U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LOC4339868 probable polygalacturonase [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4339868, updated on 12-Jul-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC4339868
    Gene description
    probable polygalacturonase
    Locus tag
    OSNPB_060106800
    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
    Broad expression in flower buds (RPKM 19.1), roots before flowering (RPKM 12.8) and 4 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC4339868 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (595052..597454, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (439059..441546, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4339866 Neighboring gene uncharacterized LOC107281230 Neighboring gene uncharacterized LOC4339867 Neighboring gene uncharacterized LOC4339869 Neighboring gene uncharacterized LOC4339870

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: 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

    Go to the top of the pageHelp

    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

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables polygalacturonase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    probable polygalacturonase
    Names
    Os06g0106800
    P0644B06.40
    putative polygalacturonase

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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
      595052..597454 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788293.3 → XP_015643779.1  probable polygalacturonase

      UniProtKB/TrEMBL
      A0A0P0WS09, A2Y8D0, A3B7L5, Q5VS63
      Conserved Domains (2) summary
      pfam12708
      Location:59 → 310
      Pectate_lyase_3; Pectate lyase superfamily protein
      cl19188
      Location:63 → 442
      PL-6; Polysaccharide Lyase Family 6
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials