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    DEK domain-containing chromatin associated protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 828770, updated on 18-Sep-2024

    Summary

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    Official Full Name
    DEK domain-containing chromatin associated protein
    Primary source
    TAIR:AT4G26630
    Locus tag
    AT4G26630
    See related
    Araport:AT4G26630
    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
    DEK-domain containing protein 3; DEK3; T15N24.80; T15N24_80
    Summary
    Encodes a chromatin-associated protein that specifically binds histones H3 and H4 and contributes to modulation of Arabidopsis chromatin structure and function.
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    Genomic context

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    Location:
    chromosome: 4
    Exon count:
    12
    Sequence:
    Chromosome: 4; NC_003075.7 (13430405..13435770, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein Neighboring gene D6 protein kinase like 1 Neighboring gene Sucrase/ferredoxin-like family protein Neighboring gene WRKY family transcription factor family protein Neighboring gene RNA-binding (RRM/RBD/RNP motifs) family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. GSK3-mediated phosphorylation of DEK3 regulates chromatin accessibility and stress tolerance in Arabidopsis. Waidmann S, et al. FEBS J, 2022 Jan. PMID 34492159
    2. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. Waidmann S, et al. Plant Cell, 2014 Nov. PMID 25387881, Free PMC Article
    3. Interactomics of Qa-SNARE in Arabidopsis thaliana. Fujiwara M, et al. Plant Cell Physiol, 2014 Apr. PMID 24556609
    4. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Pendle AF, et al. Mol Biol Cell, 2005 Jan. PMID 15496452, Free PMC Article
    5. Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. McBride Z, et al. Mol Cell Proteomics, 2017 Nov. PMID 28887381, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GSK3-mediated phosphorylation of DEK3 regulates chromatin accessibility and stress tolerance in Arabidopsis.
      Title: GSK3-mediated phosphorylation of DEK3 regulates chromatin accessibility and stress tolerance in Arabidopsis.
    2. DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Functional levels of DEK3 are crucial for stress tolerance.
      Title: A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    NM_001036647.3
    NM_118797.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding 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 chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to salt stress IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to salt stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol HDA PubMed 
    located_in nucleolus 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

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    Preferred Names
    DEK domain-containing chromatin associated protein
    NP_001031724.1
    • DEK domain-containing chromatin associated protein; CONTAINS InterPro DOMAIN/s: DEK, C-terminal (InterPro:IPR014876); BEST Arabidopsis thaliana protein match is: DEK domain-containing chromatin associated protein (TAIR:AT5G55660.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_194393.3
    • DEK domain-containing chromatin associated protein; CONTAINS InterPro DOMAIN/s: DEK, C-terminal (InterPro:IPR014876); BEST Arabidopsis thaliana protein match is: DEK domain-containing chromatin associated protein (TAIR:AT5G55660.1); Has 293195 Blast hits to 121176 proteins in 3836 species: Archae - 1379; Bacteria - 45347; Metazoa - 110567; Fungi - 36004; Plants - 15140; Viruses - 1802; Other Eukaryotes - 82956 (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_003075.7 Reference assembly

      Range
      13430405..13435770 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_118797.5 → NP_194393.3  DEK domain-containing chromatin associated protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_194393.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DFH7, Q0WN52, Q0WSS7, Q0WW14, Q8RWF6, Q9SUA1
      UniProtKB/TrEMBL
      A0A654FT16
      Conserved Domains (3) summary
      PTZ00108
      Location:466 → 675
      PTZ00108; DNA topoisomerase 2-like protein; Provisional
      TIGR00927
      Location:20 → 281
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam08766
      Location:677 → 730
      DEK_C; DEK C terminal domain

    2. NM_001036647.3 → NP_001031724.1  DEK domain-containing chromatin associated protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031724.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DFH7, Q0WN52, Q0WSS7, Q0WW14, Q8RWF6, Q9SUA1
      UniProtKB/TrEMBL
      A0A654FT16
      Conserved Domains (3) summary
      PTZ00108
      Location:466 → 675
      PTZ00108; DNA topoisomerase 2-like protein; Provisional
      TIGR00927
      Location:20 → 281
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam08766
      Location:677 → 730
      DEK_C; DEK C terminal domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SUA1.1

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