U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    ATX1 homologue of trithorax [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 817721, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    ATX1
    Official Full Name
    homologue of trithorax
    Primary source
    TAIR:AT2G31650
    Locus tag
    AT2G31650
    See related
    Araport:AT2G31650
    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
    homologue of trithorax; SDG27; SET DOMAIN PROTEIN 27; T9H9.17; T9H9_17
    Summary
    Encodes a homolog of trithorax, a histone-lysine N-methyltransferase. Involved in trimethylating histone H3-lysine 4. Involved in the formation, placement, and identity of flower organs. Role in regulation of homeotic genes. Functions as a receptor of phosphatidylinositol 5-phosphate. Localizes to cytoplasm, plasma membrane and nuclei, shifting to nuclei in the presence of PI5P.
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See ATX1 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    24
    Sequence:
    Chromosome: 2; NC_003071.7 (13455272..13462431, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene Receptor-like protein kinase-related family protein Neighboring gene miscRNA Neighboring gene ARM repeat superfamily protein Neighboring gene Stress responsive alpha-beta barrel domain protein

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Alvarez-Venegas R, et al. Curr Biol, 2003 Apr 15. PMID 12699618
    2. Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem. Wang X, et al. Nucleic Acids Res, 2021 Jan 11. PMID 33332564, Free PMC Article
    3. Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants. Alvarez-Venegas R, et al. Nucleic Acids Res, 2005. PMID 16157865, Free PMC Article
    4. Arabidopsis homolog of trithorax1 (ATX1) is required for cell production, patterning, and morphogenesis in root development. Napsucialy-Mendivil S, et al. J Exp Bot, 2014 Dec. PMID 25205583, Free PMC Article
    5. Evolution and pleiotropy of TRITHORAX function in Arabidopsis. Avramova Z. Int J Dev Biol, 2009. PMID 19412892

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis.
      Title: ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis.
    2. Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem.
      Title: Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem.
    3. ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1.
      Title: ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1.
    4. SEC transfers an O-GlcNAc group on Ser947 of ATX1, which resides in the SET domain, thereby activating ATX1. Taken together, these results uncover a novel post-translational O-GlcNAc modification-mediated mechanism for regulation of HKMT activity and establish the function of O-GlcNAc signaling in epigenetic processes in plants.
      Title: Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering.
    5. Our study provided genetic evidence for the first time that, copper ions necessary for ethylene receptor biogenesis and signaling are transported from ATX1 to RAN1.
      Title: Triplin, a small molecule, reveals copper ion transport in ethylene signaling from ATX1 to RAN1.
    6. review of role in gene activation
      Title: ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes?
    7. ATX1 is involved in the timing of root development, stem cell niche maintenance, and cell patterning during primary and lateral root development.
      Title: Arabidopsis homolog of trithorax1 (ATX1) is required for cell production, patterning, and morphogenesis in root development.
    8. We demonstrate that ATX1 and AtCOMPASS-like have distinct effects on PIC (transcription preinitiation complex )formation and the transition to transcription elongation. ATX1 and AtCOMPASS-like are required for efficient PIC formation.
      Title: ATX1-generated H3K4me3 is required for efficient elongation of transcription, not initiation, at ATX1-regulated genes.
    9. overexpression of ATX1 resulted in hypersensitivity to severe Cu deficiency... However, overexpression of mutated ATX1, replacing the Cu-binding motif MXCXXC with MXGXXG, abolished the hypersensitivity...
      Title: Overexpression of Arabidopsis ATX1 retards plant growth under severe copper deficiency.
    10. Loss of ATX1 function caused lower seed germination, larger stomatal apertures, increased water loss and sensitivity to dehydration stress.
      Title: The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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
    NM_179839.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 trimethyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables phosphatidylinositol-5-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in abscisic acid-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in actin cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-lysine methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in quiescent center organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of flower development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of lateral root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of root morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of stomatal closure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to water deprivation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within specification of floral organ identity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Set1C/COMPASS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm 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
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    homologue of trithorax
    NP_850170.1
    • homologue of trithorax (ATX1); CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), FY-rich, C-terminal (InterPro:IPR003889), Post-SET domain (InterPro:IPR003616), FY-rich, N-terminal (InterPro:IPR003888), Protein kinase C-like, phorbol ester/diacylglycerol binding (InterPro:IPR002219), Lamin-B receptor of TUDOR domain (InterPro:IPR019023), FY-rich, C-terminal subgroup (InterPro:IPR018516), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), PWWP (InterPro:IPR000313), FY-rich, N-terminal subgroup (InterPro:IPR018518), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: trithorax-like protein 2 (TAIR:AT1G05830.2); Has 7192 Blast hits to 6948 proteins in 474 species: Archae - 2; Bacteria - 393; Metazoa - 3480; Fungi - 840; Plants - 1251; Viruses - 0; Other Eukaryotes - 1226 (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_003071.7 Reference assembly

      Range
      13455272..13462431 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_179839.3 → NP_850170.1  homologue of trithorax [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850170.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q84WP4, Q9C5X4, Q9SIP3
      UniProtKB/TrEMBL
      A0A178VQ34, A0A5S9X3I0
      Conserved Domains (7) summary
      smart00317
      Location:898 → 1017
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd15494
      Location:611 → 657
      PHD_ATX1_2_like; PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins
      cd15662
      Location:668 → 784
      ePHD_ATX1_2_like; Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins
      pfam00855
      Location:299 → 389
      PWWP; PWWP domain
      pfam05964
      Location:448 → 497
      FYRN; F/Y-rich N-terminus
      cl02573
      Location:215 → 248
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      cl02651
      Location:508 → 597
      FYRC; F/Y rich C-terminus
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C5X4.2

    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