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Gene 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	10 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	86B3-86B3	Sequence location	3R:6,213,985..6,226,477 [+]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene clockwork orange is referred to in FlyBase by the symbol Dmel\cwo (CG17100, FBgn0259938). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: negative regulation of transcription from RNA polymerase II promoter; circadian regulation of gene expression; regulation of circadian rhythm. 17 alleles are reported. No phenotypic data is available. It has 3 annotated transcripts and 3 annotated polypeptides. Protein features are: Helix-loop-helix DNA-binding; Orange; Orange subgroup. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Nearly all larval and adult tissues/organs expressed at moderate levels. Expression at high levels in the following post-embryonic organs or tissues: adult heart, adult fat body. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1623277_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of cwo. Gene sequence location is 3R:6213985..6226477.
External Summaries
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2012_01	References Fathallah-Shaykh, 2010, PLoS ONE 5(10): e11207 Controlled Vocabulary Terms negative regulation of transcription from RNA polymerase II promoter sequence-specific DNA binding transcription factor activity Sequence features HFA17072 BKN30145
FB2011_10	References Paquet et al., 2008, PLoS Comput. Biol. 4(2): e38
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
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)j8B6j8B6 and P{PZ}hth05745
Experimentally Determined Cytological Location
Cytogenetic map Notes References 86B-86B     (Prokopenko, 1999.11.10)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\cwo for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) cwo-RA FBtr0082246  NM_080036   4627   698 cwo-RB FBtr0305151     4506   621 cwo-RC FBtr0305152     4685   621
Additional Transcript Data & 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 protein cwo-PA   FBpp0081723   75.1   698   6.95     NP_524775   AAF54527 cwo-PB   FBpp0293681   66.3   621   6.96       cwo-PC   FBpp0293682   66.3   621   6.96
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Orange subgroup (IPR018352) Orange (IPR003650) Helix-loop-helix DNA-binding (IPR011598)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA696211   AA696726   AA697487   AE014297 AAF54527   AF175947   AF175948   AF203477 AAF24476   AI239131   AI388193   AY119588   BG637546   BI592111   BI592639   BI593301   BT006022   BT029285   BT053735   CO155786   CO156326   CO186498   CO195269   CO265139   CO274372   CO275092   CO291183   CO292987   CO298815   CO299088   CO320861   CO332560   CO333194   CO333448   EC060649   EC075164   EC196662   EC198132   EC200301   EC210309   EC216717   EC217653   EC217882   EC227705   EC232218   EC239845   EC244617   EC255472   EC263912   EC267601   EV584757
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9U450 Q9VGZ5
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
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)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
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
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0259938    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0259938 Very low expression bin max Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, in adult female stages. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0259938 expression level Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (836) embryo 02-04hr  (333) embryo 04-06hr  (384) embryo 06-08hr  (687) embryo 08-10hr  (950) embryo 10-12hr  (1199) embryo 12-14hr  (1251) embryo 14-16hr  (1966) embryo 16-18hr  (2063) embryo 18-20hr  (2072) embryo 20-22hr  (2213) embryo 22-24hr  (2094) larva L1  (1470) larva L2  (1046) larva L3 12hr old  (691) larva L3 puffstage 1-2  (624) larva L3 puffstage 3-6  (794) larva L3 puffstage 7-9  (767) white prepupae new  (825) white prepupae 12hr  (1183) white prepupae 24hr  (1076) pupae 2d postWPP  (918) pupae 3d postWPP  (713) pupae 4d postWPP  (613) adult male 01day  (1036) adult male 05day  (1095) adult male 30day  (1162) adult female 01day  (1470) adult female 05day  (1180) adult female 30day  (1320) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr  (1966) embryo 16-18hr  (2063) embryo 18-20hr  (2072) embryo 20-22hr  (2213) embryo 22-24hr  (2094) larva L1  1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day  1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0259938 expression level Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (836) embryo 02-04hr  (333) embryo 04-06hr  (384) embryo 