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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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