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

Gene ID: 4344703, updated on 1-Aug-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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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 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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

  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

    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

  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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/TrEMBL
    B8BAW6

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

    UniProtKB/Swiss-Prot
    A0A0P0XBU0, B9FZ59, Q0J7W9, Q6ZD85
    UniProtKB/TrEMBL
    B8BAW6
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A0A0P0XBU0.1 GenPept UniProtKB/Swiss-Prot:A0A0P0XBU0

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