containing 16

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Alcoholism, organism-specific biosystem (from KEGG)
    Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Alcoholism, conserved biosystem (from KEGG)
    Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Apelin signaling pathway, organism-specific biosystem (from KEGG)
    Apelin signaling pathway, organism-specific biosystemApelin is an endogenous peptide capable of binding the apelin receptor (APJ), which was originally described as an orphan G-protein-coupled receptor. Apelin and APJ are widely expressed in various ti...
  • Cell cycle, organism-specific biosystem (from WikiPathways)
    Cell cycle, organism-specific biosystem(From http://en.wikipedia.org/wiki/Cell_cycle) The cell cycle is the series of events that takes place in a cell leading to its division and duplication (replication). Regulation of the cell cycle in...
  • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
    Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Epstein-Barr virus infection, conserved biosystem (from KEGG)
    Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Estrogen signaling, organism-specific biosystem (from WikiPathways)
    Estrogen signaling, organism-specific biosystemEstrogen receptor refers to a group of receptors which are activated by the hormone 17β-estradiol (estrogen). Two types of estrogen receptor exist: ER which is a member of the nuclear h...
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II transcription corepressor binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
histone deacetylase activity NAS
Non-traceable Author Statement
more info
PubMed 
histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity ISO
Inferred from Sequence Orthology
more info
 
protein kinase C binding IEA
Inferred from Electronic Annotation
more info
 
protein kinase C binding ISO
Inferred from Sequence Orthology
more info
 
protein kinase binding ISO
Inferred from Sequence Orthology
more info
 
repressing transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
repressing transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
transcription corepressor activity ISO
Inferred from Sequence Orthology
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
cellular response to fluid shear stress ISO
Inferred from Sequence Orthology
more info
 
cellular response to lipopolysaccharide IEP
Inferred from Expression Pattern
more info
PubMed 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
heart development ISO
Inferred from Sequence Orthology
more info
 
histone H3 deacetylation IEA
Inferred from Electronic Annotation
more info
 
histone deacetylation ISO
Inferred from Sequence Orthology
more info
 
histone deacetylation NAS
Non-traceable Author Statement
more info
PubMed 
multicellular organismal response to stress ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell migration involved in sprouting angiogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell migration involved in sprouting angiogenesis ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
negative regulation of myotube differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of myotube differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of osteoblast differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
neuron differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
osteoblast development ISO
Inferred from Sequence Orthology
more info
 
positive regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
positive regulation of neural precursor cell proliferation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of stem cell proliferation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
protein deacetylation ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression, epigenetic IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
NOT regulation of histone H3-K9 acetylation ISO
Inferred from Sequence Orthology
more info
 
regulation of myotube differentiation ISO
Inferred from Sequence Orthology
more info
 
regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
regulation of protein binding ISO
Inferred from Sequence Orthology
more info
 
regulation of skeletal muscle fiber development ISO
Inferred from Sequence Orthology
more info
 
regulation of striated muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
renal tubule morphogenesis ISO
Inferred from Sequence Orthology
more info
 
response to activity IEP
Inferred from Expression Pattern
more info
PubMed 
response to cocaine IEP
Inferred from Expression Pattern
more info
PubMed 
response to cocaine ISO
Inferred from Sequence Orthology
more info
 
response to drug IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II transcription repressor complex ISO
Inferred from Sequence Orthology
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
histone deacetylase complex IEA
Inferred from Electronic Annotation
more info
 
nuclear body ISO
Inferred from Sequence Orthology
more info
 
nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nuclear speck ISO
Inferred from Sequence Orthology
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 5
NP_445902.1

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.

mRNA and Protein(s)

  1. NM_053450.1NP_445902.1  histone deacetylase 5

    See identical proteins and their annotated locations for NP_445902.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473948
    Related
    ENSRNOP00000052059.4, ENSRNOT00000055187.4
    Conserved Domains (2) summary
    cl17011
    Location:6701086
    Arginase_HDAC; Arginase-like and histone-like hydrolases
    cl23765
    Location:68155
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005109.4 Reference Rnor_6.0 Primary Assembly

    Range
    90140183..90169853 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000078.1 Alternate Rn_Celera

    Range
    85868901..85904236 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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