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    LOC9270575 cryptochrome-1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9270575, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC9270575
    Gene description
    cryptochrome-1
    Locus tag
    OSNPB_020625000
    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
    OsCRY2
    Expression
    Ubiquitous expression in roots after flowering (RPKM 18.5), leaves after flowering (RPKM 18.5) and 6 other tissues See more
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    Genomic context

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    See LOC9270575 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (25401988..25408182)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (24915231..24922099)

    Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene inositol phosphorylceramide glucuronosyltransferase 1 Neighboring gene vegetative cell wall protein gp1-like Neighboring gene pentatricopeptide repeat-containing protein At3g29230 Neighboring gene phosphoenolpyruvate carboxylase kinase 2

    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. Involvement of rice cryptochromes in de-etiolation responses and flowering. Hirose F, et al. Plant Cell Physiol, 2006 Jul. PMID 16760221
    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
    3. 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
    4. 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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables FAD binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables blue light photoreceptor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables deoxyribodipyrimidine photo-lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blue light signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in entrainment of circadian clock by photoperiod IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cryptochrome-1
    Names
    B1215B07.27-1
    B1215B07.27-2
    Os02g0625000
    cryptochrome 2
    putative cryptochrome 2

    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
      25401988..25408182
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_026022711.2 → XP_025878496.1  cryptochrome-1 isoform X1

      UniProtKB/TrEMBL
      B9F161, Q712D5, Q852P4
      Conserved Domains (1) summary
      TIGR02766
      Location:8 → 486
      crypt_chrom_pln; cryptochrome, plant family

    2. XM_015770000.3 → XP_015625486.1  cryptochrome-1 isoform X2

      UniProtKB/TrEMBL
      Q712D5
      Conserved Domains (3) summary
      TIGR02766
      Location:8 → 486
      crypt_chrom_pln; cryptochrome, plant family
      pfam00875
      Location:7 → 170
      DNA_photolyase; DNA photolyase
      pfam03441
      Location:213 → 482
      FAD_binding_7; FAD binding domain of DNA photolyase

    3. XM_015769997.3 → XP_015625483.1  cryptochrome-1 isoform X1

      UniProtKB/TrEMBL
      B9F161, Q712D5, Q852P4
      Conserved Domains (1) summary
      TIGR02766
      Location:8 → 486
      crypt_chrom_pln; cryptochrome, plant family
    Nucleotide Protein
    Heading Accession and Version

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