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    clocka clock circadian regulator a [ Danio rerio (zebrafish) ]

    Gene ID: 30140, updated on 14-Feb-2019

    Summary

    Official Symbol
    clockaprovided by ZNC
    Official Full Name
    clock circadian regulator aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-990630-14
    See related
    Ensembl:ENSDARG00000011703
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
    Also known as
    clock; zCLOCK1; zfCLOCK1
    Orthologs

    Genomic context

    See clocka in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (22068860..22176005)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (22169277..22275698)
    103 previous assembly Zv9 (GCF_000002035.4) 20 NC_007131.5 (22140735..22248071)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene dishevelled associated activator of morphogenesis 1b Neighboring gene neuromedin U Neighboring gene transmembrane protein 165 Neighboring gene steroid 5 alpha-reductase 3

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Exercise-induced Circadian Regulation, organism-specific biosystem (from WikiPathways)
      Exercise-induced Circadian Regulation, organism-specific biosystem
      Exercise-induced Circadian Regulation
    • Herpes simplex infection, organism-specific biosystem (from KEGG)
      Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Herpes simplex infection, conserved biosystem (from KEGG)
      Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...

    General gene information

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    contributes_to DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    contributes_to protein heterodimerization activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    circadian regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    circadian rhythm IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mesoderm development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    photoperiodism IDA
    Inferred from Direct Assay
    more info
    PubMed 
    photoperiodism IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    positive regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    primitive hemopoiesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    response to light stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    response to light stimulus IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    response to temperature stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    circadian locomoter output cycles protein kaput
    Names
    Clock1a
    circadian locomotor output cycles kaput a
    clk1
    NP_571032.2
    XP_009292908.1
    XP_021324029.1

    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_130957.2NP_571032.2  circadian locomoter output cycles protein kaput

      See identical proteins and their annotated locations for NP_571032.2

      Status: VALIDATED

      Source sequence(s)
      BX088688
      UniProtKB/TrEMBL
      Q5RIV1
      Related
      ENSDARP00000014377.9, ENSDART00000025575.12
      Conserved Domains (4) summary
      cd00083
      Location:2377
      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:266364
      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 ...
      pfam00989
      Location:100169
      PAS; PAS fold
      pfam14598
      Location:265368
      PAS_11; PAS domain

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007131.7 Reference GRCz11 Primary Assembly

      Range
      22068860..22176005
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021468354.1XP_021324029.1  circadian locomoter output cycles protein kaput isoform X2

      Conserved Domains (4) summary
      cd00083
      Location:2377
      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:100169
      PAS; PAS fold
      pfam09787
      Location:514656
      Golgin_A5; Golgin subfamily A member 5
      cl25986
      Location:265368
      PAS_3; PAS fold
    2. XM_009294633.3XP_009292908.1  circadian locomoter output cycles protein kaput isoform X1

      See identical proteins and their annotated locations for XP_009292908.1

      UniProtKB/TrEMBL
      Q5RIV1
      Related
      ENSDARP00000126787.1, ENSDART00000152636.3
      Conserved Domains (4) summary
      cd00083
      Location:2377
      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:266364
      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 ...
      pfam00989
      Location:100169
      PAS; PAS fold
      pfam14598
      Location:265368
      PAS_11; PAS domain
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