06-08hr  (687) embryo 08-10hr  (950) embryo 10-12hr  (1199) embryo 12-14hr  (1251) embryo 14-16hr  (1966) embryo 16-18hr  (2063) embryo 18-20hr  (2072) embryo 20-22hr  (2213) embryo 22-24hr  (2094) larva L1  (1470) larva L2  (1046) larva L3 12hr old  (691) larva L3 puffstage 1-2  (624) larva L3 puffstage 3-6  (794) larva L3 puffstage 7-9  (767) white prepupae new  (825) white prepupae 12hr  (1183) white prepupae 24hr  (1076) pupae 2d postWPP  (918) pupae 3d postWPP  (713) pupae 4d postWPP  (613) adult male 01day  (1036) adult male 05day  (1095) adult male 30day  (1162) adult female 01day  (1470) adult female 05day  (1180) adult female 30day  (1320) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr  1966 embryo 16-18hr  2063 embryo 18-20hr  2072 embryo 20-22hr  2213 embryo 22-24hr  2094 larva L1  1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day  1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    836 embryo 02-04hr    333 embryo 04-06hr    384 embryo 06-08hr    687 embryo 08-10hr    950 embryo 10-12hr    1199 embryo 12-14hr    1251 embryo 14-16hr    1966 embryo 16-18hr    2063 embryo 18-20hr    2072 embryo 20-22hr    2213 embryo 22-24hr    2094 larva L1    1470 larva L2    1046 larva L3 12hr old    691 larva L3 puffstage 1-2    624 larva L3 puffstage 3-6    794 larva L3 puffstage 7-9    767 white prepupae new    825 white prepupae 12hr    1183 white prepupae 24hr    1076 pupae 2d postWPP    918 pupae 3d postWPP    713 pupae 4d postWPP    613 adult male 01day    1036 adult male 05day    1095 adult male 30day    1162 adult female 01day    1470 adult female 05day    1180 adult female 30day    1320 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     FlyAtlas Anatomical Expression Data for FBgn0259938    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0259938 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Nearly all larval and adult tissues/organs expressed at moderate levels. Expression at high levels in the following post-embryonic organs or tissues: adult heart, adult fat body. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval/adult carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (1000 - 25000) Linear, scaled to maximum FBgn0259938 expression level Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body  (558.6) Adult Salivary Gland    288.3 Adult Heart  (573.7) Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0259938 expression level Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body  558.6 Adult Salivary Gland    288.3 Adult Heart  573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    156.2 Larval Midgut    197.5 Larval Hindgut    311 Larval Malpighian Tubules    303.7 Larval Fat Body    397.6 Larval Salivary Gland    293.5 Larval Trachea    473.975 Larval Carcass    136.95 Adult Head    232.6 Adult Eye    303.625 Adult Brain    193.9 Adult Thoracic-Abdominal Ganglion    189.7 Adult Crop    296.5 Adult Midgut    184.3 Adult Hindgut    302.9 Adult Malpighian Tubules    341.8 Adult Fat Body    558.6 Adult Salivary Gland    288.3 Adult Heart    573.7 Adult VirginFemale Spermatheca    440.1 Adult InseminatedFemale Spermatheca    425.1 Adult Ovary    215 Adult Testis    33.4 Adult Male Accessory Gland    285 Adult Carcass    314.1 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    232.6   NA  Eye    303.625   NA  Brain    193.9   156.2  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    189.7   NA  Crop    296.5   197.5  Midgut    184.3   311  Hindgut    302.9   303.7  Malpighian Tubules    341.8   397.6  Fat Body    558.6   293.5  Salivary Gland    288.3   NA  Heart    573.7   473.975  Trachea    NA   NA  VirginFemale Spermatheca    440.1   NA  InseminatedFemale Spermatheca    425.1   NA  Ovary    215   NA  Testis    33.4   NA  Male Accessory Gland    285   136.95  Carcass    314.1 modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_09
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0259938 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG17100-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | pupal stage, with Scer\GAL4da.G32 cwoGS10340 viable cwoPB9 viable, with Scer\GAL4da.G32 cwoPB9 viable, with Scer\GAL4pnr-MD237 cwoGD1250 Other Phenotypes Allele circadian rhythm defective | adult stage (with Df(3R)RMSY) cwoPB9 circadian rhythm defective | adult stage | recessive cwoB9 cwoPB9 locomotor rhythm defective cwoe04207 cwof05073 locomotor rhythm defective, with Scer\GAL41118 cwodsRNA.IR.Scer\UAS locomotor rhythm defective, with Scer\GAL4P2.4.Pdf cwodsRNA.IR.Scer\UAS cwoΔb.Scer\UAS locomotor rhythm defective, with Scer\GAL4tim.PE cwodsRNA.Scer\UAS locomotor rhythm defective, with Scer\GAL4tim.Scer\UAS cwodsRNA.IR.Scer\UAS locomotor rhythm defective (with cwoe04207) cwof05073 locomotor rhythm defective (with cwof05073) cwoe04207 locomotor rhythm defective (with Df(3R)ED5495) cwoe04207 locomotor rhythm defective | recessive cwoe04207 cwof05073 Phenotype manifest in Allele
