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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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