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CLOCK clock circadian regulator [ Homo sapiens (human) ]

Gene ID: 9575, updated on 17-May-2020

Summary

Official Symbol
CLOCKprovided by HGNC
Official Full Name
clock circadian regulatorprovided by HGNC
Primary source
HGNC:HGNC:2082
See related
Ensembl:ENSG00000134852 MIM:601851
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KAT13D; bHLHe8
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 in certain populations and with obesity and metabolic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression
Ubiquitous expression in testis (RPKM 7.8), thyroid (RPKM 6.2) and 24 other tissues See more
Orthologs

Genomic context

See CLOCK in Genome Data Viewer
Location:
4q12
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (55427901..55547138, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (56294068..56413076, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene steroid 5 alpha-reductase 3 Neighboring gene SRD5A3 antisense RNA 1 Neighboring gene FCF1 pseudogene 8 Neighboring gene uncharacterized LOC105377659 Neighboring gene transmembrane protein 165 Neighboring gene RN7SK pseudogene 30 Neighboring gene phosducin like 2 Neighboring gene neuromedin U

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of clock homolog (mouse, CLOCK) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ39000, FLJ42446, KIAA0334, DKFZp686I23208

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 
E-box 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
histone acetyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to ionizing radiation IDA
Inferred from Direct Assay
more info
PubMed 
circadian regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian rhythm TAS
Traceable Author Statement
more info
 
histone acetylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of glucocorticoid receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
photoperiodism TAS
Traceable Author Statement
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
protein acetylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of hair cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of type B pancreatic cell development ISS
Inferred from Sequence or Structural Similarity
more info
 
response to redox state IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
chromatoid body ISS
Inferred from Sequence or Structural Similarity
more info
 
chromosome IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
circadian locomoter output cycles protein kaput
Names
circadian locomoter output cycles kaput protein
class E basic helix-loop-helix protein 8
clock homolog
NP_001254772.1
NP_004889.1
XP_005265844.1
XP_011532711.1
XP_011532712.1
XP_011532713.1
XP_016864343.1
XP_016864344.1
XP_024310052.1

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_001267843.1NP_001254772.1  circadian locomoter output cycles protein kaput

    See identical proteins and their annotated locations for NP_001254772.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC069200, BC041878
    Consensus CDS
    CCDS3500.1
    UniProtKB/Swiss-Prot
    O15516
    UniProtKB/TrEMBL
    Q3ZCT4
    Related
    ENSP00000370723.1, ENST00000381322.5
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  2. NM_004898.4NP_004889.1  circadian locomoter output cycles protein kaput

    See identical proteins and their annotated locations for NP_004889.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC069200, AK223549, DA658950
    Consensus CDS
    CCDS3500.1
    UniProtKB/Swiss-Prot
    O15516
    UniProtKB/TrEMBL
    Q53EU0
    Related
    ENSP00000426983.1, ENST00000513440.6
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    55427901..55547138 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008854.1XP_016864343.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    O15516
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  2. XM_011534410.2XP_011532712.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_011532712.1

    UniProtKB/Swiss-Prot
    O15516
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  3. XM_005265787.2XP_005265844.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_005265844.1

    UniProtKB/Swiss-Prot
    O15516
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  4. XM_011534411.2XP_011532713.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_011532713.1

    UniProtKB/Swiss-Prot
    O15516
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  5. XM_024454284.1XP_024310052.1  circadian locomoter output cycles protein kaput isoform X1

    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  6. XM_011534409.2XP_011532711.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_011532711.1

    UniProtKB/Swiss-Prot
    O15516
    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, ...
    pfam00989
    Location:109175
    PAS; PAS fold
    pfam09606
    Location:496686
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl25986
    Location:274377
    PAS_3; PAS fold
  7. XM_017008855.1XP_016864344.1  circadian locomoter output cycles protein kaput isoform X2

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