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HD1 histone deacetylase 1 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 829969, updated on 11-Oct-2018

Summary

Gene symbol
HD1
Gene description
histone deacetylase 1
Primary source
Araport:AT4G38130
Locus tag
AT4G38130
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
ARABIDOPSIS HISTONE DEACETYLASE 1; ARABIDOPSIS HISTONE DEACETYLASE 19; ATHD1; ATHDA19; ATRPD3A; F20D10.250; F20D10_250; HDA1; HDA19; HISTONE DEACETYLASE; histone deacetylase 1; HISTONE DEACETYLASE 19; HISTONE DEACETYLASE19; RPD3A
Summary
Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation.

Genomic context

See HD1 in Genome Data Viewer
Location:
chromosome: 4
Exon count:
8
Sequence:
Chromosome: 4; NC_003075.7 (17896278..17899509, complement)

Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene exportin-4 protein Neighboring gene CURVATURE THYLAKOID 1D-like protein Neighboring gene ARM repeat superfamily protein Neighboring gene RING/U-box superfamily protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene Mitochondrial transcription termination factor family protein

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

NM_001085042.1
NM_119974.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA mediated transformation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone acetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
jasmonic acid and ethylene-dependent systemic resistance IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
pathogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of stem cell population maintenance IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of multicellular organismal development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
histone deacetylase complex IPI
Inferred from Physical Interaction
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
nucleus ISM
Inferred from Sequence Model
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone deacetylase 1
NP_001078511.1
  • histone deacetylase 1 (HD1); CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 6 (TAIR:AT5G63110.1); Has 8759 Blast hits to 8549 proteins in 1452 species: Archae - 219; Bacteria - 3192; Metazoa - 1525; Fungi - 536; Plants - 478; Viruses - 0; Other Eukaryotes - 2809 (source: NCBI BLink).
NP_195526.1
  • histone deacetylase 1 (HD1); CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 6 (TAIR:AT5G63110.1); Has 8765 Blast hits to 8554 proteins in 1452 species: Archae - 219; Bacteria - 3185; Metazoa - 1529; Fungi - 558; Plants - 480; Viruses - 0; Other Eukaryotes - 2794 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

Genome Annotation

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

Reference assembly

Genomic

  1. NC_003075.7 Reference assembly

    Range
    17896278..17899509 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_119974.4NP_195526.1  histone deacetylase 1 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_195526.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    O22446
    UniProtKB/TrEMBL
    A0A178UVX8
    Conserved Domains (2) summary
    PTZ00063
    Location:16407
    PTZ00063; histone deacetylase; Provisional
    cl17011
    Location:17395
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  2. NM_001085042.1NP_001078511.1  histone deacetylase 1 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001078511.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    A8MSD0
    Conserved Domains (2) summary
    PTZ00063
    Location:16407
    PTZ00063; histone deacetylase; Provisional
    cl17011
    Location:17395
    Arginase_HDAC; Arginase-like and histone-like hydrolases
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