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    SDG29 SET domain group 29 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 835424, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SDG29
    Official Full Name
    SET domain group 29
    Primary source
    TAIR:AT5G53430
    Locus tag
    AT5G53430
    See related
    Araport:AT5G53430
    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
    ATX5; MYN8.4; MYN8_4; SET domain group 29; SET29
    Summary
    Homology Subgroup III; Orthology Group 2 - A putative histone methyltransferase (predicted to methylate H3K4) related to the Drosophila trithorax group proteins TRX and TRR and the yeast gene SET1. A plant line expressing an RNAi construct directed against this gene has reduced agrobacterium-mediated tumor formation.
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    Genomic context

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    See SDG29 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    23
    Sequence:
    Chromosome: 5; NC_003076.8 (21677146..21684122)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene F-box associated ubiquitination effector family protein Neighboring gene CCT motif family protein Neighboring gene LOW protein: zinc finger CCCH domain protein Neighboring gene OBP3-responsive protein 1 Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    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. Trithorax-group protein ATX5 mediates the glucose response via impacting the HY1-ABI4 signaling module. Liu Y, et al. Plant Mol Biol, 2018 Dec. PMID 30406469
    4. 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
    5. 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

    See all (8) citations in PubMed

    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. The findings show that a novel ATX5-HY1-ABI4 module controls the glucose response in Arabidopsis thaliana.
      Title: Trithorax-group protein ATX5 mediates the glucose response via impacting the HY1-ABI4 signaling module.
    3. 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_124722.3

    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 DNA-mediated transformation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    located_in plasmodesma HDA PubMed 

    General protein information

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    Preferred Names
    SET domain group 29
    NP_200155.2
    • SET domain group 29 (SDG29); FUNCTIONS IN: DNA binding, zinc ion binding; INVOLVED IN: DNA mediated transformation, regulation of transcription, DNA-dependent; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 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 protein 16 (TAIR:AT4G27910.1); Has 7010 Blast hits to 6787 proteins in 464 species: Archae - 2; Bacteria - 389; Metazoa - 3222; Fungi - 817; Plants - 1208; Viruses - 0; Other Eukaryotes - 1372 (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_003076.8 Reference assembly

      Range
      21677146..21684122
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_124722.3 → NP_200155.2  SET domain group 29 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200155.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8GZ42, Q941G9, Q9LV06
      UniProtKB/TrEMBL
      A0A178URM1, A0A5S9YFY7
      Conserved Domains (5) summary
      smart00317
      Location:901 → 1024
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd15495
      Location:609 → 655
      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
      cd15517
      Location:415 → 466
      PHD_TCF19_like; PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins
      cd15663
      Location:664 → 775
      ePHD_ATX3_4_5_like; Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins
      cl02554
      Location:221 → 324
      PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8GZ42.1

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