U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LOC4342137 phytoene synthase 2, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4342137, updated on 10-Oct-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC4342137
    Gene description
    phytoene synthase 2, chloroplastic
    Locus tag
    OSNPB_060729000
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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
    PSY1; OsPSY1; OsJ_22735
    Expression
    Broad expression in leaves before flowering (RPKM 78.7), roots after flowering (RPKM 39.4) 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 LOC4342137 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (31922649..31926637, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (31051987..31055921, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene protein REVEILLE 1 Neighboring gene callose synthase 3 Neighboring gene protein argonaute 1D-like Neighboring gene snakin-2 Neighboring gene uncharacterized LOC4342140

    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 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. Provitamin A accumulation in cassava (Manihot esculenta) roots driven by a single nucleotide polymorphism in a phytoene synthase gene. Welsch R, et al. Plant Cell, 2010 Oct. PMID 20889914, Free PMC Article
    2. Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Jantasuriyarat C, et al. Plant Physiol, 2005 May. PMID 15888683, Free PMC Article
    3. 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

    Pathways from PubChem

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables 15-cis-phytoene synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables farnesyltranstransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables geranylgeranyl-diphosphate geranylgeranyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carotenoid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    phytoene synthase 1, chloroplastic
    Names
    OSJNBa0069C14.4-1
    OSJNBa0069C14.4-2
    phytoene synthase-like
    NP_001389894.1
    XP_015642514.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001402965.1 → NP_001389894.1  phytoene synthase 1, chloroplastic

      Status: VALIDATED

      Source sequence(s)
      AK059535, CB678958, CI258582, CI551742, CI594433
      UniProtKB/Swiss-Prot
      Q5Z5B7, Q6KBZ6

    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
      31922649..31926637 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015787028.3 → XP_015642514.1  phytoene synthase 1, chloroplastic isoform X1

      UniProtKB/Swiss-Prot
      Q5Z5B7, Q6KBZ6
      UniProtKB/TrEMBL
      A2YH75
      Conserved Domains (1) summary
      PLN02632
      Location:77 → 414
      PLN02632; phytoene synthase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5Z5B7.1 GenPept UniProtKB/Swiss-Prot:Q5Z5B7

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials