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

Gene ID: 352927, updated on 3-Oct-2019

Summary

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
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
clock3; zfClock3

Genomic context

See clockb in Genome Data Viewer
Location:
chromosome: 1
Exon count:
21
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (19432969..19467497)
105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (18740026..18774815)
103 previous assembly Zv9 (GCF_000002035.4) 1 NC_007112.5 (18174854..18209395)

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

Pathways from BioSystems

  • 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

Markers

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
circadian rhythm IGI
Inferred from Genetic Interaction
more info
PubMed 
photoperiodism IEP
Inferred from Expression Pattern
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
response to light stimulus IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

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_178295.2NP_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
    B3DH92
    Related
    ENSDARP00000014344.8, ENSDART00000012552.9
    Conserved Domains (4) summary
    smart00091
    Location:99160
    PAS; PAS domain
    cd00083
    Location:2276
    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:264362
    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:263366
    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_007112.7 Reference GRCz11 Primary Assembly

    Range
    19432969..19467497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005168339.4XP_005168396.1  clock circadian regulator b isoform X1

    See identical proteins and their annotated locations for XP_005168396.1

    UniProtKB/TrEMBL
    B3DH92
    Related
    ENSDARP00000120780.1, ENSDART00000133959.3
    Conserved Domains (4) summary
    smart00091
    Location:99160
    PAS; PAS domain
    cd00083
    Location:2276
    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:264362
    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:263366
    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)
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