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

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 AllianceGenome:ZFIN:ZDB-GENE-990630-14
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: clock; zCLOCK1; zfCLOCK1
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Contributes to DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including photoperiodism; primitive hemopoiesis; and regulation of gene expression. Part of CLOCK-BMAL transcription complex. Is active in chromatin. Is expressed in brain; head; ovary; and photoreceptor cell. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human CLOCK (clock circadian regulator). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

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)

Chromosome 20 - NC_007131.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circadian clock1a coordinates neutrophil recruitment via nfe212a/duox-reactive oxygen species pathway in zebrafish.
Title: Circadian clock1a coordinates neutrophil recruitment via nfe212a/duox-reactive oxygen species pathway in zebrafish.
Data suggest that Clock1a coordinates mesoderm development and primitive hematopoiesis in embryos by up-regulating Nodal-Smad3 signaling; Clock1a alterations produce embryonic defects with shortened body length, lack of ventral tail fin, or partial defect of the eyes; Clock1a activates Smad3a promoter via its E-box1 element. (Clock1a = clock circadian regulator a; Nodal = nodal modulator 1; Smad3a = SMAD family member 3a)
Title: Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.
Clock plays important roles in regulating the circadian rhythms in photoreceptor cells
Title: CLOCK is required for maintaining the circadian rhythms of Opsin mRNA expression in photoreceptor cells.
endogenous CLOCK is essential for the transcriptional regulation of period1 in the embryo
Title: Autonomous onset of the circadian clock in the zebrafish embryo.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
contributes_to DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
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 histone acetyltransferase activity	IEA Inferred from Electronic Annotation 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
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 regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within circadian rhythm	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesoderm development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within photoperiodism	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within photoperiodism	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within primitive hemopoiesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to light stimulus	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within response to temperature stimulus	IDA Inferred from Direct Assay 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
part_of CLOCK-BMAL transcription complex	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
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 protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: circadian locomoter output cycles protein kaput

Names: Clock1a; circadian locomotor output cycles kaput a; clk1

NP_571032.2

EC 2.3.1.48

XP_009292908.1

EC 2.3.1.48

XP_021324029.1

EC 2.3.1.48

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)

NM_130957.2 → NP_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

A0A8M1PB05, Q5RIV1

Related

ENSDARP00000014377.9, ENSDART00000025575.12

Conserved Domains (4) summary

cd00083
Location:23 → 77

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:266 → 364

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:100 → 169

PAS; PAS fold

pfam14598
Location:265 → 368

PAS_11; PAS domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007131.7 Reference GRCz11 Primary Assembly

Range

22068860..22176005

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8M9PH45

Conserved Domains (4) summary

cd00083
Location:23 → 77

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:100 → 169

PAS; PAS fold

pfam09787
Location:514 → 656

Golgin_A5; Golgin subfamily A member 5

cl25986
Location:265 → 368

PAS_3; PAS fold
XM_009294633.3 → XP_009292908.1 circadian locomoter output cycles protein kaput isoform X1

See identical proteins and their annotated locations for XP_009292908.1

UniProtKB/TrEMBL

A0A8M1PB05, Q5RIV1

Related

ENSDARP00000126787.1, ENSDART00000152636.3

Conserved Domains (4) summary

cd00083
Location:23 → 77

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:266 → 364

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:100 → 169

PAS; PAS fold

pfam14598
Location:265 → 368

PAS_11; PAS domain