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    HD domain-containing metal-dependent phosphohydrolase family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 834025, updated on 18-Sep-2024

    Summary

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    Official Full Name
    HD domain-containing metal-dependent phosphohydrolase family protein
    Primary source
    TAIR:AT5G40270
    Locus tag
    AT5G40270
    See related
    Araport:AT5G40270
    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
    MSN9.18; MSN9_18
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    Genomic context

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    Location:
    chromosome: 5
    Exon count:
    19
    Sequence:
    Chromosome: 5; NC_003076.8 (16093035..16097245, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene RING/U-box superfamily protein Neighboring gene Nodulin MtN3 family protein Neighboring gene ncRNA Neighboring gene Prenyltransferase 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. VENOSA4, a Human dNTPase SAMHD1 Homolog, Contributes to Chloroplast Development and Abiotic Stress Tolerance. Xu D, et al. Plant Physiol, 2020 Feb. PMID 31792148, Free PMC Article
    2. The Arabidopsis phyB-9 Mutant Has a Second-Site Mutation in the VENOSA4 Gene That Alters Chloroplast Size, Photosynthetic Traits, and Leaf Growth. Yoshida Y, et al. Plant Physiol, 2018 Sep. PMID 30194261, Free PMC Article
    3. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. McWhite CD, et al. Cell, 2020 Apr 16. PMID 32191846, Free PMC Article
    4. 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. VENOSA4, a Human dNTPase SAMHD1 Homolog, Contributes to Chloroplast Development and Abiotic Stress Tolerance.
      Title: VENOSA4, a Human dNTPase SAMHD1 Homolog, Contributes to Chloroplast Development and Abiotic Stress Tolerance.
    2. Data show that loss of phytochrome B (phyB) results in longer hypocotyl than the wild type under white or red light, and this visible phenotype has been considered useful to assess phyB activity, and isolated several venosa4 (ven4) alleles that cause a reticulate phenotype.
      Title: The Arabidopsis phyB-9 Mutant Has a Second-Site Mutation in the VENOSA4 Gene That Alters Chloroplast Size, Photosynthetic Traits, and Leaf Growth.
    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_001344318.1
    NM_123391.4

    Gene Ontology Provided by TAIR

    Process Evidence Code Pubs
    acts_upstream_of_or_within chloroplast organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plastid translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    HD domain-containing metal-dependent phosphohydrolase family protein
    NP_568580.1
    • HD domain-containing metal-dependent phosphohydrolase family protein; FUNCTIONS IN: catalytic activity; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Metal-dependent phosphohydrolase, HD subdomain (InterPro:IPR006674), Metal-dependent phosphohydrolase, HD domain (InterPro:IPR003607); BEST Arabidopsis thaliana protein match is: HD domain-containing metal-dependent phosphohydrolase family protein (TAIR:AT5G40290.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (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
      16093035..16097245 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_123391.4 → NP_568580.1  HD domain-containing metal-dependent phosphohydrolase family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_568580.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9YA52, A0A654G6R4, Q9FL05
      Conserved Domains (1) summary
      COG1078
      Location:26 → 449
      YdhJ; HD superfamily phosphohydrolase [General function prediction only]

    2. NM_001344318.1 → NP_001330625.1  HD domain-containing metal-dependent phosphohydrolase family protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BBF4, A0A5S9YA52
    Nucleotide Protein
    Heading Accession and Version

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