help  | faq  | software  | ARAPORT

Gene : HD1 A. thaliana

Gene ID  ? AT4G38130
Brief Description  histone deacetylase 1  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? 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).  Source: TAIR, Jun 30, 2015.
Curator 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.  Source: TAIR, Jun 30, 2015.
Name  ? histone deacetylase 1
  • synonyms:
  • ATHDA19,
  • HDA1,
  • HDA19,
  • RPD3A,
  • ATHD1

Locus History Displayer

Publication Counts Displayer

11 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
HDA19 may regulate gene expression involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis.[HDA19] 15749761
Data suggest that AtHD1 is a nuclear protein and possesses histone deacetylase activities responsible for global transcriptional regulation important to plant growth and development. 16699543
These results suggest that acetylation of specific histone Lys residues, regulated by GCN5, TAF1, and HD1, is required for light-regulated gene expression. 17085686
These results suggest that during germination in Arabidopsis, HDA6 and HDA19 redundantly regulate the repression of embryonic properties directly or indirectly via repression of embryo-specific gene function. 18024558
Disruption of HDA19 leads to compromised resistance, whereas its overexpression results in enhanced resistance to P. syringae. 18776063
HDA6 and HDA19 may play a redundant role in modulating seed germination and salt stress response, as well as ABA- and salt stress-induced gene expression in Arabidopsis.[HDA19] 20930557
HDA19 plays a negative role in basal defense mediated by the salicylic acid-dependent signaling pathway. 22381007
findings show that AP2 represses its target genes by physically recruiting the co-repressor TOPLESS and the histone deacetylase HDA19 23034631
HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. HDA19 and HSL1 may play a vital role during embryogenesis. 23362207
HDC1 is a ubiquitously expressed nuclear protein that interacts with at least two deacetylases (HDA6 and HDA19), promotes histone deacetylation, and attenuates derepression of genes under water stress. 24058159
SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings. 26129778


Sequence Feature Displayer

Gene Structure Displayer

J Browse Displayer

Overlapping Features Displayer

12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT4G38130 0.5kb upstream 0.5kb upstream 3732   true Chr4: 17896278-17900009
AT4G38130 0.5kb upstream 0.5kb upstream 500   false Chr4: 17899510-17900009
AT4G38130 0.5kb downstream 0.5kb downstream 3732   true Chr4: 17895778-17899509
AT4G38130 0.5kb downstream 0.5kb downstream 500   false Chr4: 17895778-17896277
AT4G38130 1.0kb upstream 1.0kb upstream 4232   true Chr4: 17896278-17900509
AT4G38130 1.0kb upstream 1.0kb upstream 1000   false Chr4: 17899510-17900509
AT4G38130 1.0kb downstream 1.0kb downstream 4232   true Chr4: 17895278-17899509
AT4G38130 1.0kb downstream 1.0kb downstream 1000   false Chr4: 17895278-17896277
AT4G38130 3.0kb upstream 3.0kb upstream 6232   true Chr4: 17896278-17902509
AT4G38130 3.0kb upstream 3.0kb upstream 3000   false Chr4: 17899510-17902509
AT4G38130 3.0kb downstream 3.0kb downstream 6232   true Chr4: 17893278-17899509
AT4G38130 3.0kb downstream 3.0kb downstream 3000   false Chr4: 17893278-17896277


Protein Displayer


Gene Ontology Displayer

0 Pathways

Data Source: KEGG

Gene --> Ontology term

Gene --> Pathways


Plant Ontology Displayer

Bar Efp Browser Displayer

Array Expression

RNA-seq Expression


Save / Export






Cytoscape Network Displayer


Homologue Displayer

Phytomine Ortholog Displayer


Alelle Table Displayer

Stock Gene Table Displayer



11 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from TIGR GO annotations assigned by TIGR Arabidopsis annotation effort 8/01/2016
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139