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    SDE5 silencing defective 5 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820778, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SDE5
    Official Full Name
    silencing defective 5
    Primary source
    TAIR:AT3G15390
    Locus tag
    AT3G15390
    See related
    Araport:AT3G15390
    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 5
    Summary
    Encodes a novel protein that is similar to PRL1 interacting factor and is involved in virus induced silencing.
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    Genomic context

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    See SDE5 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    13
    Sequence:
    Chromosome: 3; NC_003074.8 (5196522..5200394, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene thioredoxin M-type 4 Neighboring gene expansin 12 Neighboring gene Plasma-membrane choline transporter family protein Neighboring gene HrpN-interacting protein from malus protein Neighboring gene anther 20

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA. Hernandez-Pinzon I, et al. Plant J, 2007 Apr. PMID 17397509
    2. A proteomic strategy for global analysis of plant protein complexes. Aryal UK, et al. Plant Cell, 2014 Oct. PMID 25293756, Free PMC Article
    3. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat M, et al. Nature, 2000 Dec 14. PMID 11130713

    GeneRIFs: Gene References Into Functions

    General gene information

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    NM_001202971.2
    NM_001338166.1
    NM_112407.5

    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 ta-siRNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in cytosol HDA PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    silencing defective 5
    NP_001189900.1
    • silencing defective 5 (SDE5); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: production of ta-siRNAs involved in RNA interference; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Domain of unknown function DUF1771 (InterPro:IPR013899); BEST Arabidopsis thaliana protein match is: smr (Small MutS Related) domain-containing protein (TAIR:AT5G58720.1).
    NP_188158.4
    • silencing defective 5 (SDE5); CONTAINS InterPro DOMAIN/s: Domain of unknown function DUF1771 (InterPro:IPR013899); BEST Arabidopsis thaliana protein match is: smr (Small MutS Related) domain-containing protein (TAIR:AT5G58720.1); Has 92 Blast hits to 92 proteins in 30 species: Archae - 0; Bacteria - 4; Metazoa - 16; Fungi - 4; Plants - 47; Viruses - 0; Other Eukaryotes - 21 (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_003074.8 Reference assembly

      Range
      5196522..5200394 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001202971.2 → NP_001189900.1  silencing defective 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001189900.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V8M2, A0A178V9A6, A0A384LHF2, F4IYR0
      Conserved Domains (1) summary
      pfam08590
      Location:140 → 196
      DUF1771; Domain of unknown function (DUF1771)

    2. NM_112407.5 → NP_188158.4  silencing defective 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_188158.4

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LUQ3, Q9M7X0
      UniProtKB/TrEMBL
      A0A5S9XCD0, A0A654F7F4
      Conserved Domains (1) summary
      pfam08590
      Location:331 → 390
      DUF1771; Domain of unknown function (DUF1771)

    3. NM_001338166.1 → NP_001327652.1  silencing defective 5 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V8M2, A0A1I9LSZ6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LUQ3.1

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