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    SDE3 P-loop containing nucleoside triphosphate hydrolases superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 837047, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SDE3
    Official Full Name
    P-loop containing nucleoside triphosphate hydrolases superfamily protein
    Primary source
    TAIR:AT1G05460
    Locus tag
    AT1G05460
    See related
    Araport:AT1G05460
    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
    SILENCING DEFECTIVE; T25N20.11; T25N20_11
    Summary
    Encodes a protein with similarity to RNA helicases. Mutants are defective in post-transcriptional gene silencing.
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    Genomic context

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    See SDE3 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    5
    Sequence:
    Chromosome: 1; NC_003070.9 (1601148..1605034, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene C-8 sterol isomerase Neighboring gene Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein Neighboring gene DNAse I-like superfamily protein Neighboring gene chromatin remodeling 31

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions. Garcia D, et al. Mol Cell, 2012 Oct 12. PMID 22940249
    2. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. Dalmay T, et al. EMBO J, 2001 Apr 17. PMID 11296239, Free PMC Article
    3. The RING E3 Ligase KEEP ON GOING Modulates JASMONATE ZIM-DOMAIN12 Stability. Pauwels L, et al. Plant Physiol, 2015 Oct. PMID 26320228, Free PMC Article
    4. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001331549.1
    NM_100425.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 5'-3' RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNAi-mediated antiviral immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulatory ncRNA-mediated post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    P-loop containing nucleoside triphosphate hydrolases superfamily protein
    NP_172037.1
    • SILENCING DEFECTIVE (SDE3); FUNCTIONS IN: RNA helicase activity; INVOLVED IN: virus induced gene silencing; LOCATED IN: cellular_component unknown; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: Restriction endonuclease, type I, R subunit/Type III, Res subunit (InterPro:IPR006935), DNA helicase, UvrD/REP type (InterPro:IPR000212); BEST Arabidopsis thaliana protein match is: RNA helicase, putative (TAIR:AT5G47010.1); Has 8827 Blast hits to 7137 proteins in 1206 species: Archae - 219; Bacteria - 2402; Metazoa - 1784; Fungi - 1431; Plants - 666; Viruses - 219; Other Eukaryotes - 2106 (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_003070.9 Reference assembly

      Range
      1601148..1605034 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_100425.4 → NP_172037.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_172037.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8GYD9, Q94KS1, Q9LR48
      UniProtKB/TrEMBL
      A0A178WDE7, A0A654EHN2
      Conserved Domains (3) summary
      cd18038
      Location:396 → 622
      DEXXQc_Helz-like; DEXXQ/H-box helicase domain of Helz-like helicase
      pfam10427
      Location:830 → 957
      Ago_hook; Argonaute hook
      pfam13087
      Location:592 → 796
      AAA_12; AAA domain

    2. NM_001331549.1 → NP_001320371.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178WDE7, A0A1P8AMM9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8GYD9.1

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