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CLOCK clock circadian regulator [ Homo sapiens (human) ]

Gene ID: 9575, updated on 7-Apr-2024

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; AllianceGenome:HGNC:2082
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
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Genomic context

See CLOCK in Genome Data Viewer
Location:
4q12
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (55427903..55546909, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (58916047..59035037, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (56294070..56413076, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:56230743-56231431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:56231432-56232119 Neighboring gene steroid 5 alpha-reductase 3 Neighboring gene SRD5A3 antisense RNA 1 Neighboring gene FCF1 pseudogene 8 Neighboring gene long intergenic non-protein coding RNA 2928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21574 Neighboring gene transmembrane protein 165 Neighboring gene Sharpr-MPRA regulatory region 15506 Neighboring gene Sharpr-MPRA regulatory region 12160 Neighboring gene uncharacterized LOC124900704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15442 Neighboring gene RN7SK pseudogene 30 Neighboring gene phosducin like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15443 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501035-56501786 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:56501787-56502538 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

Clone Names

  • FLJ39000, FLJ42446, KIAA0334, DKFZp686I23208

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
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 ISA
Inferred from Sequence Alignment
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 
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 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
enables chromatin DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone acetyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA damage checkpoint signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to ionizing radiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in circadian rhythm TAS
Traceable Author Statement
more info
PubMed 
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of glucocorticoid receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in photoperiodism TAS
Traceable Author Statement
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of NF-kappaB transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of circadian rhythm IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein acetylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of hair cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in response to redox state IDA
Inferred from Direct Assay
more info
PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
PubMed 
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
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 chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in chromatoid body ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
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_011532712.1
XP_011532713.1
XP_016864343.1
XP_024310052.1
XP_047272387.1
XP_047272388.1
XP_047272389.1
XP_047272390.1
XP_047272391.1
XP_047272392.1
XP_047272393.1
XP_047272394.1
XP_047272395.1
XP_047272396.1
XP_054207263.1
XP_054207264.1
XP_054207265.1
XP_054207266.1
XP_054207267.1
XP_054207268.1
XP_054207269.1
XP_054207270.1
XP_054207271.1
XP_054207272.1
XP_054207273.1
XP_054207274.1
XP_054207275.1
XP_054207276.1
XP_054207277.1
XP_054207278.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001267843.2NP_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
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, 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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    55427903..55546909 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534410.3XP_011532712.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_011532712.1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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_047416432.1XP_047272388.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  3. XM_047416436.1XP_047272392.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  4. XM_017008854.2XP_016864343.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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_047416433.1XP_047272389.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  6. XM_011534411.3XP_011532713.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_011532713.1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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_047416439.1XP_047272395.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  8. XM_047416437.1XP_047272393.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  9. XM_005265787.3XP_005265844.1  circadian locomoter output cycles protein kaput isoform X1

    See identical proteins and their annotated locations for XP_005265844.1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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
  10. XM_047416431.1XP_047272387.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  11. XM_047416434.1XP_047272390.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  12. XM_047416435.1XP_047272391.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  13. XM_024454284.2XP_024310052.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
    UniProtKB/TrEMBL
    Q3ZCT4, Q53EU0
    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
  14. XM_047416438.1XP_047272394.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  15. XM_047416440.1XP_047272396.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    58916047..59035037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351289.1XP_054207264.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  2. XM_054351290.1XP_054207265.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  3. XM_054351294.1XP_054207269.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  4. XM_054351288.1XP_054207263.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  5. XM_054351292.1XP_054207267.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  6. XM_054351297.1XP_054207272.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  7. XM_054351301.1XP_054207276.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  8. XM_054351296.1XP_054207271.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  9. XM_054351293.1XP_054207268.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  10. XM_054351295.1XP_054207270.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  11. XM_054351300.1XP_054207275.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  12. XM_054351302.1XP_054207277.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  13. XM_054351291.1XP_054207266.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  14. XM_054351299.1XP_054207274.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  15. XM_054351298.1XP_054207273.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8
  16. XM_054351303.1XP_054207278.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/Swiss-Prot
    A0AV01, A2I2N9, O14516, O15516, Q9UIT8