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

Summary

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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: human all
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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)

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clock knockout in inhibitory neurons reduces predisposition to epilepsy and influences anxiety-like behaviors in mice.
Title: Clock knockout in inhibitory neurons reduces predisposition to epilepsy and influences anxiety-like behaviors in mice.
Sleep deprivation reduced LPS-induced IgG2b production by up-regulating BMAL1 and CLOCK expression.
Title: Sleep deprivation reduced LPS-induced IgG2b production by up-regulating BMAL1 and CLOCK expression.
Clock gene Per3 deficiency disrupts circadian alterations of gut microbiota in mice.
Title: Clock gene Per3 deficiency disrupts circadian alterations of gut microbiota in mice.
CPEB4-CLOCK crosstalk during temporal lobe epilepsy.
Title: CPEB4-CLOCK crosstalk during temporal lobe epilepsy.
miR34a-5p impedes CLOCK expression in chronodisruptive C57BL/6J mice and potentiates pro-atherogenic manifestations.
Title: miR34a-5p impedes CLOCK expression in chronodisruptive C57BL/6J mice and potentiates pro-atherogenic manifestations.
The Clock gene regulates kainic acid-induced seizures through inhibiting ferroptosis in mice.
Title: The Clock gene regulates kainic acid-induced seizures through inhibiting ferroptosis in mice.
Circadian Regulator CLOCK Drives Immunosuppression in Glioblastoma.
Title: Circadian Regulator CLOCK Drives Immunosuppression in Glioblastoma.
Mitochondrial autophagy and cell survival is regulated by the circadian Clock gene in cardiac myocytes during ischemic stress.
Title: Mitochondrial autophagy and cell survival is regulated by the circadian Clock gene in cardiac myocytes during ischemic stress.
Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids.
Title: Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids.
Susceptibility rhythm to bacterial endotoxin in myeloid clock-knockout mice.
Title: Susceptibility rhythm to bacterial endotoxin in myeloid clock-knockout mice.

Submit: New GeneRIF Correction See all GeneRIFs (221)

Variation

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Alleles

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

Gene trapped (1)
Targeted (3) 1 citation
Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BI276488 (e-PCR)
- UniSTS:249867

RH134641 (e-PCR)
- UniSTS:217920

G54151 (e-PCR)
- UniSTS:109388

Clock (e-PCR), detects polymorphism
- UniSTS:506803

Clock (e-PCR), detects polymorphism
- UniSTS:547570

AF000998 (e-PCR)
- UniSTS:179187

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
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
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	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 DNA damage response	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
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
involved_in 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 DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of glucocorticoid receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
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 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
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
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
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
part_of CLOCK-BMAL transcription complex	IPI Inferred from Physical Interaction more info	PubMed
part_of CLOCK-BMAL transcription complex	ISO Inferred from Sequence Orthology more info
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 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
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

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Preferred Names: circadian locomoter output cycles protein kaput

Names: circadian locomotor output cycles kaput

NP_001276755.1

EC 2.3.1.48

NP_001292151.1

EC 2.3.1.48

NP_031741.1

EC 2.3.1.48

XP_011247704.1

EC 2.3.1.48

XP_017176137.1

EC 2.3.1.48

XP_017176138.1

EC 2.3.1.48

XP_017176139.1

EC 2.3.1.48

XP_017176140.1

EC 2.3.1.48

XP_030109961.1

EC 2.3.1.48

XP_030109962.1

EC 2.3.1.48

XP_030109963.1

EC 2.3.1.48

XP_036020664.1

EC 2.3.1.48

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)

NM_001289826.2 → NP_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:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
NM_001305222.2 → NP_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:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
NM_001428477.1 → NP_001415406.1 circadian locomoter output cycles protein kaput isoform 2

Status: VALIDATED

Source sequence(s)

AC147239

UniProtKB/TrEMBL

A0A0J9YU61
NM_001428478.1 → NP_001415407.1 circadian locomoter output cycles protein kaput isoform 3

Status: VALIDATED

Source sequence(s)

AC147239
NM_001428479.1 → NP_001415408.1 circadian locomoter output cycles protein kaput isoform 3

Status: VALIDATED

Source sequence(s)

AC147239
NM_001428480.1 → NP_001415409.1 circadian locomoter output cycles protein kaput isoform 4

Status: VALIDATED

Source sequence(s)

AC147239
NM_001428481.1 → NP_001415410.1 circadian locomoter output cycles protein kaput isoform 5

Status: VALIDATED

Source sequence(s)

AC147239
NM_001428482.1 → NP_001415411.1 circadian locomoter output cycles protein kaput isoform 6

Status: VALIDATED

Source sequence(s)

AC147239
NM_007715.7 → NP_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:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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

NR_190371.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC147239
NR_190372.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC147239
NR_190373.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC147239
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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

76357715..76452675 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_017320651.3 → XP_017176140.1 circadian locomoter output cycles protein kaput isoform X4

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_017320650.3 → XP_017176139.1 circadian locomoter output cycles protein kaput isoform X3

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_017320648.3 → XP_017176137.1 circadian locomoter output cycles protein kaput isoform X1

UniProtKB/Swiss-Prot

O08785

UniProtKB/TrEMBL

Q6ZQD6

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_036164771.1 → XP_036020664.1 circadian locomoter output cycles protein kaput isoform X5

UniProtKB/TrEMBL

Q6ZQD6

Conserved Domains (2) summary

cd00130
Location:3 → 91

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:149 → 252

PAS_11; PAS domain
XM_030254101.2 → XP_030109961.1 circadian locomoter output cycles protein kaput isoform X1

UniProtKB/Swiss-Prot

O08785

UniProtKB/TrEMBL

Q6ZQD6

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_030254103.2 → XP_030109963.1 circadian locomoter output cycles protein kaput isoform X3

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_030254102.2 → XP_030109962.1 circadian locomoter output cycles protein kaput isoform X1

UniProtKB/Swiss-Prot

O08785

UniProtKB/TrEMBL

Q6ZQD6

Conserved Domains (3) summary

pfam00989
Location:109 → 177

PAS; PAS fold

pfam14598
Location:274 → 377

PAS_11; PAS domain

cd19734
Location:29 → 89

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
XM_011249402.3 → XP_011247704.1 circadian locomoter output cycles protein kaput isoform X5

UniProtKB/TrEMBL

Q6ZQD6

Conserved Domains (2) summary

cd00130
Location:3 → 91

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:149 → 252

PAS_11; PAS domain