U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    zinc finger CCCH domain protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 830744, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Full Name
    zinc finger CCCH domain protein
    Primary source
    TAIR:AT5G08450
    Locus tag
    AT5G08450
    See related
    Araport:AT5G08450
    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
    F8L15.180; F8L15_180; HDC1; Histone Deacetylation Complex 1; RXT3-like
    Summary
    Component of histone-deacetylase complexes. Interacts with HDA6 and HDA19 and facilitates histone deacetylation. Several salt-inducible genes are de-repressed in hdc1 mutants. Mutants are hypersensitive to ABA during germination, grow less and flower later than wildtype. HDC1-overexpressing plants display opposite phenotypes.
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    chromosome: 5
    Exon count:
    12
    Sequence:
    Chromosome: 5; NC_003076.8 (2727613..2732925, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene RNA-binding KH domain-containing protein Neighboring gene SWIB/MDM2 and Plus-3 and GYF domain-containing protein Neighboring gene uncharacterized protein Neighboring gene GDSL-like Lipase/Acylhydrolase superfamily protein Neighboring gene peroxisome 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. Perrella G, et al. New Phytol, 2024 Jan. PMID 37565540, Free PMC Article
    2. Histone deacetylase complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis. Perrella G, et al. Plant Cell, 2013 Sep. PMID 24058159, Free PMC Article
    3. Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Budhiraja R, et al. Plant Physiol, 2009 Mar. PMID 19151129, Free PMC Article
    4. Arabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. Feng C, et al. J Genet Genomics, 2021 May 20. PMID 34144927
    5. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. McWhite CD, et al. Cell, 2020 Apr 16. PMID 32191846, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings.
      Title: Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings.
    2. 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.
      Title: Histone deacetylase complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Homology

    NM_001036780.1
    NM_120930.5
    NM_180702.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within developmental vegetative growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to abscisic acid IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to salt IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Sin3-type complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    zinc finger CCCH domain protein
    NP_001031857.1
    • FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Histone deacetylation protein Rxt3 (InterPro:IPR013951); Has 34444 Blast hits to 20801 proteins in 1175 species: Archae - 64; Bacteria - 2390; Metazoa - 15568; Fungi - 3729; Plants - 1886; Viruses - 208; Other Eukaryotes - 10599 (source: NCBI BLink).
    NP_196462.2
    • CONTAINS InterPro DOMAIN/s: Histone deacetylation protein Rxt3 (InterPro:IPR013951); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_851033.1
    • CONTAINS InterPro DOMAIN/s: Histone deacetylation protein Rxt3 (InterPro:IPR013951); Has 34444 Blast hits to 20801 proteins in 1175 species: Archae - 64; Bacteria - 2390; Metazoa - 15568; Fungi - 3729; Plants - 1886; Viruses - 208; Other Eukaryotes - 10599 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      2727613..2732925 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_180702.3 → NP_851033.1  zinc finger CCCH domain protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_851033.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9Y2W4, A0A654FZG0, Q8RWV9
      Conserved Domains (2) summary
      TIGR01622
      Location:395 → 536
      SF-CC1; splicing factor, CC1-like family
      cl02694
      Location:603 → 685
      LCCL; LCCL domain

    2. NM_120930.5 → NP_196462.2  zinc finger CCCH domain protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_196462.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9Y2W4, A0A654FZG0, Q8RWV9
      Conserved Domains (2) summary
      TIGR01622
      Location:395 → 536
      SF-CC1; splicing factor, CC1-like family
      cl02694
      Location:603 → 685
      LCCL; LCCL domain

    3. NM_001036780.1 → NP_001031857.1  zinc finger CCCH domain protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031857.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9Y2W4, A0A654FZG0, Q8RWV9
      Conserved Domains (2) summary
      TIGR01622
      Location:395 → 536
      SF-CC1; splicing factor, CC1-like family
      cl02694
      Location:603 → 685
      LCCL; LCCL domain
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools