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LOC4347165 probable polygalacturonase [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4347165, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4347165
Gene description
probable polygalacturonase
Locus tag
OSNPB_090439400
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
OJ1344_B01.15
Expression
Ubiquitous expression in roots before flowering (RPKM 33.4), roots after flowering (RPKM 31.7) and 6 other tissues See more
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Genomic context

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See LOC4347165 in Genome Data Viewer
Location:
chromosome: 9
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 9 NC_089043.1 (20662818..20667161)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 9 NC_029264.1 (16282690..16287188)

Chromosome 9 - NC_089043.1Genomic Context describing neighboring genes Neighboring gene probable glucomannan 4-beta-mannosyltransferase 4 Neighboring gene protein TIFY 10c-like Neighboring gene photosystem I chlorophyll a/b-binding protein 6, chloroplastic Neighboring gene exocyst complex component EXO70A1

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

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
Os09g0439400
P0556H01.31
putative polygalacturonase

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
    20662818..20667161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015756872.3 → XP_015612358.1  probable polygalacturonase isoform X1

    UniProtKB/TrEMBL
    B8BCE9, Q0J1H7, Q69P92
    Conserved Domains (1) summary
    COG5434
    Location:51 → 428
    Pgu1; Polygalacturonase [Carbohydrate transport and metabolism]

  2. XM_026020306.2 → XP_025876091.1  probable polygalacturonase isoform X2

    UniProtKB/TrEMBL
    B8BCE9
    Conserved Domains (1) summary
    cl26318
    Location:51 → 399
    Glyco_hydro_28; Glycosyl hydrolases family 28
Nucleotide Protein
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