FlyBase Gene Report: Dmel\cwo

General Information

Symbol

Dmel\cwo

Species

D. melanogaster

Name

clockwork orange

Annotation Symbol

CG17100

Feature Type

protein_coding_gene

FlyBase ID

FBgn0259938

Gene Model Status

Current

Stock Availability

17 publicly available

Gene Snapshot

clockwork orange (cwo) encodes a basic-helix-loop-helix-Orange transcription factor that can both activate and repress transcription. It regulates rhythmic gene expression within the transcriptional feedback loop that keeps circadian time. [Date last reviewed: 2019-02-28]

Other Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

86B3-86B3

Sequence location

3R:10,388,258..10,400,752 [+]

Recombination map

3-49

RefSeq locus

NT_033777 REGION:10388258..10400752

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (14 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables DNA-binding transcription factor activity

inferred from direct assay

(Kadener et al., 2007, Matsumoto et al., 2007)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

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

inferred from biological aspect of ancestor with PANTHER:PTN004213585

(assigned by GO_Central )

(Gaudet et al., 2011)

enables protein dimerization activity

inferred from electronic annotation with InterPro:IPR011598

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

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

inferred from biological aspect of ancestor with PANTHER:PTN004213585

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (9 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in circadian regulation of gene expression

inferred from mutant phenotype

(Richier et al., 2008)

involved_in dendrite morphogenesis

inferred from mutant phenotype

(Iyer et al., 2013)

involved_in negative regulation of transcription by RNA polymerase II

inferred from direct assay

(Kadener et al., 2007, Matsumoto et al., 2007)

involved_in regulation of circadian rhythm

inferred from mutant phenotype

(Kadener et al., 2007, Lim et al., 2007, Matsumoto et al., 2007)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

involved_in anterior/posterior pattern specification

inferred from biological aspect of ancestor with PANTHER:PTN000105428

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in peripheral nervous system development

traceable author statement

(Salzberg et al., 1994)

involved_in regulation of circadian rhythm

inferred from biological aspect of ancestor with PANTHER:PTN000862430

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of neurogenesis

inferred from biological aspect of ancestor with PANTHER:PTN000105428

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN004213585

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of transcription, DNA-templated

inferred from sequence or structural similarity with FLYBASE:Hey; FB:FBgn0027788

(Peyrefitte et al., 2001)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Matsumoto et al., 2007)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN004213585

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

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)

Plays a role in the regulation of circadian rhythms (PubMed:17555964, PubMed:17578907, PubMed:17578908, PubMed:27814361). Transcriptional repressor which inhibits Clock-mediated transcriptional activation by binding to E boxes in the promoters of Clock target genes and repressing their transcription (PubMed:17555964, PubMed:17578907, PubMed:17578908, PubMed:27814361). E box binding activity is time-dependent with higher binding activity seen in the early morning (zeitgeber time 2) than early evening (zeitgeber time 14) and is dependent on the presence of the circadian protein per (PubMed:27814361). It is likely that per binds to Clock-cycle heterodimers, reducing their affinity for E box binding and allowing cwo to bind instead (PubMed:27814361). Negatively regulates its own expression (PubMed:17578908, PubMed:18375860).

(UniProt, Q9VGZ5)

Summary (Interactive Fly)

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\cwo 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

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cwo-RA

FBtr0082246

NM_080036

4632

698

cwo-RB

FBtr0305151

NM_001260095

4508

621

cwo-RC

FBtr0305152

NM_001260096

5092

621

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

cwo-PA

FBpp0081723

75.1

698

6.95

NP_524775

AAF54527

cwo-PB

FBpp0293681

66.3

621

6.96

NP_001247024

AFH06342

cwo-PC

FBpp0293682

66.3

621

6.96

NP_001247025

AFH06343

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

621 aa isoforms: cwo-PB, cwo-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

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\cwo using the Feature Mapper tool.

External Data

Crossreferences

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

cwo_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 10 -- 12

anterior midgut primordium

(Peyrefitte et al., 2001)

posterior midgut primordium

(Peyrefitte et al., 2001)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

clypeo-labral primordium

(Fisher et al., 2012)

hindgut proper primordium

(Fisher et al., 2012)

Malpighian tubule primordium

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic epipharynx

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

adult stage | male

adult fat body

(Ellis and Carney, 2011)

abdominal adult fat mass

(Ellis and Carney, 2011)

adult brain

(Ellis and Carney, 2011)

mutational analysis

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

organism

Comment: circadian cycling, peak at ZT14

(Kadener et al., 2007)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

Comment: oscillating expression

(Matsumoto et al., 2007)

organism

Comment: circadian cycling, peak at ZT14

(Kadener et al., 2007)

adult stage | male

head

Comment: circadian oscillating expression

(Rakshit et al., 2012)

Additional Descriptive Data

Expression oscillates with the circadian cycle and peaks at ZT12, with the peak becoming less pronounced as flies age.

