U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

clockb clock circadian regulator b [ Danio rerio (zebrafish) ]

Gene ID: 352927, updated on 4-Jan-2025

Summary

Go to the top of the page Help
Official Symbol
clockbprovided by ZNC
Official Full Name
clock circadian regulator bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030408-2
See related
Ensembl:ENSDARG00000003631 AllianceGenome:ZFIN:ZDB-GENE-030408-2
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
clock3; zfClock3
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and E-box binding activity. Acts upstream of or within circadian rhythm and photoperiodism. Predicted to be located in cytosol and nucleus. Predicted to be part of CLOCK-BMAL transcription complex. Human ortholog(s) of this gene implicated in Alzheimer's disease and alcohol use disorder. Orthologous to human CLOCK (clock circadian regulator). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See clockb in Genome Data Viewer
Location:
chromosome: 1
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (19432991..19468703)
105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (18740026..18774815)

Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 47 Neighboring gene leucine aminopeptidase 3 Neighboring gene KIT proto-oncogene, receptor tyrosine kinase b Neighboring gene clarin 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Circadian oscillation of TNF-α gene expression regulated by clock gene, BMAL1 and CLOCK1, in the Japanese medaka (Oryzias latipes). Onoue T, et al. Int Immunopharmacol, 2019 May. PMID 30852291
  2. CLOCK:BMAL-independent circadian oscillation of zebrafish Cryptochrome1a gene. Miyamura N, et al. Biol Pharm Bull, 2009 Jul. PMID 19571382
  3. Cloning of circadian rhythmic pathway genes and perturbation of oscillation patterns in endocrine disrupting chemicals (EDCs)-exposed mangrove killifish Kryptolebias marmoratus. Rhee JS, et al. Comp Biochem Physiol C Toxicol Pharmacol, 2014 Aug. PMID 24726801
  4. The orphan receptor Rev-erbalpha gene is a target of the circadian clock pacemaker. Triqueneaux G, et al. J Mol Endocrinol, 2004 Dec. PMID 15591021, Free PMC Article
  5. Temperature regulates transcription in the zebrafish circadian clock. Lahiri K, et al. PLoS Biol, 2005 Nov. PMID 16176122, Free PMC Article

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  
enables E-box binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in circadian regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within circadian regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within circadian rhythm IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within photoperiodism IEP
Inferred from Expression Pattern
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within response to light stimulus IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within rhythmic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of CLOCK-BMAL transcription complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
clock circadian regulator b
Names
Clock1b
circadian locomotor output cycles kaput b
clock homolog 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_178295.2 → NP_840080.2  clock circadian regulator b

    See identical proteins and their annotated locations for NP_840080.2

    Status: VALIDATED

    Source sequence(s)
    BX901913, CR926462, CT669240
    UniProtKB/TrEMBL
    A0A8M2BFM7, B3DH92, F1QQF0
    Related
    ENSDARP00000014344.8, ENSDART00000012552.9
    Conserved Domains (4) summary
    smart00091
    Location:99 → 160
    PAS; PAS domain
    cd00083
    Location:22 → 76
    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:264 → 362
    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:263 → 366
    PAS_11; PAS domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007112.7 Reference GRCz11 Primary Assembly

    Range
    19432991..19468703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005168339.5 → XP_005168396.1  clock circadian regulator b isoform X1

    See identical proteins and their annotated locations for XP_005168396.1

    UniProtKB/TrEMBL
    A0A8M2BFM7, B3DH92, F1QQF0
    Related
    ENSDARP00000120780.1, ENSDART00000133959.3
    Conserved Domains (4) summary
    smart00091
    Location:99 → 160
    PAS; PAS domain
    cd00083
    Location:22 → 76
    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:264 → 362
    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:263 → 366
    PAS_11; PAS domain

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394474.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    3042..3637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials
Tools