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Clock clock circadian regulator [ Mus musculus (house mouse) ]

Gene ID: 12753, updated on 13-Jan-2025

Summary

Official Symbol
Clockprovided by MGI
Official Full Name
clock circadian regulatorprovided by MGI
Primary source
MGI:MGI:99698
See related
Ensembl:ENSMUSG00000029238 AllianceGenome:MGI:99698
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
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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
RS_2024_02 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)

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 STARR-seq mESC enhancer starr_13445 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

General gene information

Clone Names

  • bHLHe8, mKIAA0334

Gene Ontology Provided by MGI

Items 1 - 25 of 39
Function Evidence Code Pubs
enables DNA binding  
enables DNA binding  
enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific  
enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
enables E-box binding  
enables E-box binding PubMed 
enables E-box binding  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
enables chromatin DNA binding PubMed 
enables histone H2AK5 acetyltransferase activity  
enables histone H2AK9 acetyltransferase activity  
enables histone H2BK12 acetyltransferase activity  
enables histone H2BK5 acetyltransferase activity  
enables histone H3K122 acetyltransferase activity  
enables histone H3K14 acetyltransferase activity  
enables histone H3K18 acetyltransferase activity  
enables histone H3K23 acetyltransferase activity  
enables histone H3K27 acetyltransferase activity  
enables histone H3K36 acetyltransferase activity  
enables histone H3K4 acetyltransferase activity  
enables histone H3K56 acetyltransferase activity  
enables histone H3K9 acetyltransferase activity  
enables histone H4K12 acetyltransferase activity  
enables histone H4K16 acetyltransferase activity  
enables histone H4K5 acetyltransferase activity  
enables histone H4K8 acetyltransferase activity  
enables histone acetyltransferase activity PubMed 
enables histone acetyltransferase activity  
enables histone acetyltransferase activity  
enables protein binding PubMed 
enables protein dimerization activity  
enables sequence-specific DNA binding PubMed 
enables sequence-specific double-stranded DNA binding  
enables transcription factor binding PubMed 
Items 1 - 25 of 39
Items 1 - 25 of 40
Process Evidence Code Pubs
involved_in DNA damage checkpoint signaling  
involved_in DNA damage checkpoint signaling  
involved_in cellular response to ionizing radiation  
involved_in cellular response to ionizing radiation  
involved_in chromatin remodeling  
involved_in circadian regulation of gene expression  
involved_in circadian regulation of gene expression PubMed 
involved_in circadian regulation of gene expression  
involved_in circadian regulation of gene expression  
acts_upstream_of_or_within circadian rhythm PubMed 
involved_in circadian rhythm PubMed 
acts_upstream_of_or_within circadian rhythm PubMed 
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of glucocorticoid receptor signaling pathway PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription  
involved_in positive regulation of NF-kappaB transcription factor activity PubMed 
involved_in positive regulation of circadian rhythm PubMed 
involved_in positive regulation of circadian rhythm  
involved_in positive regulation of circadian rhythm  
involved_in positive regulation of inflammatory response PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process PubMed 
involved_in protein acetylation PubMed 
involved_in protein acetylation  
acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
involved_in regulation of DNA-templated transcription PubMed 
involved_in regulation of circadian rhythm PubMed 
involved_in regulation of hair cycle  
involved_in regulation of hair cycle  
involved_in regulation of insulin secretion PubMed 
involved_in regulation of transcription by RNA polymerase II  
involved_in regulation of type B pancreatic cell development PubMed 
involved_in response to redox state  
involved_in response to redox state  
involved_in spermatogenesis PubMed 
Items 1 - 25 of 40
Component Evidence Code Pubs
part_of CLOCK-BMAL transcription complex  
part_of CLOCK-BMAL transcription complex PubMed 
part_of CLOCK-BMAL transcription complex  
located_in chromatoid body PubMed 
located_in chromosome  
located_in chromosome  
located_in cytoplasm PubMed 
located_in cytosol  
located_in cytosol  
located_in cytosol  
located_in intracellular membrane-bounded organelle  
located_in nucleoplasm  
located_in nucleoplasm  
located_in nucleus PubMed 
located_in nucleus  
located_in perichromatin fibrils  
part_of transcription regulator complex PubMed 
part_of transcription regulator complex  

General protein information

Preferred Names
circadian locomoter output cycles protein kaput
Names
circadian locomotor output cycles 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)

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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_001289826.2NP_001276755.1  circadian locomoter output cycles protein kaput isoform 1

    See identical proteins and their annotated locations for NP_001276755.1

    Status: VALIDATED

    Source sequence(s)
    AC147239
    Consensus CDS
    CCDS19360.1
    UniProtKB/Swiss-Prot
    O08785
    UniProtKB/TrEMBL
    Q6ZQD6
    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_001305222.2NP_001292151.1  circadian locomoter output cycles protein kaput isoform 2

    See identical proteins and their annotated locations for NP_001292151.1

    Status: VALIDATED

    Source sequence(s)
    AC147239
    Consensus CDS
    CCDS84889.1
    UniProtKB/TrEMBL
    A0A0J9YU61, 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_001428477.1NP_001415406.1  circadian locomoter output cycles protein kaput isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC147239
    UniProtKB/TrEMBL
    A0A0J9YU61, Q6ZQD6
  4. NM_001428478.1NP_001415407.1  circadian locomoter output cycles protein kaput isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC147239
    UniProtKB/TrEMBL
    Q6ZQD6
  5. NM_001428479.1NP_001415408.1  circadian locomoter output cycles protein kaput isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC147239
    UniProtKB/TrEMBL
    Q6ZQD6
  6. NM_001428480.1NP_001415409.1  circadian locomoter output cycles protein kaput isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC147239
    UniProtKB/TrEMBL
    Q6ZQD6
  7. NM_001428481.1NP_001415410.1  circadian locomoter output cycles protein kaput isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC147239
  8. NM_001428482.1NP_001415411.1  circadian locomoter output cycles protein kaput isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC147239
  9. NM_007715.7NP_031741.1  circadian locomoter output cycles protein kaput isoform 1

    See identical proteins and their annotated locations for NP_031741.1

    Status: VALIDATED

    Source sequence(s)
    AC147239
    Consensus CDS
    CCDS19360.1
    UniProtKB/Swiss-Prot
    O08785
    UniProtKB/TrEMBL
    Q6ZQD6
    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

RNA

  1. NR_190371.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC147239
  2. NR_190372.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC147239
  3. NR_190373.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC147239
  4. NR_190374.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC147239

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    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

    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
    UniProtKB/TrEMBL
    Q6ZQD6
    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

    UniProtKB/TrEMBL
    Q6ZQD6
    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

    UniProtKB/Swiss-Prot
    O08785
    UniProtKB/TrEMBL
    Q6ZQD6
    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

    UniProtKB/Swiss-Prot
    O08785
    UniProtKB/TrEMBL
    Q6ZQD6
    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

    UniProtKB/TrEMBL
    Q6ZQD6
    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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