(Rakshit et al., 2012)

cwo transcript levels rhythmically oscillate in the adult fly head, peaking in closely phase with per and tim expression.

(Matsumoto et al., 2007)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult DN period neuron

(Matsumoto et al., 2007)

pacemaker neuron

(Richier et al., 2008)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood & male -- day 7 of adulthood & male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

cwo protein is expressed in three cell clusters in the adult lateral brain, coinciding wiht per expression

(Matsumoto et al., 2007)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Matsumoto et al., 2007)

Expression Deduced from Reporters

Reporter: P{GSV6}GS10340

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

pacemaker neuron

(Richier et al., 2008)

larval s-LNv neuron

(Richier et al., 2008)

l-LNv neuron

(Richier et al., 2008)

larval DN1 neuron

(Richier et al., 2008)

larval DN2 neuron

(Richier et al., 2008)

larval LN period neuron

Comment: 5th LN

(Richier et al., 2008)

adult stage

pacemaker neuron

(Richier et al., 2008)

DN1 neuron

(Richier et al., 2008)

DN2 neuron

(Richier et al., 2008)

DN3 neuron

(Richier et al., 2008)

s-LNv neuron

(Richier et al., 2008)

l-LNv neuron

(Richier et al., 2008)

LNd neuron

(Richier et al., 2008)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\cwo in GBrowse 2

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

View exonic expression by developmental stage for Dmel\cwo

View exonic expression by tissue for Dmel\cwo

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

FBgn0259938

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0259938

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG17100-RA

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

CG17100

Flygut - An atlas of the Drosophila adult midgut

FBgn0259938

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 10 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 15 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of cwo

Transgenic constructs containing regulatory region of cwo

Deletions and Duplications ( 2 )

Disrupted in

Df(3R)Exel6266

(Ryder, 2004.4.26)

Df(3R)RMSY

(Richier et al., 2008)

Phenotypes

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

Lethality

Allele

lethal - all die before end of pupal stage, with Scer\GAL4^da.G32

cwo^GS10340

viable

cwo^PB9

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

cwo^GD1250

viable, with Scer\GAL4^da.G32

cwo^PB9

viable, with Scer\GAL4^Mef2.PR

cwo^GD1250

viable, with Scer\GAL4^pnr-MD237

cwo^GD1250

viable, with Scer\GAL4^tin.CΔ4

cwo^GD1250

Other Phenotypes

Allele

circadian rhythm defective | adult stage (with Df(3R)RMSY)

cwo^PB9

circadian rhythm defective | adult stage | recessive

flightless, with Scer\GAL4^Mef2.PR

cwo^GD1250

locomotor rhythm defective

locomotor rhythm defective, with Scer\GAL4¹¹¹⁸

cwo^dsRNA.IR.UAS

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

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

cwo^dsRNA.UAS

locomotor rhythm defective, with Scer\GAL4^tim.UAS

cwo^dsRNA.IR.UAS

locomotor rhythm defective (with cwo^e04207)

cwo^f05073

locomotor rhythm defective (with cwo^f05073)

cwo^e04207

locomotor rhythm defective (with Df(3R)ED5495)

cwo^e04207

locomotor rhythm defective | recessive

neuroanatomy defective, with Scer\GAL4²²¹

neuroanatomy defective, with Scer\GAL4^ppk.1.9

some die during pupal stage, with Scer\GAL4^da.G32

cwo^GS10340

visible | male limited, with Scer\GAL4^Bx-MS1096

cwo^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

abdominal anterior ventral multidendritic neuron vdaa, with Scer\GAL4^ppk.1.9

larval dorsal multidendritic neuron ddaC, with Scer\GAL4^ppk.1.9

larval dorsal multidendritic neuron ddaD, with Scer\GAL4²²¹

wing | male limited, with Scer\GAL4^Bx-MS1096

cwo^{UAS.ORF.GW.Tag:HA}

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (13)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\HELT

3 of 15

Yes

Hsap\HEY1

3 of 15

Yes

Hsap\HEY2

3 of 15

Yes

Hsap\HEYL

3 of 15

Yes

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (12)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Hey1

3 of 15

Yes

Mmus\Hey2

3 of 15

Yes

Mmus\Heyl

3 of 15

Yes

Mmus\Bhlhe40

2 of 15

Mmus\Bhlhe41

2 of 15

Mmus\Helt

2 of 15

Yes

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

1 of 15

Rattus norvegicus (Norway rat) (12)

Rnor\Helt

3 of 13

Yes

Rnor\Hey2

3 of 13

Yes

Rnor\Heyl

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

Xenopus tropicalis (Western clawed frog) (17)

