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    LCL1 LHY/CCA1-like 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 831766, updated on 18-Sep-2024

    Summary

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    Official Symbol
    LCL1
    Official Full Name
    LHY/CCA1-like 1
    Primary source
    TAIR:AT5G02840
    Locus tag
    AT5G02840
    See related
    Araport:AT5G02840
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    F9G14.150; F9G14_150; LHY/CCA1-like 1; REVEILLE 4; RVE4
    Summary
    CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.
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    Genomic context

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    See LCL1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    10
    Sequence:
    Chromosome: 5; NC_003076.8 (648648..651979)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Spo11/DNA topoisomerase VI, subunit A protein Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein Neighboring gene ncRNA Neighboring gene hydroxyproline-rich glycoprotein family protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Lu SX, et al. Plant Physiol, 2009 Jun. PMID 19218364, Free PMC Article
    2. The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size. Gray JA, et al. Plant Physiol, 2017 Apr. PMID 28254761, Free PMC Article
    3. Accurate timekeeping is controlled by a cycling activator in Arabidopsis. Hsu PY, et al. Elife, 2013 Apr 30. PMID 23638299, Free PMC Article
    4. LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. Xie Q, et al. Plant Cell, 2014 Jul. PMID 25012192, Free PMC Article
    5. Transcriptional regulation of nitrogen-associated metabolism and growth. Gaudinier A, et al. Nature, 2018 Nov. PMID 30356219

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. REVEILLE clock genes rve3 4 5 6 8 mutants are much larger than wild-type plants, with both increased leaf area and biomass.
      Title: The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001036746.2
    NM_001342672.1
    NM_001342673.1
    NM_120362.4
    NM_180425.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of circadian rhythm IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    LHY/CCA1-like 1
    NP_001031823.1
    • LHY/CCA1-like 1 (LCL1); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT3G09600.1); Has 1341 Blast hits to 1331 proteins in 115 species: Archae - 0; Bacteria - 0; Metazoa - 91; Fungi - 0; Plants - 1058; Viruses - 0; Other Eukaryotes - 192 (source: NCBI BLink).
    NP_568108.1
    • LHY/CCA1-like 1 (LCL1); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT3G09600.2); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_850756.1
    • LHY/CCA1-like 1 (LCL1); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT3G09600.2); Has 1339 Blast hits to 1329 proteins in 114 species: Archae - 0; Bacteria - 0; Metazoa - 92; Fungi - 0; Plants - 1059; Viruses - 0; Other Eukaryotes - 188 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      648648..651979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_120362.4 → NP_568108.1  LHY/CCA1-like 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_568108.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DG39, Q6R0G4, Q94B26
      UniProtKB/TrEMBL
      A0A178U8Z5, A0A5S9Y0V6, Q9LZ01
      Conserved Domains (1) summary
      TIGR01557
      Location:46 → 96
      myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

    2. NM_001036746.2 → NP_001031823.1  LHY/CCA1-like 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031823.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2F4L8, Q9LZ01
      Conserved Domains (1) summary
      TIGR01557
      Location:46 → 96
      myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

    3. NM_001342672.1 → NP_001332134.1  LHY/CCA1-like 1 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BFY6, Q9LZ01

    4. NM_180425.2 → NP_850756.1  LHY/CCA1-like 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850756.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DG39, Q6R0G4, Q94B26
      UniProtKB/TrEMBL
      A0A178U8Z5, A0A5S9Y0V6, Q9LZ01
      Conserved Domains (1) summary
      TIGR01557
      Location:46 → 96
      myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

    5. NM_001342673.1 → NP_001332135.1  LHY/CCA1-like 1 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BFZ8, Q9LZ01
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6R0G4.1

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