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    VCR varicose-like protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820529, updated on 18-Sep-2024

    Summary

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    Official Symbol
    VCR
    Official Full Name
    varicose-like protein
    Primary source
    TAIR:AT3G13290
    Locus tag
    AT3G13290
    See related
    Araport:AT3G13290
    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
    varicose-related
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    Genomic context

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    See VCR in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    12
    Sequence:
    Chromosome: 3; NC_003074.8 (4297282..4303634)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene Putative endonuclease or glycosyl hydrolase Neighboring gene Transducin/WD40 repeat-like superfamily protein Neighboring gene Chaperone DnaJ-domain superfamily protein

    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. Components of the Arabidopsis mRNA decapping complex are required for early seedling development. Goeres DC, et al. Plant Cell, 2007 May. PMID 17513503, Free PMC Article
    2. A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern. Schiaffini M, et al. Plant Physiol, 2022 Feb 4. PMID 34791434, Free PMC Article
    3. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Xu J, et al. Plant Cell, 2006 Dec. PMID 17158604, Free PMC Article
    4. Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. Kim TW, et al. Plant Cell, 2023 Mar 15. PMID 36660928, Free PMC Article
    5. 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    • At3g13290_Arabidopsis_lyrata_ssp._lyrata_CAN11 (e-PCR)
    • At3g13290_Arabidopsis_lyrata_ssp._petraea_GER1 (e-PCR)
    NM_112174.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in deadenylation-independent decapping of nuclear-transcribed mRNA ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mRNA catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in P-body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    varicose-like protein
    NP_187937.2
    • varicose-related (VCR); FUNCTIONS IN: nucleotide binding; LOCATED IN: cellular_component unknown; EXPRESSED IN: male gametophyte, cultured cell, pollen tube; EXPRESSED DURING: L mature pollen stage, M germinated pollen stage; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), WD40 repeat 2 (InterPro:IPR019782), WD40-repeat-containing domain (InterPro:IPR017986), WD40 repeat (InterPro:IPR001680), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: Transducin/WD40 repeat-like superfamily protein (TAIR:AT3G13300.1); Has 1082 Blast hits to 861 proteins in 259 species: Archae - 6; Bacteria - 246; Metazoa - 313; Fungi - 205; Plants - 136; Viruses - 0; Other Eukaryotes - 176 (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
      4297282..4303634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_112174.4 → NP_187937.2  varicose-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_187937.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LTT9
      UniProtKB/TrEMBL
      A0A5S9XD39
      Conserved Domains (3) summary
      pfam16529
      Location:170 → 478
      Ge1_WD40; WD40 region of Ge1, enhancer of mRNA-decapping protein
      sd00039
      Location:224 → 265
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:213 → 440
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LTT9.1

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