Xtro\hey1

3 of 12

Yes

Xtro\hey2

3 of 12

Yes

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (25)

Drer\helt

3 of 15

Yes

Drer\hey1

3 of 15

Yes

Drer\hey2

3 of 15

Yes

Drer\heyl

3 of 15

Yes

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\lin-22

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\NAI1

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\PHO4

2 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091905JT )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA14324

Drosophila persimilis

Dper\GL23696

Drosophila willistoni

Dwil\GK11546

Drosophila virilis

Dvir\GJ23560

Drosophila mojavensis

Dmoj\GI23585

Drosophila grimshawi

Dgri\GH19128

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091503ME )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17012058

Glossina morsitans

Tsetse fly

Gmor\GMOY007975

Mayetiola destructor

Hessian fly

Mdes\Mdes013645

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL010513

Anopheles gambiae

Malaria mosquito

Agam\AGAP003844

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ002379

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0J3H )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA010929

Danaus plexippus

Monarch butterfly

Dple\DPOGS209925-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL016750

Apis florea

Little honeybee

Aflo\2299741620

Apis mellifera

Western honey bee

Amel\GB52039

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP10206

Bombus terrestris

Buff-tailed bumblebee

Bter\15213043

Linepithema humile

Argentine ant

Lhum\LH22530

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:0004f8

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG012954

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG012953

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_10078

Tribolium castaneum

Red flour beetle

Tcas\TC012119

Pediculus humanus

Human body louse

Phum\PHUM134640

Rhodnius prolixus

Kissing bug

Rpro\cwo

Cimex lectularius

Bed bug

Clec\CLEC008475

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI24234

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_06851

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0J7Y )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR008480

Ixodes scapularis

Black-legged tick

Isca\ISCW004855

Stegodyphus mimosarum

African social velvet spider

Smim\KFM71673.1

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_317068

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )

No non-Arthropod Metazoa orthologies identified

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (12)

Gene Symbol

Score

Source

Alignment

dpn

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

2 of 10

Hey

2 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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 ( 1 )

Allele

Disease

Interaction

References

cwo^EP3470

exacerbates Alzheimer's disease

modeled by Hsap\APP^{Aβ42.GMR.Tag:SS(rPENK)}

(Cao et al., 2008)

Disease Associations of Human Orthologs (via DIOPT v8.0 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?

HELT; helt bHLH transcription factor

3 of 15

3 of 15

3 of 15

3 of 15

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

esyN Network Diagram

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

cwo - Atx2

anti tag coimmunoprecipitation, primer specific pcr

(Lim and Allada, 2013)

RNA-RNA

Physical Interaction

Assay

References

cwo - mir-let7

quantitative reverse transcription pcr, luminiscence technology, necessary binding region

(Chen et al., 2014)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

cwo

enhanceable

per

(Richier et al., 2008)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0259938

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

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

Transcription regulation of cwo gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-49

Cytogenetic map

86B3-86B3

Sequence location

3R:10,388,258..10,400,752 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

86B3-86B3

Limits computationally determined from genome sequence between P{PZ}jumu⁰⁶⁴³⁹&P{lacW}l(3)j8B6^j8B6 and P{PZ}hth⁰⁵⁷⁴⁵

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

86B-86B

(Prokopenko, 1999.11.10)

Experimentally Determined Recombination Data

Location

3-49

(FlyBase, 2016)

3-46.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

Bloomington

66745

w¹¹¹⁸; P{cwo-GFP.FPTB}attP40

26476

w¹¹¹⁸; Mi{ET1}cwo^MB09389

26318

y¹ v¹; P{TRiP.JF02091}attP2

27736

y¹ v¹; P{TRiP.JF02820}attP2

63786

w¹¹¹⁸; PBac{IT.GAL4}cwo^0794-G4

17508

y¹ w^67c23; P{EPgy2}cwo^EY15652

85593

w¹¹¹⁸; PBac{RB}cwo^e04207/TM6B, Tb¹

FlyORF

F000668

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

F004875

M{UAS-cwo.ORF-VNshort}ZH-86Fb

VDRC

v106783

P{KK110145}VIE-260B

v42821

w¹¹¹⁸; P{GD1250}v42821

v42822

w¹¹¹⁸; P{GD1250}v42822

More stocks available...

Genomic Clones (24)

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

cDNA Clones (43)

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 sequenced

BDGP DGC clones

Other clones

RT01038

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.

FBgn0259938

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0259938

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

44669

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Richier et al., 2008)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: cwo CG17100

(Lim et al., 2007)

Source for database merge of

Additional comments

Flanking sequence recovered from either side of the P{lacW} insertion in "stich1^S143702" are located at least 28kb apart on the genomic sequence. This suggests that there may be 2 different P{lacW} elements that map 28kb apart in the "l(3)S143702" line, or the P{lacW}stich1^S143702 insertion may be associated with a 28kb deletion. One set of flanking sequence indicates that the P{lacW} element is inserted approximately 90bp upstream of the 5' end of the GM05287 cDNA. The other set of flanking sequence maps within the first intron of "jumu", suggesting that both GM05287 and "jumu" may be affected in the "l(3)S143702" line. The molecular nature of the "stich1^D233" mutation is not known.

(Prokopenko et al., 2000)

It is not clear which gene is affected in "stich1" mutants, since the lesion in the "l(3)S143702" "stich1" mutant allele contains a deficiency which removes both "jumu" and "Rfx" sequences, associated with a P{lacW} insertion which is within the "jumu" gene and maps only approximately 90bp upstream of the 5' end of the "CG17100" GM05287 cDNA. "stich1" mutants complement "Rfx" mutants, so "stich1" likely corresponds to one of "jumu" and "CG17100" (see FBrf0151940 and FBrf0131381).

(FlyBase, 1992-)

Other Comments

Origin and Etymology

Discoverer

Etymology

The gene is dubbed "clockwork orange" given its potential clock function and the presence of an Orange domain.

(Lim et al., 2007)

Identification

External Crossreferences and Linkouts ( 37 )

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.

44669

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

Q9VGZ5

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q8MRI9

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0259938

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

FBgn0259938

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

cwo_1

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

CG17100

Flygut - An atlas of the Drosophila adult midgut

FBgn0259938

FlyMine - An integrated database for Drosophila genomics

FBgn0259938

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

432599

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

44669

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

TC012119

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

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

Dmel_CG17100

modMine - A data warehouse for the modENCODE project

FBgn0259938

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0259938

DRSC - Results frm RNAi screens

FBgn0259938

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0259938

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG17100-RA

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

Interactive Fly

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

Transcription regulation of cwo gene

Synonyms and Secondary IDs (13)

Reported As

Symbol Synonym

AAF24476.1

(Ledent and Vervoort, 2001)

CG17100

(Japanese National Institute of Genetics, 2012.5.21, Ellis and Carney, 2011, Ni et al., 2011.7.19, Nagoshi et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Perkins et al., 2009.3.31, Stevens et al., 2008, Stevens et al., 2008, Kadener et al., 2007, Keegan et al., 2007, Lim et al., 2007, Matsumoto et al., 2007, Shafer et al., 2006)

CWO

(He et al., 2017, Mendoza-Viveros et al., 2017, Ki et al., 2015, Lerner et al., 2015, Jackson, 2011, Lim et al., 2011)

Cwo

(Lerner et al., 2015, Kux et al., 2013, Tokusumi et al., 2012)

GM05287

(Prokopenko et al., 2000)

bHLHe49

(Stevens et al., 2008)

cwo

(Hung et al., 2020, Arnes et al., 2019, Faragó et al., 2019, Foley et al., 2019, Hsieh et al., 2019, Martin Anduaga et al., 2019, Meltzer et al., 2019, Bischof et al., 2018, Xue and Zhang, 2018, Abruzzi et al., 2017, Clandinin and Owens, 2016-, Schertel et al., 2015, Tataroglu and Emery, 2015, Alic et al., 2014, Chen et al., 2014, Weiss et al., 2014, Iyer et al., 2013, Lim and Allada, 2013, Mehta and Cheng, 2013, Pandey et al., 2013, Ling et al., 2012, Rakshit et al., 2012, Abruzzi et al., 2011, Ellis and Carney, 2011, Goda et al., 2011, Scribner and Fathallah-Shaykh, 2011, Allada and Chung, 2010, Duncan and Dearden, 2010, Fathallah-Shaykh, 2010, Kula-Eversole et al., 2010, Nagoshi et al., 2010, Wasbrough et al., 2010, Fathallah-Shaykh et al., 2009, Kadener et al., 2009, Kilman and Allada, 2009, Richier et al., 2008, Yang et al., 2008, Kadener et al., 2007, Lim et al., 2007, Matsumoto et al., 2007)

dcwo

(Fu et al., 2016)

mel_cwo

(Paquet et al., 2008)

Name Synonyms

CG17100

CLOCKWORK ORANGE

(Lerner et al., 2015)

Stich

(Cao et al., 2008)

clockwork orange

(Iyer et al., 2013, Rakshit et al., 2012, Scribner and Fathallah-Shaykh, 2011, Kadener et al., 2007, Keegan et al., 2007, Lim et al., 2007, Matsumoto et al., 2007)

clockworkorange

(Kadener et al., 2009)

Secondary FlyBase IDs

FBgn0259894
FBgn0016941
FBgn0011718
FBgn0037813

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (97)

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