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

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

    Summary

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    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
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    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

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    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

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    Preferred Names
    clock circadian regulator b
    Names
    Clock1b
    circadian locomotor output cycles kaput b
    clock homolog 3

    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_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

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