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    SDG16 SET domain protein 16 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 828904, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SDG16
    Official Full Name
    SET domain protein 16
    Primary source
    TAIR:AT4G27910
    Locus tag
    AT4G27910
    See related
    Araport:AT4G27910
    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
    ATX4; SET domain protein 16; T13J8.20; T13J8_20
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    Genomic context

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    See SDG16 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    23
    Sequence:
    Chromosome: 4; NC_003075.7 (13893915..13900630)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene HSP20-like chaperones superfamily protein Neighboring gene CCT motif family protein Neighboring gene PYR1-like 10 Neighboring gene manganese tracking factor for mitochondrial SOD2

    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. Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. Liu Y, et al. New Phytol, 2018 Mar. PMID 29250818
    2. Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation. Shang JY, et al. J Integr Plant Biol, 2022 Dec. PMID 36354145
    3. ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development. Chen LQ, et al. Plant Physiol, 2017 Jul. PMID 28550207, Free PMC Article
    4. COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis. Shang JY, et al. Plant Cell, 2021 Oct 11. PMID 34270751, Free PMC Article
    5. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Mayer K, et al. Nature, 1999 Dec 16. PMID 10617198

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATX4 and ATX5 occupancies at AHG3 are dramatically increased under abscissic acid treatment, and are also essential for RNA polymerase II (RNAPII) occupancies.
      Title: Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses.
    2. ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome.
      Title: ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development.
    Submit: New GeneRIF Correction

    General gene information

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    NM_118929.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within epigenetic regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Ino80 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Set1C/COMPASS complex 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
    SET domain protein 16
    NP_194520.3
    • SET domain protein 16 (SDG16); FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Post-SET domain (InterPro:IPR003616), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), PWWP (InterPro:IPR000313), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: SET domain group 29 (TAIR:AT5G53430.1); Has 6853 Blast hits to 6701 proteins in 480 species: Archae - 2; Bacteria - 423; Metazoa - 3089; Fungi - 828; Plants - 1148; Viruses - 0; Other Eukaryotes - 1363 (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
      13893915..13900630
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_118929.5 → NP_194520.3  SET domain protein 16 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_194520.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q941H0, Q9SUE7
      UniProtKB/TrEMBL
      A0A178UVA2, A0A654FTK5
      Conserved Domains (5) summary
      cd05838
      Location:205 → 308
      WHSC1_related; The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as ...
      cd15495
      Location:594 → 640
      PHD_ATX3_4_5_like; PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins
      cd15663
      Location:649 → 760
      ePHD_ATX3_4_5_like; Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins
      cd10518
      Location:872 → 1023
      SET_SETD1-like; SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins
      cl22851
      Location:401 → 451
      PHD_SF; PHD finger superfamily
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SUE7.3

    Gene LinkOut

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