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    Clock circadian locomotor output cycles kaput [ Mus musculus (house mouse) ]

    Gene ID: 12753, updated on 27-Jul-2021

    Summary

    Official Symbol
    Clockprovided by MGI
    Official Full Name
    circadian locomotor output cycles kaputprovided by MGI
    Primary source
    MGI:MGI:99698
    See related
    Ensembl:ENSMUSG00000029238
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    KAT13; bHLHe; KAT13D; 5330400M04Rik
    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 the same protein have been found for this gene. [provided by RefSeq, Jan 2014]
    Expression
    Ubiquitous expression in subcutaneous fat pad adult (RPKM 6.4), cerebellum adult (RPKM 6.2) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Clock in Genome Data Viewer
    Location:
    5 C3.3; 5 40.63 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (76357715..76452675, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (76209868..76305603, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (76641202..76733573, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene steroid 5 alpha-reductase 3 Neighboring gene predicted gene, 33938 Neighboring gene transmembrane protein 165 Neighboring gene adenomatosis polyposis coli, pseudogene 1 Neighboring gene ubiquitin-conjugating enzyme E2N, pseudogene 1 Neighboring gene predicted gene 7467 Neighboring gene phosducin-like 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • bHLHe8, mKIAA0334

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IC
    Inferred by Curator
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISA
    Inferred from Sequence Alignment
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables E-box binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables E-box binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables E-box binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables acyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone acetyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables histone acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone acetyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription factor binding ISA
    Inferred from Sequence Alignment
    more info
    PubMed 
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in DNA damage checkpoint signaling ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cellular response to DNA damage stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to ionizing radiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in circadian regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in circadian regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within circadian rhythm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within circadian rhythm IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of glucocorticoid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein acetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein acetylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of hair cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of insulin secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of type B pancreatic cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to redox state ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of CLOCK-BMAL transcription complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in chromatoid body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
     
    located_in rough endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    circadian locomoter output cycles protein kaput
    NP_001276755.1
    NP_001292151.1
    NP_031741.1
    XP_011247704.1
    XP_017176137.1
    XP_017176138.1
    XP_017176139.1
    XP_017176140.1
    XP_030109961.1
    XP_030109962.1
    XP_030109963.1
    XP_036020664.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001289826.1NP_001276755.1  circadian locomoter output cycles protein kaput isoform 1

      See identical proteins and their annotated locations for NP_001276755.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AC147239, AK030352, AK040337, BX526669
      Consensus CDS
      CCDS19360.1
      UniProtKB/Swiss-Prot
      O08785
      UniProtKB/TrEMBL
      Q8C9W6
      Related
      ENSMUSP00000143939.2, ENSMUST00000202651.4
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    2. NM_001305222.1NP_001292151.1  circadian locomoter output cycles protein kaput isoform 2

      See identical proteins and their annotated locations for NP_001292151.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice acceptor site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK129118, AK136367, BX526669
      Consensus CDS
      CCDS84889.1
      UniProtKB/TrEMBL
      A0A0J9YU61, Q3UWG6, Q6ZQD6
      Related
      ENSMUSP00000144022.2, ENSMUST00000202122.2
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    3. NM_007715.6NP_031741.1  circadian locomoter output cycles protein kaput isoform 1

      See identical proteins and their annotated locations for NP_031741.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AC147239, AK030352, AK040337, BX526669
      Consensus CDS
      CCDS19360.1
      UniProtKB/Swiss-Prot
      O08785
      UniProtKB/TrEMBL
      Q8C9W6
      Related
      ENSMUSP00000074656.2, ENSMUST00000075159.5
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      76357715..76452675 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017320649.3XP_017176138.1  circadian locomoter output cycles protein kaput isoform X2

      UniProtKB/TrEMBL
      A0A0J9YU61
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    2. XM_017320651.3XP_017176140.1  circadian locomoter output cycles protein kaput isoform X4

      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    3. XM_017320650.3XP_017176139.1  circadian locomoter output cycles protein kaput isoform X3

      UniProtKB/Swiss-Prot
      O08785
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    4. XM_017320648.3XP_017176137.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/Swiss-Prot
      O08785
      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    5. XM_036164771.1XP_036020664.1  circadian locomoter output cycles protein kaput isoform X5

      Conserved Domains (2) summary
      cd00130
      Location:391
      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
    6. XM_030254101.2XP_030109961.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    7. XM_030254103.2XP_030109963.1  circadian locomoter output cycles protein kaput isoform X3

      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    8. XM_030254102.2XP_030109962.1  circadian locomoter output cycles protein kaput isoform X1

      Conserved Domains (3) summary
      pfam00989
      Location:109177
      PAS; PAS fold
      pfam14598
      Location:274377
      PAS_11; PAS domain
      cd19734
      Location:2989
      bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
    9. XM_011249402.3XP_011247704.1  circadian locomoter output cycles protein kaput isoform X5

      Conserved Domains (2) summary
      cd00130
      Location:391
      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_001784602.3 RNA Sequence

    2. XR_001784601.3 RNA Sequence

    3. XR_004942433.1 RNA Sequence

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