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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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