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HDT4 histone deacetylase-related / HD-like protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 817331, updated on 18-Sep-2024

Summary

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Official Symbol
HDT4
Official Full Name
histone deacetylase-related / HD-like protein
Primary source
TAIR:AT2G27840
Locus tag
AT2G27840
See related
Araport:AT2G27840
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
F15K20.6; F15K20_6; HD2D; HDA13; HDT04; HISTONE DEACETYLASE; HISTONE DEACETYLASE 13; histone deacetylase 2D
Summary
Belongs to the plant specific HD2 type proteins; similar to nucleolar Zea mays histone deacetylase; HD2-p39
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Genomic context

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See HDT4 in Genome Data Viewer
Location:
chromosome: 2
Exon count:
8
Sequence:
Chromosome: 2; NC_003071.7 (11861806..11863908)

Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene prephenate dehydratase 1 Neighboring gene uncharacterized protein Neighboring gene tRNA-Gly Neighboring gene UDP-D-apiose/UDP-D-xylose synthase 1

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003071.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis. Chu Y, et al. J Plant Physiol, 2024 Jun. PMID 38614048
  2. Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Lee WK, et al. Nucleic Acids Res, 2016 Jun 2. PMID 26857545, Free PMC Article
  3. Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. Yano R, et al. Plant J, 2013 Jun. PMID 23464703
  4. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. He XJ, et al. Genes Dev, 2009 Feb 1. PMID 19204117, Free PMC Article
  5. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Pandey R, et al. Nucleic Acids Res, 2002 Dec 1. PMID 12466527, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis.
    Title: AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis.
  2. TRB2 interacts with HD2-type histone deacetylase HDT4.HDT4 is associated with Arabidopsis telomeres.
    Title: Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_001336129.1
NM_001336130.1
NM_179778.1

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables histone deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within seed dormancy process IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within siRNA processing IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleolus HDA PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
histone deacetylase-related / HD-like protein
NP_001318300.1
  • HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 3 (TAIR:AT3G44750.2); Has 818 Blast hits to 747 proteins in 183 species: Archae - 0; Bacteria - 171; Metazoa - 199; Fungi - 55; Plants - 177; Viruses - 17; Other Eukaryotes - 199 (source: NCBI BLink).
NP_850109.1
  • HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 2B (TAIR:AT5G22650.2); Has 725 Blast hits to 661 proteins in 171 species: Archae - 0; Bacteria - 166; Metazoa - 184; Fungi - 55; Plants - 136; Viruses - 17; Other Eukaryotes - 167 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

  1. NC_003071.7 Reference assembly

    Range
    11861806..11863908
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_128344.4 → NP_565661.2  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_565661.2

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q0WN36, Q9M4T3, Q9ZUY5
    UniProtKB/TrEMBL
    A0A178VVQ4

  2. NM_001336129.1 → NP_001318300.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A2H1ZE29

  3. NM_001336130.1 → NP_001324791.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1P8B163

  4. NM_179778.1 → NP_850109.1  histone deacetylase-related / HD-like protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_850109.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A178VVQ4, F4IGT4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9M4T3.1

Gene LinkOut

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