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    LOC4344703 protein LHY [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4344703, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4344703
    Gene description
    protein LHY
    Locus tag
    OSNPB_080157600
    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
    LHY; CCA1; COC1; OsLHY; OsCCA1; OsJ_26106
    Expression
    Ubiquitous expression in milk grains (RPKM 16.6), roots after flowering (RPKM 15.3) and 6 other tissues See more
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    Genomic context

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    See LOC4344703 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 8 NC_089042.1 (3407602..3420147)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (3360845..3373396)

    Chromosome 8 - NC_089042.1Genomic Context describing neighboring genes Neighboring gene brassinosteroid-responsive RING protein 1 Neighboring gene flavone 3'-O-methyltransferase 1-like Neighboring gene putative B3 domain-containing protein Os08g0157700 Neighboring gene uncharacterized LOC4344704

    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. The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing. Wang F, et al. Plant Cell, 2020 Oct. PMID 32796126, 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

    What's a GeneRIF?
    1. The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing.
      Title: The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing.
    Submit: New GeneRIF Correction

    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 

    General protein information

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    Preferred Names
    protein CCA1
    Names
    LOC_Os08g06110
    MYB-related transcription factor CCA1
    Os08g0157600
    P0438H08.34
    Protein CCA1
    Protein CIRCADIAN CLOCK ASSOCIATED 1
    Protein LATE ELONGATED HYPOCOTYL homolog
    circadian oscillator component
    putative LHY protein

    NCBI Reference Sequences (RefSeq)

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    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_001422441.1 → NP_001409370.1  protein CCA1

      Status: VALIDATED

      Source sequence(s)
      AK111893, AK242771, CB642160, CB675761, CF309491, CI191999
      UniProtKB/Swiss-Prot
      A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
      UniProtKB/TrEMBL
      B8BAW6

    2. NM_001422442.1 → NP_001409371.1  protein CCA1

      Status: VALIDATED

      Source sequence(s)
      AK111893, CB642160, CB675761, CF309491, CI191999
      UniProtKB/Swiss-Prot
      A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
      UniProtKB/TrEMBL
      B8BAW6

    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_089042.1 Reference ASM3414082v1 Primary Assembly

      Range
      3407602..3420147
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066312859.1 → XP_066168956.1  protein CCA1 isoform X2

    2. XM_066312854.1 → XP_066168951.1  protein CCA1 isoform X2

    3. XM_066312855.1 → XP_066168952.1  protein CCA1 isoform X2

    4. XM_066312860.1 → XP_066168957.1  protein CCA1 isoform X2

    5. XM_015794350.2 → XP_015649836.1  protein CCA1 isoform X1

      UniProtKB/TrEMBL
      B8BAW6
      Conserved Domains (1) summary
      cl21498
      Location:22 → 72
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    6. XM_066312850.1 → XP_066168947.1  protein CCA1 isoform X1

    7. XM_066312858.1 → XP_066168955.1  protein CCA1 isoform X2

    8. XM_015794349.2 → XP_015649835.1  protein CCA1 isoform X1

      UniProtKB/TrEMBL
      B8BAW6
      Conserved Domains (1) summary
      cl21498
      Location:22 → 72
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    9. XM_066312853.1 → XP_066168950.1  protein CCA1 isoform X2

    10. XM_066312847.1 → XP_066168944.1  protein CCA1 isoform X1

    11. XM_066312863.1 → XP_066168960.1  protein CCA1 isoform X2

    12. XM_066312849.1 → XP_066168946.1  protein CCA1 isoform X1

    13. XM_066312857.1 → XP_066168954.1  protein CCA1 isoform X2

    14. XM_066312846.1 → XP_066168943.1  protein CCA1 isoform X1

    15. XM_066312852.1 → XP_066168949.1  protein CCA1 isoform X2

    16. XM_066312861.1 → XP_066168958.1  protein CCA1 isoform X2

    17. XM_066312848.1 → XP_066168945.1  protein CCA1 isoform X1

    18. XM_066312856.1 → XP_066168953.1  protein CCA1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0A0P0XBU0.1 GenPept UniProtKB/Swiss-Prot:A0A0P0XBU0

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