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    LOC4345438 phosphoglucan phosphatase LSF1, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4345438, updated on 13-Jul-2024

    Summary

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    Gene symbol
    LOC4345438
    Gene description
    phosphoglucan phosphatase LSF1, chloroplastic
    Locus tag
    OSNPB_080379300
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Also known as
    RNG2
    Expression
    Ubiquitous expression in leaves before flowering (RPKM 38.2), roots after flowering (RPKM 29.9) and 6 other tissues See more
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    Genomic context

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    See LOC4345438 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 8 NC_089042.1 (17987462..17991497)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (17851900..17856030)

    Chromosome 8 - NC_089042.1Genomic Context describing neighboring genes Neighboring gene pre-mRNA-processing factor 39-2 Neighboring gene probable phospholipid-transporting ATPase 8 Neighboring gene 2-methylene-furan-3-one reductase Neighboring gene uncharacterized LOC136351350 Neighboring gene BURP domain-containing protein 12-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome profiling of various organs at different developmental stages in rice Transcriptome profiling of various organs at different developmental stages in rice
    • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
    • BioProject: PRJNA243371
    • Publication: PMID 26387578
    • Analysis date: Fri Dec 15 20:02:59 2017

    Bibliography

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    Related articles in PubMed

    1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764
    2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables carbohydrate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein tyrosine/serine/threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in starch catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in starch grain IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phosphoglucan phosphatase LSF1, chloroplastic
    Names
    OSJNBb0011E04.124
    Os08g0379300
    P0709D11.14

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

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

    Reference ASM3414082v1 Primary Assembly

    Genomic

    1. NC_089042.1 Reference ASM3414082v1 Primary Assembly

      Range
      17987462..17991497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015795275.3 → XP_015650761.1  phosphoglucan phosphatase LSF1, chloroplastic isoform X1

      UniProtKB/TrEMBL
      A2YUR2, Q0J611, Q7EYM9
      Conserved Domains (3) summary
      cd02859
      Location:456 → 537
      E_set_AMPKbeta_like_N; N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit
      cd14526
      Location:289 → 435
      DSP_laforin-like; dual specificity phosphatase domain of laforin and similar domains
      cl21460
      Location:95 → 121
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    2. XM_026019959.2 → XP_025875744.1  phosphoglucan phosphatase LSF1, chloroplastic isoform X2

      Conserved Domains (2) summary
      cd02859
      Location:314 → 395
      E_set_AMPKbeta_like_N; N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit
      cl21483
      Location:150 → 284
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    3. XM_066303291.1 → XP_066159388.1  phosphoglucan phosphatase LSF1, chloroplastic isoform X2

    Nucleotide Protein
    Heading Accession and Version

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