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

    Gene ID: 12753, updated on 10-Jun-2017
    Official Symbol
    Clockprovided by MGI
    Official Full Name
    circadian locomotor output cycles kaputprovided by MGI
    Primary source
    MGI:MGI:99698
    See related
    Ensembl:ENSMUSG00000029238 Vega:OTTMUSG00000056120
    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
    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]
    Orthologs
    Location:
    5 C3.3; 5 40.63 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 5 NC_000071.6 (76209868..76305000, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (76641202..76733573, complement)

    Chromosome 5 - NC_000071.6Genomic Context describing neighboring genes 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 RIKEN cDNA 4930432L08 gene Neighboring gene phosducin-like 2 Neighboring gene neuromedin U

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • bHLHe8, mKIAA0334

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    E-box binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    E-box binding ISO
    Inferred from Sequence Orthology
    more info
     
    RNA polymerase II core promoter proximal region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    core promoter binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone acetyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding ISA
    Inferred from Sequence Alignment
    more info
    PubMed 
    transcription factor binding ISA
    Inferred from Sequence Alignment
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IC
    Inferred by Curator
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    transferase activity, transferring acyl groups IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    DNA damage checkpoint ISO
    Inferred from Sequence Orthology
    more info
     
    cellular response to DNA damage stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to ionizing radiation ISO
    Inferred from Sequence Orthology
    more info
     
    circadian regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    circadian rhythm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    circadian rhythm IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of glucocorticoid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of hair cycle ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of insulin secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of type B pancreatic cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to redox state ISO
    Inferred from Sequence Orthology
    more info
     
    rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    chromatoid body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromosome ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
     
    rough endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor complex ISO
    Inferred from Sequence Orthology
    more info
     
    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

    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
      ENSMUSP00000143939.1, OTTMUSP00000072919, ENSMUST00000202651.3, OTTMUST00000138780
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    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
      ENSMUSP00000144022.1, OTTMUSP00000072921, ENSMUST00000202122.1, OTTMUST00000138782
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    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
      ENSMUSP00000074656.1, OTTMUSP00000072920, ENSMUST00000075159.4, OTTMUST00000138781
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain

    RefSeqs of Annotated Genomes: Mus musculus 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 GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000071.6 Reference GRCm38.p4 C57BL/6J

      Range
      76209868..76305000 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017320648.1XP_017176137.1  circadian locomoter output cycles protein kaput isoform X1

      UniProtKB/Swiss-Prot
      O08785
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    2. XM_017320651.1XP_017176140.1  circadian locomoter output cycles protein kaput isoform X4

      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    3. XM_017320650.1XP_017176139.1  circadian locomoter output cycles protein kaput isoform X3

      UniProtKB/Swiss-Prot
      O08785
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    4. XM_017320649.1XP_017176138.1  circadian locomoter output cycles protein kaput isoform X2

      UniProtKB/TrEMBL
      A0A0J9YU61
      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:119223
      PAS_9; PAS domain
      pfam14598
      Location:274377
      PAS_11; PAS domain
    5. XM_011249402.1XP_011247704.1  circadian locomoter output cycles protein kaput isoform X5

      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_001784602.1 RNA Sequence

    2. XR_001784601.1 RNA Sequence

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