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

Gene ID: 12753, updated on 13-Apr-2019

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
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

Genomic context

See Clock in Genome Data Viewer
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

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 FunctionsWhat's a GeneRIF?

Variation

Alleles

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

Pathways from BioSystems

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
DNA binding ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription activator activity, RNA polymerase II-specific IC
Inferred by Curator
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity ISA
Inferred from Sequence Alignment
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
E-box binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II distal enhancer sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin 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 binding ISA
Inferred from Sequence Alignment
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 by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription by RNA polymerase II 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 
protein acetylation IDA
Inferred from Direct Assay
more info
PubMed 
protein acetylation ISO
Inferred from Sequence Orthology
more info
 
regulation of circadian rhythm IMP
Inferred from Mutant Phenotype
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 
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 
cytosol ISO
Inferred from Sequence Orthology
more info
 
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
 

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

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_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, ENSMUST00000202651.3
    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: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, ENSMUST00000202122.1
    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: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, ENSMUST00000075159.4
    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

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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