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    LOC4341389 pectate lyase [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4341389, updated on 1-Aug-2024

    Summary

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    Gene symbol
    LOC4341389
    Gene description
    pectate lyase
    Locus tag
    OSNPB_060583900
    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
    Expression
    Biased expression in flowers (RPKM 126.9) and flower buds (RPKM 74.6) See more
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    Genomic context

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    See LOC4341389 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (23679936..23681989)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (22821032..22823348)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene receptor kinase-like protein Xa21 Neighboring gene uncharacterized LOC136357056 Neighboring gene pectate lyase-like Neighboring gene uncharacterized LOC136356826

    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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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables pectate lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pectate lyase
    Names
    Os06g0583900
    P0498C03.34
    putative pectate lyase

    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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      23679936..23681989
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066311377.1 → XP_066167474.1  pectate lyase

      UniProtKB/TrEMBL
      A0A0P0WY87, B8B435, Q5VP91

    2. XM_026026010.2 → XP_025881795.1  pectate lyase

      UniProtKB/TrEMBL
      A0A0P0WY87, B8B435, Q5VP91
      Conserved Domains (2) summary
      smart00656
      Location:174 → 369
      Amb_all; Amb_all domain
      pfam04431
      Location:35 → 84
      Pec_lyase_N; Pectate lyase, N terminus
    Nucleotide Protein
    Heading Accession and Version

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