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    RDM4 RNA-directed DNA methylation 4 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 817578, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RDM4
    Official Full Name
    RNA-directed DNA methylation 4
    Primary source
    TAIR:AT2G30280
    Locus tag
    AT2G30280
    See related
    Araport:AT2G30280
    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
    DEFECTIVE IN MERISTEM SILENCING 4; DMS4; RNA-directed DNA methylation 4; T9D9.9; T9D9_9
    Summary
    Encodes RDM4, a transcriptional regulator functioning in RNA-directed DNA methylation and plant development.
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    Genomic context

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    See RDM4 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Sequence:
    Chromosome: 2; NC_003071.7 (12909551..12912416, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene U2 small nuclear ribonucleoprotein B Neighboring gene LURP-one-like protein (DUF567) Neighboring gene VACUOLAR SORTING RECEPTOR 2 Neighboring gene Major facilitator superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. Kanno T, et al. EMBO Rep, 2010 Jan. PMID 20010803, Free PMC Article
    2. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. He XJ, et al. Genes Dev, 2009 Dec 1. PMID 19903758, Free PMC Article
    3. RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. Chan Z, et al. New Phytol, 2016 Mar. PMID 26522658, Free PMC Article
    4. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. Law JA, et al. PLoS Genet, 2011 Jul. PMID 21811420, Free PMC Article
    5. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Lin X, et al. Nature, 1999 Dec 16. PMID 10617197

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3.
      Title: RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway.
    2. Data show that SHH1(AT1G15215), RDR2, CLASSY1, and RDM4 were co-purified with NRPD1(At1g63020), the largest subunit of Pol-IV.
      Title: SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.
    3. Data suggest that DMS4 might be a regulatory factor for several RNA polymerases, thus explaining its diverse roles in the plant. [DMS4]
      Title: RNA-directed DNA methylation and plant development require an IWR1-type transcription factor.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_128581.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within developmental process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within post-embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNA-directed DNA methylation 4
    NP_180587.2
    • RNA-directed DNA methylation 4 (RDM4); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1762 (InterPro:IPR013883); Has 44351 Blast hits to 18281 proteins in 1030 species: Archae - 135; Bacteria - 13377; Metazoa - 12547; Fungi - 4712; Plants - 1881; Viruses - 609; Other Eukaryotes - 11090 (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_003071.7 Reference assembly

      Range
      12909551..12912416 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_128581.4 → NP_180587.2  RNA-directed DNA methylation 4 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_180587.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O22924, Q8GYP3
      UniProtKB/TrEMBL
      A0A654EXG6
      Conserved Domains (1) summary
      pfam08574
      Location:218 → 278
      DUF1762; Protein of unknown function (DUF1762)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8GYP3.1

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