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    Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 841886, updated on 14-Nov-2024

    Summary

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    Official Full Name
    Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein
    Primary source
    TAIR:AT1G54440
    Locus tag
    AT1G54440
    See related
    Araport:AT1G54440
    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
    F20D21.26; F20D21_26
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    Genomic context

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    Location:
    chromosome: 1
    Exon count:
    14
    Sequence:
    Chromosome: 1; NC_003070.9 (20322964..20328238)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene pseudo Neighboring gene ncRNA Neighboring gene Protein of unknown function (PD694200) Neighboring gene Calcium-binding EF-hand family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Zhang H, et al. Mol Cell, 2014 May 8. PMID 24726328, Free PMC Article
    2. AtRRP6L1, a homolog of conserved yeast Exosomal Rrp6p, plays an important role in transcriptional gene silencing in arabidopsis. Hsu YF, et al. Mol Plant, 2014 Sep. PMID 24719467
    3. Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis. Shin JH, et al. PLoS Genet, 2014 Sep. PMID 25211139, Free PMC Article
    4. Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana. Lange H, et al. Mol Cell Biol, 2008 May. PMID 18285452, Free PMC Article
    5. Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Elrouby N, et al. Proc Natl Acad Sci U S A, 2010 Oct 5. PMID 20855607, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AtRRP6L1 plays an important role in transcriptional gene silencing in Arabidopsis. [AtRRP6L1]
      Title: AtRRP6L1, a homolog of conserved yeast Exosomal Rrp6p, plays an important role in transcriptional gene silencing in arabidopsis.
    2. AtRRP6L1 functions in epigenetic regulation by helping with the retention of noncoding RNAs in normal cells.
      Title: An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis.
    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_001198293.1
    NM_001333649.1
    NM_104322.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 3'-5'-RNA exonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within RNA localization to chromatin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of siRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase V IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein
    NP_001185222.1
    • Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain; FUNCTIONS IN: 3'-5' exonuclease activity, nucleic acid binding; INVOLVED IN: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; LOCATED IN: intracellular; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), 3'-5' exonuclease (InterPro:IPR002562), Helicase/RNase D C-terminal, HRDC domain (InterPro:IPR002121); BEST Arabidopsis thaliana protein match is: Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain (TAIR:AT5G35910.1).
    NP_175846.3
    • Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain; FUNCTIONS IN: 3'-5' exonuclease activity, nucleic acid binding; INVOLVED IN: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; LOCATED IN: intracellular; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Polynucleotidyl transferase, ribonuclease H fold (InterPro:IPR012337), Helicase/RNase D C-terminal, HRDC domain (InterPro:IPR002121), 3'-5' exonuclease (InterPro:IPR002562); BEST Arabidopsis thaliana protein match is: Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain (TAIR:AT5G35910.1); Has 4852 Blast hits to 4794 proteins in 1324 species: Archae - 0; Bacteria - 2587; Metazoa - 382; Fungi - 243; Plants - 209; Viruses - 1; Other Eukaryotes - 1430 (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_003070.9 Reference assembly

      Range
      20322964..20328238
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001333647.1 → NP_001323051.1  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AVS7, A0A5S9WPP9

    2. NM_001333648.1 → NP_001323053.1  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AVX1, A0A5S9WPP9

    3. NM_104322.5 → NP_175846.3  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_175846.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WMR6, Q0WVE8, Q9SLI9
      UniProtKB/TrEMBL
      A0A178W683, A0A5S9WPP9
      Conserved Domains (2) summary
      cd06147
      Location:111 → 303
      Rrp6p_like_exo; DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins
      pfam00570
      Location:337 → 404
      HRDC; HRDC domain

    4. NM_001198293.1 → NP_001185222.1  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001185222.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9WPP9, F4HWX0
      Conserved Domains (2) summary
      cd06147
      Location:111 → 303
      Rrp6p_like_exo; DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins
      pfam00570
      Location:337 → 404
      HRDC; HRDC domain

    5. NM_001333649.1 → NP_001323052.1  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AVW8, A0A5S9WPP9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0WVE8.1

    Gene LinkOut

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