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    LOC4340090 probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340090, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4340090
    Gene description
    probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
    Locus tag
    OSNPB_060142900
    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
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    Genomic context

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    See LOC4340090 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (2408576..2414174, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (2251017..2256638, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene putative cytochrome c oxidase subunit 5b-like Neighboring gene protein arginine N-methyltransferase PRMT10-like Neighboring gene superoxide dismutase [Fe] 2, chloroplastic-like Neighboring gene palmitoyl-acyl carrier protein thioesterase, chloroplastic

    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 1-deoxy-D-xylulose-5-phosphate synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in terpenoid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
    Names
    1-deoxy-D-xylulose 5-phosphate synthase 1-like
    Os06g0142900
    P0535G04.30-1
    P0535G04.30-2
    putative 1-deoxy-D-xylulose 5-phosphate synthase 1

    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
      2408576..2414174 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015787006.3 → XP_015642492.1  probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic isoform X2

      UniProtKB/TrEMBL
      B7F7X3, Q5VSB8
      Conserved Domains (4) summary
      cd07033
      Location:297 → 450
      TPP_PYR_DXS_TK_like; Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins
      COG1154
      Location:14 → 604
      Dxs; Deoxyxylulose-5-phosphate synthase [Coenzyme transport and metabolism, Lipid transport and metabolism]
      pfam02780
      Location:469 → 592
      Transketolase_C; Transketolase, C-terminal domain
      pfam13292
      Location:9 → 253
      DXP_synthase_N; 1-deoxy-D-xylulose-5-phosphate synthase

    2. XM_015787005.3 → XP_015642491.1  probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic isoform X2

      UniProtKB/TrEMBL
      B7F7X3, Q5VSB8
      Conserved Domains (4) summary
      cd07033
      Location:297 → 450
      TPP_PYR_DXS_TK_like; Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins
      COG1154
      Location:14 → 604
      Dxs; Deoxyxylulose-5-phosphate synthase [Coenzyme transport and metabolism, Lipid transport and metabolism]
      pfam02780
      Location:469 → 592
      Transketolase_C; Transketolase, C-terminal domain
      pfam13292
      Location:9 → 253
      DXP_synthase_N; 1-deoxy-D-xylulose-5-phosphate synthase

    3. XM_015787004.3 → XP_015642490.1  probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic isoform X1

      Conserved Domains (1) summary
      PLN02582
      Location:54 → 721
      PLN02582; 1-deoxy-D-xylulose-5-phosphate synthase
    Nucleotide Protein
    Heading Accession and Version

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