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    vacuolar protein sorting-associated protein, putative (DUF1162) [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 832543, updated on 18-Sep-2024

    Summary

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    Official Full Name
    vacuolar protein sorting-associated protein, putative (DUF1162)
    Primary source
    TAIR:AT5G24740
    Locus tag
    AT5G24740
    See related
    Araport:AT5G24740
    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
    SHBY; SHRUBBY; T4C12.10
    Summary
    Encodes a vacuolar sorting protein that interacts with the plant-specific GRAS family transcription factor SHORT-ROOT and acts in a pathway that controls root growth and radial patterning. It provides a connections between gibberellic acid, SHR and PLT signaling in the root.
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    Genomic context

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    Location:
    chromosome: 5
    Exon count:
    47
    Sequence:
    Chromosome: 5; NC_003076.8 (8469711..8489867, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Transducin/WD40 repeat-like superfamily protein Neighboring gene ncRNA Neighboring gene UDP-Glycosyltransferase superfamily protein Neighboring gene GroES-like zinc-binding dehydrogenase family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning. Koizumi K, et al. Development, 2013 Mar. PMID 23444357
    2. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Klopffleisch K, et al. Mol Syst Biol, 2011 Sep 27. PMID 21952135, Free PMC Article
    3. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Tabata S, et al. Nature, 2000 Dec 14. PMID 11130714

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SHRUBBY (At5g24740) controls root growth downstream of gibberellic acid in part through the regulation of SHORT-ROOT and SCARECROW.
      Title: Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_122383.8

    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 ground tissue pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of root meristem growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within root morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein, putative (DUF1162)
    NP_001318641.1
    • EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: calcium-dependent lipid-binding family protein (TAIR:AT1G48090.1).
    NP_568451.7
    • INVOLVED IN: protein localization; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Vacuolar protein sorting-associated protein (InterPro:IPR009543); BEST Arabidopsis thaliana protein match is: calcium-dependent lipid-binding family protein (TAIR:AT1G48090.1); Has 2219 Blast hits to 1322 proteins in 202 species: Archae - 0; Bacteria - 2; Metazoa - 1077; Fungi - 361; Plants - 231; Viruses - 0; Other Eukaryotes - 548 (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_003076.8 Reference assembly

      Range
      8469711..8489867 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001343896.1 → NP_001331614.1  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BEF0, A0A654G3T6

    2. NM_001343894.1 → NP_001318641.1  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654G3T6, F4KII0

    3. NM_001343895.1 → NP_001331612.1  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BEE1, A0A654G3T6

    4. NM_001343897.1 → NP_001331613.1  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BED7, A0A654G3T6

    5. NM_001343898.1 → NP_001331615.1  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178U996, A0A1P8BEE6

    6. NM_122383.8 → NP_568451.7  vacuolar protein sorting-associated protein, putative (DUF1162) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_568451.7

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654G3T6, F4KIH9
      Conserved Domains (6) summary
      pfam04800
      Location:3407 → 3435
      ETC_C1_NDUFA4; ETC complex I subunit conserved region
      pfam06650
      Location:2490 → 2701
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:3 → 115
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:141 → 341
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:3018 → 3185
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:550 → 784
      VPS13_mid_rpt; Repeating coiled region of VPS13
    Nucleotide Protein
    Heading Accession and Version

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