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    DPD1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 832752, updated on 18-Sep-2024

    Summary

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    Official Symbol
    DPD1
    Official Full Name
    Polynucleotidyl transferase, ribonuclease H-like superfamily protein
    Primary source
    TAIR:AT5G26940
    Locus tag
    AT5G26940
    See related
    Araport:AT5G26940
    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
    defective in pollen organelle DNA degradation1; F2P16.200; F2P16_200
    Summary
    Encodes a Mg2+-dependent DNA exonuclease that degrades organelle DNA during Arabidopsis pollen development.
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    Genomic context

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    See DPD1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    5
    Sequence:
    Chromosome: 5; NC_003076.8 (9480308..9482818)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Cam-binding protein 60-like G Neighboring gene GATA transcription factor 23 Neighboring gene uncharacterized protein Neighboring gene AGAMOUS-like 93 Neighboring gene Galactose oxidase/kelch repeat superfamily 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. Tissue-specific organelle DNA degradation mediated by DPD1 exonuclease. Tang LY, et al. Plant Signal Behav, 2011 Sep. PMID 21852754, Free PMC Article
    2. A conserved, Mg²+-dependent exonuclease degrades organelle DNA during Arabidopsis pollen development. Matsushima R, et al. Plant Cell, 2011 Apr. PMID 21521697, Free PMC Article
    3. Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease. Tang LY, et al. Plant J, 2012 May. PMID 22239102
    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. Data show that the defects in ribonucleotide reductase DPD2 (At2g21790) indirectly compromise the activity of DPD1 nuclease (At5g26940) in plastids, suggesting a different regulation of organellar DNA degradation in pollen.
      Title: Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease.
    2. Data discuss a possible role of organelle DNA degradation mediated by DPD1, based on a DPD1 expression profile studied using in silico analyses.
      Title: Tissue-specific organelle DNA degradation mediated by DPD1 exonuclease.
    3. DPD1 encodes a protein belonging to the exonuclease family. It has Mg2+-dependent exonuclease activity and is dual-targeted to plastids and mitochondria. [DPD1]
      Title: A conserved, Mg²+-dependent exonuclease degrades organelle DNA during Arabidopsis pollen development.
    Submit: New GeneRIF Correction

    General gene information

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    NM_122576.5
    NM_180751.2
    NM_180752.3
    NM_203113.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 3'-5' exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA catabolic process 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 
    located_in plastid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    Polynucleotidyl transferase, ribonuclease H-like superfamily protein
    NP_198046.1
    • Polynucleotidyl transferase, ribonuclease H-like superfamily protein; FUNCTIONS IN: exonuclease activity, nucleic acid binding; LOCATED IN: intracellular, chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Exonuclease (InterPro:IPR006055), Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), Exonuclease, RNase T/DNA polymerase III (InterPro:IPR013520); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink).
    NP_851082.1
    • Polynucleotidyl transferase, ribonuclease H-like superfamily protein; FUNCTIONS IN: exonuclease activity, nucleic acid binding; LOCATED IN: intracellular, chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Exonuclease (InterPro:IPR006055), Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), Exonuclease, RNase T/DNA polymerase III (InterPro:IPR013520); Has 3712 Blast hits to 3712 proteins in 1305 species: Archae - 2; Bacteria - 3079; Metazoa - 40; Fungi - 0; Plants - 53; Viruses - 4; Other Eukaryotes - 534 (source: NCBI BLink).
    NP_851083.1
    • Polynucleotidyl transferase, ribonuclease H-like superfamily protein; FUNCTIONS IN: exonuclease activity, nucleic acid binding; LOCATED IN: intracellular, chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Exonuclease (InterPro:IPR006055), Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), Exonuclease, RNase T/DNA polymerase III (InterPro:IPR013520); Has 3689 Blast hits to 3689 proteins in 1295 species: Archae - 2; Bacteria - 3056; Metazoa - 40; Fungi - 0; Plants - 53; Viruses - 4; Other Eukaryotes - 534 (source: NCBI BLink).
    NP_974842.1
    • Polynucleotidyl transferase, ribonuclease H-like superfamily protein; FUNCTIONS IN: exonuclease activity, nucleic acid binding; LOCATED IN: intracellular, chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Exonuclease (InterPro:IPR006055), Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), Exonuclease, RNase T/DNA polymerase III (InterPro:IPR013520); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (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
      9480308..9482818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_203113.3 → NP_974842.1  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_974842.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q681U1, Q682U6, Q8LBK8
      UniProtKB/TrEMBL
      A0A5S9Y826, A0A654G4R5
      Conserved Domains (1) summary
      smart00479
      Location:110 → 290
      EXOIII; exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases

    2. NM_122576.5 → NP_198046.1  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_198046.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q681U1, Q682U6, Q8LBK8
      UniProtKB/TrEMBL
      A0A5S9Y826, A0A654G4R5
      Conserved Domains (1) summary
      smart00479
      Location:110 → 290
      EXOIII; exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases

    3. NM_180752.3 → NP_851083.1  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_851083.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q681U1, Q682U6, Q8LBK8
      UniProtKB/TrEMBL
      A0A5S9Y826, A0A654G4R5
      Conserved Domains (1) summary
      smart00479
      Location:110 → 290
      EXOIII; exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases

    4. NM_180751.2 → NP_851082.1  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_851082.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q681U1, Q682U6, Q8LBK8
      UniProtKB/TrEMBL
      A0A5S9Y826, A0A654G4R5
      Conserved Domains (1) summary
      smart00479
      Location:110 → 290
      EXOIII; exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q682U6.1

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