General Information
Symbol
Dmel\cyc
Species
D. melanogaster
Name
cycle
Annotation Symbol
CG8727
Feature Type
FlyBase ID
FBgn0023094
Gene Model Status
Stock Availability
Gene Snapshot
cycle (cyc) is a circadian clock gene. It encodes a transcription factor of the BHLH-PAS family and activates transcription of key clock genes as well as downstream clock-regulated genes. [Date last reviewed: 2018-09-20]
Also Known As
CYCLE, dbmal1, Bmal1, dCYC
Genomic Location
Cytogenetic map
Sequence location
3L:19,813,770..19,815,938 [-]
Recombination map
3-46
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Summaries
Gene Group Membership
BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS -
Basic helix-loop-helix (bHLH) transcription factors are sequence-specific DNA-binding proteins that regulate transcription. They are characterized by a 60 amino acid region comprising a basic DNA binding domain followed by a HLH motif formed from two amphipathic α-helices connected by a loop. bHLH transcription factors form homo- and hetero-dimeric complexes, which bind to a E box consensus sequence. (Adapted from PMID:15186484).
UniProt Contributed Function Data
Putative transcription factor involved in the generation of biological rhythms. Activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.
(UniProt, O61734)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\cyc or the JBrowse view of Dmel\cyc for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Gene model reviewed during 5.45
Gene model reviewed during 5.43
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.46
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074924
1625
413
Additional Transcript Data and Comments
Reported size (kB)
1.7 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0074693
47.6
413
7.71
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with Clock in order to activate PER and TIM transcription.
(UniProt, O61734)
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\cyc using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (20 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from physical interaction with UniProtKB:O61735
inferred from physical interaction with FLYBASE:Clk; FB:FBgn0023076
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001067
(assigned by InterPro )
non-traceable author statement
Biological Process (13 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (10 terms)
CV Term
Evidence
References
traceable author statement
non-traceable author statement
traceable author statement
non-traceable author statement
non-traceable author statement
traceable author statement
non-traceable author statement
traceable author statement
traceable author statement
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001067
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR001067
(assigned by InterPro )
non-traceable author statement
inferred from electronic annotation with InterPro:IPR001067
(assigned by InterPro )
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
cyc transcripts are detected in adult head RNA. They do not exhibit any temporal cycling.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\cyc in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 5 )
For All Classical and Insertion Alleles Show
 
Allele of cyc
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Other relevant insertions
Transgenic Constructs ( 18 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of cyc
Allele of cyc
Mutagen
Associated Transgenic Construct
Stocks
Transgenic constructs containing regulatory region of cyc
Deletions and Duplications ( 1 )
Summary of Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
11 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
12 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (5)
10 of 13
Yes
Yes
4 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (2)
7 of 12
Yes
Yes
1 of 12
No
Yes
Danio rerio (Zebrafish) (9)
12 of 15
Yes
Yes
7 of 15
No
Yes
4 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
1 of 15
Yes
No
1 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (1)
1 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No orthologs reported.
Schizosaccharomyces pombe (Fission yeast) (0)
No orthologs reported.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091909J9 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091505IK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W05FK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X05BK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G126J )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with Clock in order to activate PER and TIM transcription.
    (UniProt, O61734 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-46
    Cytogenetic map
    Sequence location
    3L:19,813,770..19,815,938 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    76C6-76C6
    Limits computationally determined from genome sequence between P{lacW}l(3)L3809L3809 and P{lacW}l(3)L1243L1243&P{lacW}Mi-2j3D4
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    76C-76C
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (8)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (20)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Source for merge of: cyc Mop3
    Additional comments
    Source for merge of cyc Mop3 was sequence comparison ( date:000202 ).
    Other Comments
    DNA-protein interactions: genome-wide binding profile (ChIP-chip) assayed for cyc protein in adult heads; see GEO_GSE32613 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32613).
    Clk and cyc proteins interact in the cytoplasm of S2R+ cells and heterodimerisation promotes nuclear import as well as phosphorylation of cytoplasmic Clk protein.
    cry functions as a repressor of Clk/cyc-activated transcription.
    dco-mediated hyperphosphorylation of Clk does not require cyc or the DNA-binding domain of Clk.
