FlyBase Gene Report: Dmel\cyc

General Information

Symbol

Dmel\cyc

Species

D. melanogaster

Name

cycle

Annotation Symbol

CG8727

Feature Type

protein_coding_gene

FlyBase ID

FBgn0023094

Gene Model Status

Current

Stock Availability

20 publicly available

Gene Summary

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] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dbmal1, BMAL1, dCYC

Key Links

Genomic Location

Cytogenetic map

76C6-76C6

Sequence location

3L:19,813,770..19,815,938 [-]

Recombination map

3-46

RefSeq locus

NT_037436 REGION:19813770..19815938

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (24 terms)

Molecular Function (7 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables DNA binding

inferred from direct assay

(Yu et al., 2006)

enables protein heterodimerization activity

inferred from physical interaction with UniProtKB:O61735

(Maurer et al., 2009)

contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from physical interaction with FLYBASE:Clk; FB:FBgn0023076

(Lee et al., 1999)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN000548496

(GO Reference Genome Project, 2011-)

enables DNA-binding transcription factor activity

inferred from electronic annotation with InterPro:IPR001067

(InterPro Project Members, 2004-)

enables protein dimerization activity

inferred from electronic annotation with InterPro:IPR011598, InterPro:IPR036638

(InterPro Project Members, 2004-)

enables RNA polymerase II cis-regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000548496

(GO Reference Genome Project, 2011-)

Biological Process (13 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in circadian regulation of gene expression

inferred from mutant phenotype

(Hung et al., 2007)

involved_in circadian regulation of heart rate

inferred from mutant phenotype

(Gill et al., 2015)

involved_in regulation of circadian sleep/wake cycle, sleep

inferred from mutant phenotype

(Yuan et al., 2006, Shaw et al., 2002)

involved_in response to starvation

inferred from direct assay

(Xu et al., 2008)

Terms Based on Predictions or Assertions (10 terms)

CV Term

Evidence

References

involved_in behavioral response to cocaine

traceable author statement

(Rothenfluh and Heberlein, 2002)

involved_in circadian rhythm

traceable author statement

(Emery and Reppert, 2004, Shaw and Franken, 2003, Glossop and Hardin, 2002, Panda et al., 2002, Hardin, 2000)

non-traceable author statement

(Sokolowski, 2001)

involved_in eclosion rhythm

traceable author statement

(Stanewsky, 2003)

involved_in locomotor rhythm

traceable author statement

(Stanewsky, 2003)

involved_in positive regulation of DNA-templated transcription

traceable author statement

(Glossop and Hardin, 2002)

involved_in positive regulation of transcription by RNA polymerase II

traceable author statement

(Stanewsky, 2003)

involved_in regulation of circadian sleep/wake cycle, sleep

traceable author statement

(Hendricks, 2003, Shaw and Franken, 2003)

involved_in regulation of DNA-templated transcription

inferred from electronic annotation with InterPro:IPR001067, InterPro:IPR013767

(InterPro Project Members, 2004-)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000548496

(GO Reference Genome Project, 2011-)

involved_in rhythmic behavior

traceable author statement

(Stanewsky, 2003)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

part_of aryl hydrocarbon receptor complex

inferred from biological aspect of ancestor with PANTHER:PTN000548496

(GO Reference Genome Project, 2011-)

located_in cytoplasm

inferred from electronic annotation with InterPro:IPR001067

(InterPro Project Members, 2004-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000548496

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred from electronic annotation with InterPro:IPR001067

(InterPro Project Members, 2004-)

part_of transcription regulator complex

inferred from electronic annotation with InterPro:IPR001067

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

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).

Protein Function (UniProtKB)

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)

Summary (Interactive Fly)

transcription factor - bHLH, pas domain - photoperiod response - Clock-Cycle heterodimer binds canonical E-box sequences to activate the transcription of direct targets clockwork orange, period, timeless, vrille and par domain protein 1

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry O61734)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

PDB - An information portal to biological macromolecular structures

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cyc-RA

FBtr0074924

NM_079444

1625

413

Additional Transcript Data and Comments

Reported size (kB)

1.7 (northern blot)

(Rutila et al., 1998)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

cyc-PA

FBpp0074693

47.6

413

7.71

O61734

NP_524168

AAF49107

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)

413 (aa)

(Darlington et al., 1998, Rutila et al., 1998)

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)

Crossreferences

InterPro - A database of protein families, domains and functional sites

PDB - An information portal to biological macromolecular structures

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

O61734

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.

cyc_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.52

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

lineage MNB primary interneuron

(Kearney et al., 2004)

larval MP1 neuron

(Kearney et al., 2004)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

head

(Rutila et al., 1998)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

organism

(Rakshit et al., 2012)

Additional Descriptive Data

The amount of cyc is reduced slightly in old flies compared to young flies, with the difference being slightly more pronounced in heads than in bodies.

(Rakshit et al., 2012)

cyc transcripts are detected in adult head RNA. They do not exhibit any temporal cycling.

(Rutila et al., 1998)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{GFP-cyc}

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

adult LP neuron

(Liu et al., 2015)

larval s-LNv Pdf neuron

(Liu et al., 2015)

larval LNd neuron

(Liu et al., 2015)

larval DN period neuron

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cyc in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\cyc

View exonic expression by tissue for Dmel\cyc

Bulk Downloads

RNA-Seq RPKM values for all genes

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

FBgn0023094

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

40162/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0023094

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0023094

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0023094

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG8727

Flygut - An atlas of the Drosophila adult midgut

FBgn0023094

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 24 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of cyc

Transgenic constructs containing regulatory region of cyc

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)kto2

(Rutila et al., 1998)

Inferred from location ( 2 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

partially lethal, with Scer\GAL4^phtm.PO

cyc^KK101917

viable, with Scer\GAL4^Mef2.PR

cyc^GD1313

viable, with Scer\GAL4^pnr-MD237

cyc^GD1313

viable, with Scer\GAL4^tin.CΔ4

cyc^GD1313

Other Phenotypes

Allele

abnormal behavior

abnormal behavior (with Df(3L)kto2)

cyc⁰¹

abnormal circadian rhythm

cyc⁰¹

abnormal circadian rhythm, with Scer\GAL4^Or22a.8197

cyc^{Δ.UAS.Tag:MYC}

abnormal circadian rhythm, with Scer\GAL4^{Orco.2.642.Hsim\VP22}

cyc^{Δ.UAS.Tag:MYC}

abnormal circadian rhythm, with Scer\GAL4^tim.PE

cyc^{Δ.UAS.Tag:MYC}

abnormal circadian rhythm, with Scer\GAL4^to.PD

cyc^DN.UAS

abnormal circadian rhythm | adult stage, with Scer\GAL4^Pdf.PU

abnormal eclosion rhythm, with Scer\GAL4^P2.4.Pdf

cyc^{Δ.UAS.Tag:MYC}

abnormal eclosion rhythm, with Scer\GAL4^phtm.PO

cyc^{Δ.UAS.Tag:MYC}

abnormal eclosion rhythm, with Scer\GAL4^tim.PE

cyc^{Δ.UAS.Tag:MYC}

abnormal eclosion rhythm, with Scer\GAL4^tim.PE, Scer\GAL80^phtm.1.2

cyc^{Δ.UAS.Tag:MYC}

abnormal eclosion rhythm | recessive

cyc⁰¹

abnormal locomotor rhythm

cyc⁰¹

abnormal locomotor rhythm, with Scer\GAL4^Act.PU

cyc^VP16.UAS

abnormal locomotor rhythm, with Scer\GAL4^{elav.Switch.PO}

cyc^DN.UAS

abnormal locomotor rhythm, with Scer\GAL4^elav-C155

cyc^VP16.UAS

abnormal locomotor rhythm, with Scer\GAL4^P2.4.Pdf

abnormal locomotor rhythm, with Scer\GAL4^tim.PE

abnormal locomotor rhythm | adult stage

cyc⁰¹

abnormal locomotor rhythm | adult stage, with Scer\GAL4^Clk.-856

cyc^{Δ.UAS.Tag:MYC}

abnormal locomotor rhythm | adult stage, with Scer\GAL4^Clk.-856, Scer\GAL80^Pdf.PS

cyc^{Δ.UAS.Tag:MYC}

abnormal locomotor rhythm | adult stage, with Scer\GAL4^Dvir\Pdf.1.9, Scer\GAL4^GMR78G02, Scer\GAL80^Pdf.PS

cyc^{Δ.UAS.Tag:MYC}

abnormal locomotor rhythm | adult stage, with Scer\GAL4^P2.4.Pdf

cyc^{Δ.UAS.Tag:MYC}

abnormal locomotor rhythm | adult stage, with Scer\GAL4^tim.UAS

cyc^{Δ.UAS.Tag:MYC}

abnormal locomotor rhythm | recessive

abnormal mating rhythm | male, with Scer\GAL4^Desat1.PB

cyc^{Δ.UAS.Tag:MYC}

abnormal mating rhythm | male limited | recessive

cyc⁰¹

abnormal neuroanatomy | adult stage

cyc⁰¹

abnormal neuroanatomy | adult stage, with Scer\GAL4^Pdf.PU

abnormal neuroanatomy | larval stage, with Scer\GAL4^Pdf.PU

abnormal sleep

cyc⁰¹

abnormal sleep, with Scer\GAL4^P2.4.Pdf

cyc^{Δ.UAS.Tag:MYC}

abnormal visual behavior

cyc⁰¹

decreased efficacy of long-term memory | adult stage, with Scer\GAL4^tim.PU, cyc⁰¹

decreased efficacy of long-term memory | adult stage, with Scer\GAL4^tim.PU, cyc^F311fs.UAS

cyc⁰¹

decreased efficacy of long-term memory | adult stage, with Scer\GAL4^tim.PU, cyc^I161T.UAS

cyc⁰¹

decreased efficacy of short-term memory | adult stage, with Scer\GAL4^tim.PU, cyc⁰¹

decreased efficacy of short-term memory | adult stage, with Scer\GAL4^tim.PU, cyc^F311fs.UAS

cyc⁰¹

decreased efficacy of short-term memory | adult stage, with Scer\GAL4^tim.PU, cyc^I161T.UAS

cyc⁰¹

Phenotype manifest in

Allele

adult heart

cyc⁰¹

adult s-LNv neuron

cyc⁰¹

adult s-LNv neuron, with Scer\GAL4^Pdf.PU

larval s-LNv neuron, with Scer\GAL4^Pdf.PU

LN period neuron

neuron projection | adult stage

cyc⁰¹

neuron projection | adult stage, with Scer\GAL4^Pdf.PU

neuron projection | larval stage, with Scer\GAL4^Pdf.PU

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (38)

Hsap\BMAL1

12 of 14

Yes

Hsap\ARNTL2

11 of 14

Yes

4 of 14

4 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (31)

Rnor\Arntl

12 of 14

Yes

Rnor\Arntl2

9 of 14

Yes

4 of 14

4 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (32)

Mmus\Arntl

12 of 14

Yes

Mmus\Arntl2

11 of 14

Yes

4 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (31)

Xtro\arntl

8 of 13

Yes

Xtro\arntl2

6 of 13

Yes

3 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\sim1

1 of 13

Danio rerio (Zebrafish) (51)

Drer\arntl1a

11 of 14

Yes

Drer\arntl1b

10 of 14

Yes

Drer\arntl2

10 of 14

Yes

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\aha-1

4 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (19)

Agam\AgaP_AGAP005655

12 of 12

Yes

Agam\AgaP_AGAP012873

5 of 12

Yes

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (7)

Atha\ALC

1 of 13

Yes

Atha\AT2G41130

1 of 13

Yes

Atha\AT3G56770

1 of 13

Yes

Atha\AT4G28800

1 of 13

Yes

Atha\AT5G62610

1 of 13

Yes

Atha\PIF3

1 of 13

Yes

Atha\PIL1

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\CBF1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:cyc. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (19)

tgo

6 of 13

gce

3 of 13

Met

3 of 13

Clk

2 of 13

cwo

1 of 13

dpn

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Hey

1 of 13

hry

1 of 13

per

1 of 13

Sidpn

1 of 13

sima

1 of 13

sim

1 of 13

tai

1 of 13

trh

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

alcohol, response to, circadian genes

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

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

DO term

Complementation?

Transgene?

