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    VCL1 vacuoleless1 (VCL1) [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 818380, updated on 18-Sep-2024

    Summary

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    Official Symbol
    VCL1
    Official Full Name
    vacuoleless1 (VCL1)
    Primary source
    TAIR:AT2G38020
    Locus tag
    AT2G38020
    See related
    Araport:AT2G38020
    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
    EMB258; MAN; MANGLED; T8P21.7; T8P21_7; VACUOLELESS 1
    Summary
    necessary for proper vacuole formation and morphogenesis in Arabidopsis
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    Genomic context

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    See VCL1 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    16
    Sequence:
    Chromosome: 2; NC_003071.7 (15909908..15914711, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene O-fucosyltransferase family protein Neighboring gene ribosome biogenesis regulatory protein (RRS1) family protein Neighboring gene chaperone protein dnaJ-like protein Neighboring gene Neutral/alkaline non-lysosomal ceramidase Neighboring gene Cysteine proteinases superfamily protein Neighboring gene tRNA-Glu

    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. VPS18-regulated vesicle trafficking controls the secretion of pectin and its modifying enzyme during pollen tube growth in Arabidopsis. Hou S, et al. Plant Cell, 2021 Sep 24. PMID 34125904, Free PMC Article
    2. The AtC-VPS protein complex is localized to the tonoplast and the prevacuolar compartment in arabidopsis. Rojo E, et al. Mol Biol Cell, 2003 Feb. PMID 12589039, Free PMC Article
    3. Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases mediate membrane fusion at the vacuole in Arabidopsis. Takemoto K, et al. Proc Natl Acad Sci U S A, 2018 Mar 6. PMID 29463724, Free PMC Article
    4. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Kim DY, et al. Plant Cell, 2013 May. PMID 23667124, Free PMC Article
    5. Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. McBride Z, et al. Mol Cell Proteomics, 2017 Nov. PMID 28887381, Free PMC Article

    See all (6) citations in PubMed

    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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    Homology

    NM_001084551.1
    NM_129359.4

    Gene Ontology Provided by TAIR

    Process Evidence Code Pubs
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within pollen tube growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vacuole organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of CORVET complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum HDA PubMed 
    is_active_in multivesicular body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plant-type vacuole membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plant-type vacuole membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuoleless1 (VCL1)
    NP_001078020.1
    • VACUOLELESS 1 (VCL1); CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), Vps16, N-terminal (InterPro:IPR006926), Vacuolar protein sorting-associated protein 16 (InterPro:IPR016534), Vps16, C-terminal (InterPro:IPR006925); Has 455 Blast hits to 406 proteins in 191 species: Archae - 0; Bacteria - 0; Metazoa - 145; Fungi - 134; Plants - 46; Viruses - 0; Other Eukaryotes - 130 (source: NCBI BLink).
    NP_565879.1
    • VACUOLELESS 1 (VCL1); CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), Vps16, N-terminal (InterPro:IPR006926), Vacuolar protein sorting-associated protein 16 (InterPro:IPR016534), Vps16, C-terminal (InterPro:IPR006925); Has 461 Blast hits to 410 proteins in 195 species: Archae - 0; Bacteria - 0; Metazoa - 145; Fungi - 140; Plants - 46; Viruses - 0; Other Eukaryotes - 130 (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
      15909908..15914711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_129359.4 → NP_565879.1  vacuoleless1 (VCL1) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_565879.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DFU5, F4IRY5, Q93VQ0
      UniProtKB/TrEMBL
      A0A178VQK7, A0A5S9X507, A0A654F191
      Conserved Domains (2) summary
      pfam04841
      Location:8 → 427
      Vps16_N; Vps16, N-terminal region
      pfam04840
      Location:528 → 835
      Vps16_C; Vps16, C-terminal region

    2. NM_001084551.1 → NP_001078020.1  vacuoleless1 (VCL1) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078020.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VQK7, A0A654F191
      Conserved Domains (3) summary
      COG2319
      Location:63 → 271
      WD40; WD40 repeat [General function prediction only]
      pfam04841
      Location:8 → 427
      Vps16_N; Vps16, N-terminal region
      pfam04840
      Location:528 → 804
      Vps16_C; Vps16, C-terminal region
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q93VQ0.1

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