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

Gene ID: 30140, updated on 3-Oct-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 Functions

What'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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