BMAL1; basic helix-loop-helix ARNT like 1

12 of 14

602550

BMAL2; basic helix-loop-helix ARNT like 2

11 of 14

614517

ARNT2; aryl hydrocarbon receptor nuclear translocator 2

4 of 14

606036

WEBB-DATTANI SYNDROME; WEDAS

ARNT; aryl hydrocarbon receptor nuclear translocator

4 of 14

126110

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

cyc - Atx2

anti tag coimmunoprecipitation, quantitative reverse transcription pcr, primer specific pcr

(Lee et al., 2017, Lim and Allada, 2013)

protein-protein

Physical Interaction

Assay

References

cyc - CG18011

two hybrid array

(Shokri et al., 2019)

cyc - Clk

anti tag coimmunoprecipitation, anti tag western blot, autoradiography, anti bait coimmunoprecipitation, pull down, tag visualisation, two hybrid

(Wang et al., 2025, Liu et al., 2017, Lee et al., 2016, Lee et al., 2014, Cheng et al., 2013, Kazemian et al., 2013, Maurer et al., 2009, Hung et al., 2007, Ceriani et al., 1999, Lee et al., 1999, Darlington et al., 1998)

cyc - Eip78C

two hybrid array

(Shokri et al., 2019)

cyc - Hr78

two hybrid array

(Shokri et al., 2019)

cyc - foxo

two hybrid array

(Shokri et al., 2019)

cyc - hyd

anti tag coimmunoprecipitation, anti tag western blot

(Duan et al., 2024)

cyc - per

anti tag coimmunoprecipitation, autoradiography

(Lee et al., 1999)

cyc - rept

anti tag coimmunoprecipitation, anti tag western blot

(Liao et al., 2025)

cyc - tim

anti tag coimmunoprecipitation, autoradiography

(Lee et al., 1999)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

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

Clk

suppressible

cyc

(Kadener et al., 2008)

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.

65431

DroID - A comprehensive database of gene and protein interactions.

FBgn0023094

MIST (protein-protein) - An integrated Molecular Interaction Database

40162

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Circadian rhythm - fly

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-46

Cytogenetic map

76C6-76C6

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)L3809^L3809 and P{lacW}l(3)L1243^L1243&P{lacW}Mi-2^j3D4

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

76C-76D

(Rutila, 1998.5.15)

76C-76C

(Darlington, 1998.5.21)

76C-76C

(determined by in situ hybridisation)

(Darlington et al., 1998)

Experimentally Determined Recombination Data

Location

3-46

(FlyBase, 2016)

3-43.2

(Comeron et al., 2012)

(Rutila et al., 1998)

Left of (cM)

(Rutila et al., 1998)

Right of (cM)

(Rutila et al., 1998)

Notes

Stocks and Reagents

Stocks (20)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

80929

cyc⁰¹

600602

w^*; P{UAS-cyc.Δ}1

29400

y¹ v¹; P{TRiP.JF03333}attP2

31897

y¹ v¹; P{TRiP.JF02185}attP2

84182

y¹ v¹; M{WKO.P1-D10}ZH-86Fb

27950

y¹ w^*; P{EP}cyc^G4677

FlyORF

F003491

M{UAS-cyc.ORF-CC}ZH-21F

F000245

M{UAS-cyc.ORF.3xHA.GW}ZH-86Fb

8727R-1

8727R-3

v110455

v11765

w¹¹¹⁸; P{GD1313}v11765/TM3

More stocks available...

Genomic Clones (8)

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

cDNA Clones (18)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

SD27452

Other clones

FI01122

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.

FBgn0023094

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0023094

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-unspecified : Stable S2 cell lines were created expressing Clk-Tag:HA/Tag:FLAG or cyc-Tag:V5.
(Cho et al., 2019)

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).

(Abruzzi et al., 2011)

Clk and cyc proteins interact in the cytoplasm of S2R+ cells and heterodimerisation promotes nuclear import as well as phosphorylation of cytoplasmic Clk protein.

(Maurer et al., 2009)

cry functions as a repressor of Clk/cyc-activated transcription.

(Collins et al., 2006)

dco-mediated hyperphosphorylation of Clk does not require cyc or the DNA-binding domain of Clk.

(Kim and Edery, 2006)

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.

