U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    RPD1 Ubiquitin carboxyl-terminal hydrolase family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 829487, updated on 18-Sep-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    RPD1
    Official Full Name
    Ubiquitin carboxyl-terminal hydrolase family protein
    Primary source
    TAIR:AT4G33495
    Locus tag
    AT4G33495
    See related
    Araport:AT4G33495
    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
    ROOT PRIMORDIUM DEFECTIVE 1
    Summary
    A member of the RPD gene family - there are13 annotated genes and one EST encoding RPD1-like proteins in Arabidopsis. Shows no homology to any protein of known function. Abundant expression found in the shoot apex and the root. rpd1 mutant is a temperature-sensitive mutant isolated on the basis of the impairment in adventitious roots formation in hypocotyl region. Also, disruption of the RPD1 gene by a T-DNA insertion caused embryogenesis arrest at the globular to transition stages. This phenotype is consistent with the hypothesized function of RPD1 in the maintenance of active cell proliferation.
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See RPD1 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    2
    Sequence:
    Chromosome: 4; NC_003075.7 (16110712..16112604, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene histone deacetylase 14 Neighboring gene BTB/POZ domain protein TNFAIP protein Neighboring gene Eukaryotic aspartyl protease family protein Neighboring gene Protein phosphatase 2C family protein Neighboring gene 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase Neighboring gene P-type ATP-ase 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene. Wang C, et al. Nucleic Acids Res, 2024 May 8. PMID 38364869, Free PMC Article
    2. Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis. Edris R, et al. Plant Cell Physiol, 2024 May 14. PMID 37702436
    3. A novel plant-specific family gene, ROOT PRIMORDIUM DEFECTIVE 1, is required for the maintenance of active cell proliferation. Konishi M, et al. Plant Physiol, 2006 Feb. PMID 16407439, Free PMC Article
    4. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Mayer K, et al. Nature, 1999 Dec 16. PMID 10617198

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene.
      Title: Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene.
    2. Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis.
      Title: Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis.
    3. RPD1 encodes a member of a novel protein family specific to the plant kingdom and functions in the maintenance of active cell proliferation. [RPD1]
      Title: A novel plant-specific family gene, ROOT PRIMORDIUM DEFECTIVE 1, is required for the maintenance of active cell proliferation.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help
    NM_148393.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within lateral root morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    Ubiquitin carboxyl-terminal hydrolase family protein
    NP_680759.1
    • ROOT PRIMORDIUM DEFECTIVE 1 (RPD1); CONTAINS InterPro DOMAIN/s: RNA recognition domain, plant (InterPro:IPR021099); BEST Arabidopsis thaliana protein match is: Ubiquitin carboxyl-terminal hydrolase family protein (TAIR:AT5G45790.2); Has 413 Blast hits to 409 proteins in 15 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 413; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003075.7 Reference assembly

      Range
      16110712..16112604 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_148393.3 → NP_680759.1  Ubiquitin carboxyl-terminal hydrolase family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_680759.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q689D6, Q8GWI6
      UniProtKB/TrEMBL
      A0A178V474, A0A5S9Y0G9, A0A654FVN3
      Conserved Domains (1) summary
      pfam11955
      Location:47 → 387
      PORR; Plant organelle RNA recognition domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q689D6.1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Molecular Biology Databases
    Research Materials
    Tools