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LOC4347428 probable polygalacturonase [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4347428, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4347428
Gene description
probable polygalacturonase
Locus tag
OSNPB_090487600
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 flowers (RPKM 8.4), flower buds (RPKM 7.9) and 6 other tissues See more
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Genomic context

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See LOC4347428 in Genome Data Viewer
Location:
chromosome: 9
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 9 NC_089043.1 (23202974..23205482, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 9 NC_029264.1 (18801157..18803767, complement)

Chromosome 9 - NC_089043.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4347426 Neighboring gene uncharacterized LOC4347427 Neighboring gene OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 4 Neighboring gene transcription factor bHLH130

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. A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. Norton GJ, et al. Genomics, 2008 Nov. PMID 18755262
  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

GeneRIFs: Gene References Into Functions

General gene information

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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

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Preferred Names
probable polygalacturonase
Names
Os09g0487600

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_089043.1 Reference ASM3414082v1 Primary Assembly

    Range
    23202974..23205482 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015795938.3 → XP_015651424.1  probable polygalacturonase

    UniProtKB/TrEMBL
    A0A0P0XNS4, B8BCV9, B9G498
    Conserved Domains (1) summary
    COG5434
    Location:21 → 308
    Pgu1; Polygalacturonase [Carbohydrate transport and metabolism]
Nucleotide Protein
Heading Accession and Version

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