(Andretic et al., 1999)

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.

(Andretic et al., 1999)

Clk mRNA cycling is regulated by per-tim-mediated release of Clk- and cyc-dependent repression.

(Glossop et al., 1999)

Daily cycles in the association of per and tim proteins with the Clk-cyc complex may contribute to rhythmic expression of per and tim.

(Lee et al., 1999)

The tim-induced per mRNA level increase does not require cyc.

(Suri et al., 1999)

Mutation of the cyc gene produces flies that are behaviourally arrhythmic and have little per or tim transcription.

(Rutila et al., 1998)

Arrhythmic mutant. per and tim transcription levels are low and constant in cyc mutants.

(So et al., 1997)

Relationship to Other Genes

Source for database merge of

Source for merge of: cyc Mop3

(FlyBase, 1996-)

Additional comments

Source for merge of cyc Mop3 was sequence comparison ( date:000202 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (22)

Reported As

Symbol Synonym

BMAL1

(Kon et al., 2021, Hendricks et al., 2003, Darlington, 1998.5.21)

Bmal1

(Roenneberg and Merrow, 2003)

CG8727

(Ibaraki et al., 2021, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Stevens et al., 2008, Stevens et al., 2008)

CYC

(Spangler et al., 2025, Lou et al., 2024, Deppisch et al., 2022, Anna and Kannan, 2021, De and Chatterjee, 2021, Ma et al., 2021, Mosier and Hurley, 2021, Srikanta and Cermakian, 2021, Damulewicz and Mazzotta, 2020, Mahesh et al., 2020, Patke et al., 2020, Pelham et al., 2020, Schubert et al., 2020, Zhu and Belden, 2020, Kozlov and Nagoshi, 2019, Giebultowicz, 2018, Krzeptowski et al., 2018, Pilorz et al., 2018, Xue and Zhang, 2018, Young, 2018, He et al., 2017, Liu et al., 2017, Erion et al., 2016, Ito and Tomioka, 2016, Lee et al., 2016, Mazzoccoli et al., 2016, Jaumouillé et al., 2015, Lerner et al., 2015, Merbitz-Zahradnik and Wolf, 2015, Zordan and Sandrelli, 2015, Anderson and Adolphs, 2014, Chen et al., 2014, Lee et al., 2014, Tataroglu and Emery, 2014, Weiss et al., 2014, Cheng et al., 2013, Erion and Sehgal, 2013, Górska-Andrzejak, 2013, Abruzzi et al., 2011, Goda et al., 2011, Jackson, 2011, Lan and Mezić, 2011, Staiger and Koster, 2011, Weber et al., 2011, Allada and Chung, 2010, Fathallah-Shaykh, 2010, Gummadova et al., 2009, Yu et al., 2009, Dunlap, 2008, Kivimäe et al., 2008, Xu et al., 2008, Weber et al., 2007, Collins et al., 2006, Dunlap, 2006, Reppert, 2006, Yu and Hardin, 2006, Yu et al., 2006, Nawathean and Rosbash, 2004, Wang et al., 2001)

CYCLE

(Duan et al., 2024, Malik et al., 2020, Uriu and Tei, 2019, Erion and Sehgal, 2013, Goda et al., 2011, Hastings and Maywood, 2000, Lee et al., 1999)

Cyc

(Damulewicz and Mazzotta, 2025, Yan et al., 2025, Fangninou et al., 2024, Raicu et al., 2024, Bossen et al., 2023, Salgado-Canales et al., 2023, Zhao et al., 2023, Ulgherait et al., 2021, Parasram and Karpowicz, 2020, Kučerová et al., 2016, Lerner et al., 2015, Ghezzi et al., 2013, Peschel and Helfrich-Förster, 2011, Hardin, 2000, Loudon et al., 2000)

Cycle

(Liu et al., 2021, Górska-Andrzejak, 2013, Shaw and Franken, 2003)

MOP3

(Bae, 1998.6.2)

