U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LOC4327178 probable chlorophyll(ide) b reductase NYC1, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4327178, updated on 21-Dec-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC4327178
    Gene description
    probable chlorophyll(ide) b reductase NYC1, chloroplastic
    Locus tag
    OSNPB_010227100
    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
    NYC1; OsNYC1; OsJ_00960; P0452F10.6
    Expression
    Broad expression in leaves before flowering (RPKM 156.7), roots after flowering (RPKM 137.7) and 5 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 LOC4327178 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (7024291..7030593)

    Chromosome 1 - NC_029256.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4326746 Neighboring gene transcription factor GAMYB-like Neighboring gene proline-rich receptor-like protein kinase PERK1 Neighboring gene ras-related protein Rab7

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_029256.1 Chromosome 1 Reference IRGSP-1.0 Primary Assembly

    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
    • 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. Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and grana degradation during leaf senescence. Kusaba M, et al. Plant Cell, 2007 Apr. PMID 17416733, 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

    General gene information

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables chlorophyll(ide) b reductase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in PSII associated light-harvesting complex II catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in chlorophyll catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    probable chlorophyll(ide) b reductase NYC1, chloroplastic
    Names
    LOC_Os01g12710
    P0443E07.35
    Protein NON-YELLOW COLORING 1
    short-chain dehydrogenase/reductase NYC1
    XP_015621887.1

    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_001406306.1 → NP_001393235.1  probable chlorophyll(ide) b reductase NYC1, chloroplastic

      Status: VALIDATED

      Source sequence(s)
      CB644830, CB646722, CB668998, CI313349, CI575180, CI601644
      UniProtKB/Swiss-Prot
      A0A0P0V014, Q5N800

    RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference IRGSP-1.0 Primary Assembly

    Genomic

    1. NC_029256.1 Reference IRGSP-1.0 Primary Assembly

      Range
      7024291..7030593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015766401.2 → XP_015621887.1  probable chlorophyll(ide) b reductase NYC1, chloroplastic

      UniProtKB/Swiss-Prot
      Q5N800
      Conserved Domains (2) summary
      cd05233
      Location:173 → 404
      SDR_c; classical (c) SDRs
      pfam00106
      Location:171 → 377
      adh_short; short chain dehydrogenase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5N800.1 GenPept UniProtKB/Swiss-Prot:Q5N800

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials