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    Clock clock circadian regulator [ Rattus norvegicus (Norway rat) ]

    Gene ID: 60447, updated on 19-Apr-2019

    Summary

    Official Symbol
    Clockprovided by RGD
    Official Full Name
    clock circadian regulatorprovided by RGD
    Primary source
    RGD:620271
    See related
    Ensembl:ENSRNOG00000002175
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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]
    Expression
    Biased expression in Kidney (RPKM 160.4), Heart (RPKM 145.8) and 9 other tissues See more
    Orthologs

    Genomic context

    See Clock in Genome Data Viewer
    Location:
    14p11
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (34418226..34502218)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 14 NC_005113.3 (34233721..34289468)

    Chromosome 14 - NC_005113.4Genomic Context describing neighboring genes Neighboring gene neuromedin U Neighboring gene phosducin-like 2 Neighboring gene uncharacterized LOC108352740 Neighboring gene transmembrane protein 165 Neighboring gene steroid 5 alpha-reductase 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Circadian rhythm, organism-specific biosystem (from KEGG)
      Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
    • Circadian rhythm, conserved biosystem (from KEGG)
      Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
    • Dopaminergic synapse, organism-specific biosystem (from KEGG)
      Dopaminergic synapse, organism-specific biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
    • Dopaminergic synapse, conserved biosystem (from KEGG)
      Dopaminergic synapse, conserved biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
    • 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 RGD

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    E-box binding IEA
    Inferred from Electronic Annotation
    more info
     
    E-box binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    E-box binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    RNA polymerase II distal enhancer sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II distal enhancer sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    RNA polymerase II distal enhancer sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    RNA polymerase II proximal promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    chromatin DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    chromatin DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone acetyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    histone acetyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    DNA damage checkpoint IEA
    Inferred from Electronic Annotation
    more info
     
    DNA damage checkpoint ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to DNA damage stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to ionizing radiation IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to ionizing radiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    circadian regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    circadian rhythm IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    circadian rhythm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    entrainment of circadian clock IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    female pregnancy IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    histone acetylation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of glucocorticoid receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of glucocorticoid receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of glucocorticoid receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of NF-kappaB transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of NF-kappaB transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of NF-kappaB transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    proteasome-mediated ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    proteasome-mediated ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein acetylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of circadian rhythm IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of circadian rhythm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of hair cycle IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of hair cycle ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of hair cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of insulin secretion IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of insulin secretion ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of insulin secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of type B pancreatic cell development IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of type B pancreatic cell development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of type B pancreatic cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    response to light stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to redox state IEA
    Inferred from Electronic Annotation
    more info
     
    response to redox state ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to redox state ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    chromatoid body IEA
    Inferred from Electronic Annotation
    more info
     
    chromatoid body ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    chromatoid body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    chromosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    perichromatin fibrils IDA
    Inferred from Direct Assay
    more info
    PubMed 
    rough endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor complex IEA
    Inferred from Electronic Annotation
    more info
     
    transcription factor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    transcription factor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    circadian locomoter output cycles protein kaput
    Names
    circadian locomoter output cycles kaput
    rCLOCK
    NP_001276761.1
    NP_068628.1
    XP_006250931.1
    XP_006250932.1
    XP_017454850.1
    XP_017454851.1
    XP_017454852.1
    XP_017454853.1

    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_001289832.1NP_001276761.1  circadian locomoter output cycles protein kaput isoform S

      See identical proteins and their annotated locations for NP_001276761.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (S) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB019259, AC116236
      UniProtKB/Swiss-Prot
      Q9WVS9
      Related
      ENSRNOP00000002981.2, ENSRNOT00000002981.3
      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: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 ...
      pfam13426
      Location:119220
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    2. NM_021856.2NP_068628.1  circadian locomoter output cycles protein kaput isoform 1

      See identical proteins and their annotated locations for NP_068628.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB019258, AC116236
      UniProtKB/Swiss-Prot
      Q9WVS9
      Related
      ENSRNOP00000074670.1, ENSRNOT00000085991.1
      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: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 ...
      pfam13426
      Location:119220
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005113.4 Reference Rnor_6.0 Primary Assembly

      Range
      34418226..34502218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017599364.1XP_017454853.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/TrEMBL
      G3V697
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
    2. XM_017599363.1XP_017454852.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/TrEMBL
      G3V697
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
    3. XM_017599361.1XP_017454850.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/TrEMBL
      G3V697
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
    4. XM_006250870.3XP_006250932.1  circadian locomoter output cycles protein kaput isoform X2

      See identical proteins and their annotated locations for XP_006250932.1

      UniProtKB/TrEMBL
      A0A0G2K8N0
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
    5. XM_017599362.1XP_017454851.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/TrEMBL
      G3V697
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
    6. XM_006250869.3XP_006250931.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/TrEMBL
      G3V697
      Related
      ENSRNOP00000002976.3, ENSRNOT00000002976.5
      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: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 ...
      pfam00989
      Location:109202
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain

    Alternate Rn_Celera

    Genomic

    1. AC_000082.1 Alternate Rn_Celera

      Range
      31247422..31293707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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