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    CLOCK clock circadian regulator [ Gallus gallus (chicken) ]

    Gene ID: 373991, updated on 14-Feb-2019

    Summary

    Symbol
    CLOCKprovided by CGNC
    Full Name
    clock circadian regulatorprovided by CGNC
    Primary source
    CGNC:10328
    See related
    Ensembl:ENSGALG00000013793
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Gallus gallus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus
    Summary
    The protein encoded by this gene plays a central role in the regulation of circadian rhythms. The protein encodes a transcription factor of the basic helix-loop-helix (bHLH) family and contains DNA binding histone acetyltransferase activity. The encoded protein forms a heterodimer with ARNTL (BMAL1) that binds E-box enhancer elements upstream of Period (PER1, PER2, PER3) and Cryptochrome (CRY1, CRY2) genes and activates transcription of these genes. PER and CRY proteins heterodimerize and repress their own transcription by interacting in a feedback loop with CLOCK/ARNTL complexes. Polymorphisms in this gene may be associated with behavioral changes, obesity, and metabolic syndrome. Two transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2014]
    Orthologs

    Genomic context

    See CLOCK in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    104 current GRCg6a (GCF_000002315.5) 4 NC_006091.5 (65058739..65118686)
    103 previous assembly Gallus_gallus-5.0 (GCF_000002315.4) 4 NC_006091.4 (65471431..65531356)
    102 previous assembly Gallus_gallus-4.0 (GCF_000002315.3) 4 NC_006091.3 (64695956..64718266)

    Chromosome 4 - NC_006091.5Genomic Context describing neighboring genes Neighboring gene translation initiation factor IF-2-like Neighboring gene neuromedin U Neighboring gene phosducin like 2 Neighboring gene transmembrane protein 165 Neighboring gene steroid 5 alpha-reductase 3 Neighboring gene kinase insert domain receptor

    Genomic regions, transcripts, and products

    Bibliography

    Pathways from BioSystems

    • Herpes simplex infection, organism-specific biosystem (from KEGG)
      Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Herpes simplex infection, conserved biosystem (from KEGG)
      Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II distal enhancer sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cellular response to DNA damage stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    circadian regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    response to redox state ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription factor complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    circadian locomoter output cycles protein kaput
    Names
    clock homolog
    transcription regulation factor
    NP_001276763.1
    NP_989505.2
    XP_015140878.1
    XP_015140879.1
    XP_015140880.1
    XP_015140882.1
    XP_015140884.1
    XP_015140885.1
    XP_015140886.1
    XP_025005225.1

    NCBI Reference Sequences (RefSeq)

    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_001289834.2NP_001276763.1  circadian locomoter output cycles protein kaput isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AADN05000017, AF132531, BU435154
      UniProtKB/Swiss-Prot
      Q8QGQ6
      Related
      ENSGALP00000036747.4, ENSGALT00000037539.5
      Conserved Domains (3) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:275373
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam14598
      Location:274377
      PAS_11; PAS domain
    2. NM_204174.4NP_989505.2  circadian locomoter output cycles protein kaput isoform 1

      See identical proteins and their annotated locations for NP_989505.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AADN05000017, AF132531, BU435154
      UniProtKB/Swiss-Prot
      Q8QGQ6
      Related
      ENSGALP00000036748.2, ENSGALT00000037540.4
      Conserved Domains (3) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:275373
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam14598
      Location:274377
      PAS_11; PAS domain

    RefSeqs of Annotated Genomes: Gallus gallus Annotation Release 104 details...Open this link in a new tab

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

    Reference GRCg6a Primary Assembly

    Genomic

    1. NC_006091.5 Reference GRCg6a Primary Assembly

      Range
      65058739..65118686
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015285392.2XP_015140878.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (4) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:118216
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      cl02165
      Location:570674
      CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
      cl25986
      Location:274377
      PAS_3; PAS fold
    2. XM_015285399.2XP_015140885.1  circadian locomoter output cycles protein kaput isoform X3

      Conserved Domains (3) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:275373
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam14598
      Location:274377
      PAS_11; PAS domain
    3. XM_025149457.1XP_025005225.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (4) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:118216
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      cl02165
      Location:570674
      CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
      cl25986
      Location:274377
      PAS_3; PAS fold
    4. XM_015285398.2XP_015140884.1  circadian locomoter output cycles protein kaput isoform X2

      UniProtKB/TrEMBL
      F1NKI9
      Conserved Domains (3) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:275373
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam14598
      Location:274377
      PAS_11; PAS domain
    5. XM_015285394.2XP_015140880.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (4) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:118216
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      cl02165
      Location:570674
      CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
      cl25986
      Location:274377
      PAS_3; PAS fold
    6. XM_015285393.2XP_015140879.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (4) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:118216
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      cl02165
      Location:570674
      CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
      cl25986
      Location:274377
      PAS_3; PAS fold
    7. XM_015285396.2XP_015140882.1  circadian locomoter output cycles protein kaput isoform X1

      Related
      ENSGALP00000071463.1, ENSGALT00000099728.1
      Conserved Domains (4) summary
      cd00083
      Location:3286
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:118216
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      cl02165
      Location:570674
      CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
      cl25986
      Location:274377
      PAS_3; PAS fold
    8. XM_015285400.2XP_015140886.1  circadian locomoter output cycles protein kaput isoform X4

      Conserved Domains (2) summary
      cd00130
      Location:150248
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam14598
      Location:149252
      PAS_11; PAS domain

    RNA

    1. XR_003074708.1 RNA Sequence

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