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clocka clock circadian regulator a [ Cyprinus carpio (common carp) ]

Gene ID: 109044823, updated on 7-Dec-2023

Summary

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Gene symbol
clocka
Gene description
clock circadian regulator a
See related
Ensembl:ENSCCRG00000003591
Gene type
protein coding
RefSeq status
MODEL
Organism
Cyprinus carpio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Cyprininae; Cyprinus
Also known as
clock
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Genomic context

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See clocka in Genome Data Viewer
Location:
chromosome: B20
Exon count:
25
Annotation release Status Assembly Chr Location
101 current ASM1834038v1 (GCF_018340385.1) B20 NC_056616.1 (13219221..13271396)
100 previous assembly common carp genome (GCF_000951615.1) 40 NC_031736.1 (8254270..8276654, complement)

Chromosome B20 - NC_056616.1Genomic Context describing neighboring genes Neighboring gene trans-L-3-hydroxyproline dehydratase Neighboring gene disheveled-associated activator of morphogenesis 1-like Neighboring gene neuromedin-U-like Neighboring gene transmembrane protein 165 Neighboring gene steroid 5 alpha-reductase 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
  2. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables E-box binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in circadian regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of CLOCK-BMAL transcription complex IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
circadian locomoter output cycles protein kaput

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Cyprinus carpio Annotation Release 101 details...Open this link in a new tab

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

Reference ASM1834038v1 Primary Assembly

Genomic

  1. NC_056616.1 Reference ASM1834038v1 Primary Assembly

    Range
    13219221..13271396
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_042746946.1 → XP_042602880.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/TrEMBL
    A0A8C1RTV1, A0A8C2DJ69
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

  2. XM_042746949.1 → XP_042602883.1  circadian locomoter output cycles protein kaput isoform X2

    UniProtKB/TrEMBL
    A0A8C2DJ69, A0A9Q9XJB7
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

  3. XM_042746950.1 → XP_042602884.1  circadian locomoter output cycles protein kaput isoform X3

    UniProtKB/TrEMBL
    A0A8C0YGN4, A0A9Q9XJB9
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

  4. XM_042746951.1 → XP_042602885.1  circadian locomoter output cycles protein kaput isoform X4

    UniProtKB/TrEMBL
    A0A8C0YGN4, A0A9Q9XJQ9
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

  5. XM_042746948.1 → XP_042602882.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/TrEMBL
    A0A8C1RTV1, A0A8C2DJ69
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins

  6. XM_042746947.1 → XP_042602881.1  circadian locomoter output cycles protein kaput isoform X1

    UniProtKB/TrEMBL
    A0A8C1RTV1, A0A8C2DJ69
    Conserved Domains (3) summary
    cd00130
    Location:109 → 207
    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 ...
    pfam08447
    Location:277 → 364
    PAS_3; PAS fold
    cd19734
    Location:20 → 80
    bHLH-PAS_CLOCK; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins
Nucleotide Protein
Heading Accession and Version

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