    Clk and cyc, along with other circadian genes per and dco (but not tim) have roles in regulating cocaine sensitization and may function as regulators of Tdc.
    Sensitization to repeated cocaine exposures, a phenomenon also seen in humans and animal models and associated with enhanced drug craving, is eliminated in flies mutant for per, dco, Clk, and cyc but not tim.
    Clk mRNA cycling is regulated by per-tim-mediated release of Clk- and cyc-dependent repression.
    Daily cycles in the association of per and tim proteins with the Clk-cyc complex may contribute to rhythmic expression of per and tim.
    The tim-induced per mRNA level increase does not require cyc.
    Mutation of the cyc gene produces flies that are behaviourally arrhythmic and have little per or tim transcription.
    Arrhythmic mutant. per and tim transcription levels are low and constant in cyc mutants.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 47 )
    Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Synonyms and Secondary IDs (22)
    Reported As
    Symbol Synonym
    Mop3
    cyc
    (Filošević et al., 2018, Nazario-Toole et al., 2018, Noreen et al., 2018, Zhang et al., 2018, Lee et al., 2017, Liu et al., 2017, Park et al., 2017, Transgenic RNAi Project members, 2017-, Vaccaro et al., 2017, Donelson and Sanyal, 2015, Giebultowicz and Long, 2015, Gill et al., 2015, Grotewiel and Bettinger, 2015, Lerner et al., 2015, Liu et al., 2015, Pasco et al., 2015, Schertel et al., 2015, Tataroglu and Emery, 2015, Thimgan et al., 2015, Tomita et al., 2015, Zwarts et al., 2015, Liu et al., 2014, Victorsen and White, 2014.4.15, Joiner et al., 2013, Krupp et al., 2013, Lee et al., 2013, Lim and Allada, 2013, Mehta and Cheng, 2013, Pandey et al., 2013, Pohl et al., 2013, Rakshit et al., 2013, Sivachenko et al., 2013, Bywalez et al., 2012, Chen et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Kaun et al., 2012, Luo et al., 2012, Rakshit et al., 2012, Ruben et al., 2012, Abruzzi et al., 2011, Diangelo et al., 2011, Goda et al., 2011, Ito et al., 2011, Itoh et al., 2011, Lone and Sharma, 2011, Beaver et al., 2010, Blanchard et al., 2010, Chatterjee et al., 2010, Cooper et al., 2010, Fujii and Amrein, 2010, Gegear et al., 2010, Keene et al., 2010, Kula-Eversole et al., 2010, Li et al., 2010, Menet et al., 2010, Nagoshi et al., 2010, Thimgan et al., 2010, Xie et al., 2010, Bahn et al., 2009, Currie et al., 2009, Dworkin et al., 2009, Fathallah-Shaykh et al., 2009, Gummadova et al., 2009, Hung et al., 2009, Kempinger et al., 2009, Kilman and Allada, 2009, Maurer et al., 2009, Sehadova et al., 2009, Benito et al., 2008, Fujii et al., 2008, Houl et al., 2008, Ito et al., 2008, Kadener et al., 2008, Krishnan et al., 2008, Lee and Edery, 2008, Miura et al., 2008, Ogawa et al., 2008, Ratan et al., 2008, Tanoue et al., 2008, Taylor and Hardin, 2008, T et al., 2008, Xu et al., 2008, Yang et al., 2008, Fujii et al., 2007, Hung et al., 2007, Kurata et al., 2007, Lim et al., 2007, Vosshall, 2007, Williams et al., 2007, Yoshii et al., 2007, Chen et al., 2006, Ganguly-Fitzgerald et al., 2006, Ni et al., 2006, Rosbash, 2006.8.10, Seugnet et al., 2006, Van Gelder, 2006, Yuan et al., 2006, Cyran et al., 2005, Mazzoni et al., 2005, Yuan et al., 2005, Yuan et al., 2005, Beaver et al., 2003, Hendricks et al., 2003, Yoshii et al., 2002)
    Secondary FlyBase IDs
    • FBgn0024953
    • FBgn0025108
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (319)