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    LOW protein: PPR containing-like protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 821840, updated on 18-Sep-2024

    Summary

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    Official Full Name
    LOW protein: PPR containing-like protein
    Primary source
    TAIR:AT3G22690
    Locus tag
    AT3G22690
    See related
    Araport:AT3G22690
    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
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    Genomic context

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    Location:
    chromosome: 3
    Exon count:
    2
    Sequence:
    Chromosome: 3; NC_003074.8 (8021229..8024594, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene rRNA processing protein-like protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene RNA-DIRECTED DNA METHYLATION 1 Neighboring gene F-box and associated interaction domains-containing protein Neighboring gene F-box family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Natural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana. van Rooijen R, et al. Nat Commun, 2017 Nov 10. PMID 29123092, Free PMC Article
    2. The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth. Zhou W, et al. Plant J, 2009 Apr. PMID 19054358
    3. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. Dal Bosco C, et al. J Biol Chem, 2004 Jan 9. PMID 14576160
    4. Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis. Wang S, et al. PLoS Genet, 2016 May. PMID 27138552, Free PMC Article
    5. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat M, et al. Nature, 2000 Dec 14. PMID 11130713

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. YS1 (Yellow Seedlings 1) is required for correct plastid gene expression during early chloroplast development. [YS1]
      Title: The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth.
    Submit: New GeneRIF Correction

    General gene information

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    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photosystem I assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within photosystem II assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of chlorophyll biosynthetic process IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to high light intensity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within thylakoid membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    LOW protein: PPR containing-like protein
    NP_001189950.1
    • INVOLVED IN: photosystem II assembly, regulation of chlorophyll biosynthetic process, photosystem I assembly, thylakoid membrane organization, RNA modification; LOCATED IN: chloroplast; EXPRESSED IN: 13 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal differentiation and expansion stage, E expanded cotyledon stage, D bilateral stage; CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT2G29760.1).
    NP_188908.2
    • CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1685 (InterPro:IPR012881), Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT2G29760.1); Has 49784 Blast hits to 14716 proteins in 280 species: Archae - 2; Bacteria - 10; Metazoa - 107; Fungi - 167; Plants - 48594; Viruses - 0; Other Eukaryotes - 904 (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_003074.8 Reference assembly

      Range
      8021229..8024594 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001203021.2 → NP_001189950.1  LOW protein: PPR containing-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001189950.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LUJ2
      UniProtKB/TrEMBL
      A0A5S9XEN7, A0A654F9R0
      Conserved Domains (3) summary
      PLN03077
      Location:100 → 840
      PLN03077; Protein ECB2; Provisional
      PLN03081
      Location:49 → 147
      PLN03081; pentatricopeptide (PPR) repeat-containing protein; Provisional
      sd00004
      Location:101 → 128
      PPR; PPR repeat [structural motif]

    2. NM_001338595.1 → NP_001326902.1  LOW protein: PPR containing-like protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LQP2, A0A5S9XEN7

    3. NM_113168.2 → NP_188908.2  LOW protein: PPR containing-like protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_188908.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XEN7, F4J1L5
      Conserved Domains (7) summary
      TIGR00756
      Location:100 → 133
      PPR; pentatricopeptide repeat domain (PPR motif)
      sd00004
      Location:101 → 128
      PPR; PPR repeat [structural motif]
      pfam01535
      Location:201 → 229
      PPR; PPR repeat
      pfam07939
      Location:843 → 894
      DUF1685; Protein of unknown function (DUF1685)
      pfam13041
      Location:401 → 444
      PPR_2; PPR repeat family
      pfam14432
      Location:708 → 832
      DYW_deaminase; DYW family of nucleic acid deaminases
      cl03252
      Location:601 → 634
      PPR; PPR repeat
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LUJ2.1

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