Mop3

TGO_CYC

(Blatti et al., 2015)

bHLHe7

(Stevens et al., 2008)

bMAL1

(Liman, 1998)

cyc

(Liao et al., 2025, Wang et al., 2025, Liu et al., 2024, Peng et al., 2024, Peterson and Ahmad, 2024, Shirakawa et al., 2024, Anna et al., 2023, Gao et al., 2023, Khatib et al., 2023, Liu et al., 2023, Rodrigues et al., 2023, Tuo et al., 2023, Jarabo et al., 2022, Philyaw et al., 2022, Poe et al., 2022, Sebastian et al., 2022, Sheardown et al., 2022, Vaughen et al., 2022, Yildirim et al., 2022, Zhao et al., 2022, Ahmad et al., 2021, Cavieres-Lepe and Ewer, 2021, Du et al., 2021, Gunawardhana et al., 2021, Ibaraki et al., 2021, Khyati et al., 2021, Solovev et al., 2021, Zhang et al., 2021, Beer and Helfrich-Förster, 2020, Brody, 2020, Damulewicz et al., 2020, De Nobrega and Lyons, 2020, Funato, 2020, Helfrich-Förster et al., 2020, Hill et al., 2020, Lathen et al., 2020, Mahesh et al., 2020, Ulgherait et al., 2020, Wang et al., 2020, Boomgarden et al., 2019, Bulthuis et al., 2019, Cho et al., 2019, Harbison et al., 2019, Hegazi et al., 2019, Hsieh et al., 2019, Martin Anduaga et al., 2019, Meltzer, 2019-, Meltzer et al., 2019, Mendoza and Vanotti, 2019, Shokri et al., 2019, Sinigaglia et al., 2019, Solovev et al., 2019, Stone et al., 2019, Zhao et al., 2019, Bischof et al., 2018, Chatterjee et al., 2018, Doupé et al., 2018, Filošević et al., 2018, Gene Disruption Project members, 2018-, Nazario-Toole et al., 2018, Noreen et al., 2018, Parasram et al., 2018, Zhang et al., 2018, Gunawardhana and Hardin, 2017, Lee et al., 2017, Liu et al., 2017, Park et al., 2017, Selcho et al., 2017, Sharp 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, Glossop et al., 2014, 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)

cycle

(Harris-Gauthier et al., 2022, Shafer and Keene, 2021)

dBMAL

(Andretic and Hirsh, 1999)

dBMAL1

(Ishida et al., 2001, Aasland, 1998, Aasland, 1998)

dBma1

(Loudon et al., 2000)

dBmal

(Lucas and Foster, 1999)

dCYC

(Beckwith et al., 2011, Emery and Reppert, 2004)

dbmal

(Crosthwaite, 2004)

dbmal1

(Darlington et al., 1998, Green, 1998, Reppert, 1998, Schibler, 1998)

Name Synonyms

CYCLE

(Stevenson et al., 2025, Abdalla et al., 2022, Damulewicz and Mazzotta, 2020, Huang, 2018, Mendoza-Viveros et al., 2017, Jaumouillé et al., 2015, Weiss et al., 2014, Luo et al., 2012, Abruzzi et al., 2011, Beckwith et al., 2011, Yu et al., 2009, Houl et al., 2008, Dunlap, 2006, Yu and Hardin, 2006, Yu et al., 2006, Mazzoni et al., 2005)

Cycle

(Young, 2018, Mazzoccoli et al., 2016, Potdar and Sheeba, 2013, Gegear et al., 2010, T et al., 2008)

brain and muscle ARNT-like 1

(Darlington, 1998.5.21)

Secondary FlyBase IDs

FBgn0024953
FBgn0025108

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 56 )

Sequence 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.

40162

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

O61734

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

O61734

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

O61734

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0023094

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

40162/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0023094

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0023094

FlyMine - An integrated database for Drosophila genomics

FBgn0023094

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG8727

MARRVEL_MODEL - MARRVEL (model organism gene)

40162

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

65431

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0023094

DroID - A comprehensive database of gene and protein interactions.

FBgn0023094

DRSC - Results frm RNAi screens

FBgn0023094

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

cyc_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0023094

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0023094

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG8727

Flygut - An atlas of the Drosophila adult midgut

FBgn0023094

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC002494

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Circadian rhythm - fly

MIST (protein-protein) - An integrated Molecular Interaction Database

40162

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (458)

The following external sites may use different assemblies or annotations than FlyBase.

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