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    LOC4329786 protein PHYLLO, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4329786, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4329786
    Gene description
    protein PHYLLO, chloroplastic
    Locus tag
    OSNPB_020581400
    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
    PHYLLO; OJ1115_A05.21
    Expression
    Ubiquitous expression in leaves before flowering (RPKM 14.1), roots after flowering (RPKM 8.8) and 6 other tissues See more
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    Genomic context

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    See LOC4329786 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (22896831..22910559)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (22415270..22429837)

    Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene photosystem II 5 kDa protein, chloroplastic Neighboring gene ASC1-like protein 1 Neighboring gene uncharacterized LOC112937814 Neighboring gene uncharacterized LOC9269114

    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
    • 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 plant locus essential for phylloquinone (vitamin K1) biosynthesis originated from a fusion of four eubacterial genes. Gross J, et al. J Biol Chem, 2006 Jun 23. PMID 16617180
    2. 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

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables thiamine pyrophosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in amino acid catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in menaquinone biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein PHYLLO, chloroplastic
    Names
    OSJNBa0016D04.2
    Os02g0581400
    Os02g0581500
    chloroplast phylloquinone biosynthesis protein
    hydrolase-like protein

    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_089036.1 Reference ASM3414082v1 Primary Assembly

      Range
      22896831..22910559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066307275.1 → XP_066163372.1  protein PHYLLO, chloroplastic isoform X1

    2. XM_066307276.1 → XP_066163373.1  protein PHYLLO, chloroplastic isoform X2

    3. XM_066307277.1 → XP_066163374.1  protein PHYLLO, chloroplastic isoform X4

    4. XM_066307278.1 → XP_066163375.1  protein PHYLLO, chloroplastic isoform X6

    5. XM_026022610.2 → XP_025878395.1  protein PHYLLO, chloroplastic isoform X3

      UniProtKB/TrEMBL
      B9F0R7
      Conserved Domains (1) summary
      cl26190
      Location:76 → 1729
      MenC; O-succinylbenzoate synthase [Coenzyme transport and metabolism]

    6. XM_015770805.2 → XP_015626291.1  protein PHYLLO, chloroplastic isoform X5

      UniProtKB/TrEMBL
      B9F0R7, F7VJK0
      Conserved Domains (6) summary
      cd07037
      Location:378 → 537
      TPP_PYR_MenD; Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins
      PLN02980
      Location:76 → 1704
      PLN02980; 2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate binding
      cd02009
      Location:765 → 943
      TPP_SHCHC_synthase; Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key ...
      cl21457
      Location:1012 → 1331
      TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...
      cl21494
      Location:1445 → 1702
      Abhydrolase; alpha/beta hydrolases
      cl22435
      Location:553 → 786
      TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain

    7. XM_026022611.2 → XP_025878396.1  protein PHYLLO, chloroplastic isoform X7

      UniProtKB/TrEMBL
      B9F0R7
      Conserved Domains (1) summary
      cl26190
      Location:76 → 1687
      MenC; O-succinylbenzoate synthase [Coenzyme transport and metabolism]

    8. XM_066307280.1 → XP_066163377.1  protein PHYLLO, chloroplastic isoform X8

    9. XM_066307281.1 → XP_066163378.1  protein PHYLLO, chloroplastic isoform X9

    10. XM_066307279.1 → XP_066163376.1  protein PHYLLO, chloroplastic isoform X8

    Nucleotide Protein
    Heading Accession and Version

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