Classical Alleles ( 8 )
For All Classical Alleles Show
Allele of cwo Class Mutagen Stocks Known lesion cwoe04207 piggyBac transposase 1 Yes cwoEY15652 P-element activity 1 -- cwof05073 piggyBac transposase 1 Yes cwoGS10340 1 Yes cwoMB09389 1 -- cwoB9 amorphic allele - molecular evidence Delta2-3 0 Yes cwoPB9 amorphic allele - molecular evidence ethyl methanesulfonate 0 Yes cwoEP3470 0 --
Alleles Carried on Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Allele of cwo Class Mutagen Stocks Known lesion cwoGD1250 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes cwoJF02091 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cwoJF02820 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cwoKK110145 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cwodsRNA.IR.Scer\UAS in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes cwodsRNA.Scer\UAS in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes cwoScer\UAS.cKa in vitro construct - regulatory fusion 0 Yes cwoScer\UAS.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cwoΔb.Scer\UAS in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)Exel6266 (Ryder, 2004.4.26) Df(3R)RMSY (Richier et al., 2008)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{KK110145} NA P{TRiP.JF02091} NA P{TRiP.JF02820} NA P{UAS-cwo.FLAG} NA P{UAS-cwo.IR} NA P{UAS-cwo.K} NA P{UAS-cwo.RNAi} NA P{UAS-cwo.Δb} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}cwoEP3470 NA P{EPgy2}cwoEY15652 NA P{GSV6}cwoGS10340 NA miscellaneous insertions P{WF6}R32 NA PBac{RB}cwoe04207 NA PBac{WH}cwof05073 NA insertion of enhancer trap binary system Mi{ET1}cwoMB09389 No P{GawB}c632a No
Gene Ontology: Function, Process & Cellular Component ( 7 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity inferred from direct assay (Kadener et al., 2007, Matsumoto et al., 2007)
Biological Process
CV term Evidence References
circadian regulation of gene expression inferred from mutant phenotype (Richier et al., 2008) negative regulation of transcription from RNA polymerase II promoter inferred from direct assay (Kadener et al., 2007, Matsumoto et al., 2007) regulation of circadian rhythm inferred from mutant phenotype (Lim et al., 2007, Matsumoto et al., 2007, Kadener et al., 2007)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Matsumoto et al., 2007)
Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term Evidence References
DNA binding inferred from electronic annotation with InterPro:IPR003650 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
regulation of transcription, DNA-dependent inferred from sequence or structural similarity with Hey (Peyrefitte et al., 2001)
Cellular Component
CV term Evidence References
nucleus non-traceable author statement (Prokopenko, 1999.11.10)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions cwo allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0259938
Orthologs
Genome-wide drosophilid orthologs	Dana\GF17529 Dere\GG17540 Dgri\GH19128 Dmoj\GI23585 Dper\GL23696 Dpse\GA14324 Dsec\GM23880 Dsim\GD18691 Dvir\GJ23560 Dwil\GK11546 Dyak\GE26033
Curated drosophilid orthologs	Dpse\GA14324
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • XP_001121958.1 Apis mellifera (honey bee) 103107 Branchiostoma floridae (lancelet) BGIBMGA010929-PA Bombyx mori (silk worm) 196737 Capitella spl (polychaete worm) ENSP00000242728 Homo sapiens (human) ISCW004855-PA Ixodes scapularis (deer tick) ENSMODP00000020661 Monodelphis domestica (gray opossum) ENSMUSP00000032386 Mus musculus (house mouse) PHUM006980-PA Pediculus humanus (human body louse) ENSPTRP00000008155 Pan troglodytes (chimpanzee) XP_001812240.1 Tribolium castaneum (red flour beetle) ENSTRUP00000037143 Takifugu rubripes (pufferfish Takifugu)
Stocks & Reagents
Stocks Listed in FlyBase ( 10 )
Bloomington	26476 w1118; Mi{ET1}cwoMB09389 26318 y1 v1; P{TRiP.JF02091}attP2 27736 y1 v1; P{TRiP.JF02820}attP2 17508 y1 w67c23; P{EPgy2}cwoEY15652
Harvard	- PBac{RB}cwoe04207 - PBac{WH}cwof05073
Kyoto	202488 y1 w67c23; P{GSV6}cwoGS10340/TM3, Sb1 Ser1
VDRC	v106783 P{KK110145}VIE-260B v42821 w1118; P{GD1250}v42821 v42822 w1118; P{GD1250}v42822
Genomic Clones ( 1 )
	BACR03L12 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 44 )
	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	GM02743 LD15411 RE11081
Other clones	RT01038
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH19011 GM02755 GM05287 HL02604 RH09733 RH10383 RH11307
Other clones	1380 12489 14296 31637 34003 58948 72782 183544 214467.35 281304 281591 525576 527734 CK01.22A.F3 CK01.32C.D6 CK01.99B.H11 Dmel_dig_002245_0625_0494 EC39957 EK020322 EK076432 EK113923 EK116435 EK141628 EK173922 EK174458 EK201354 EK288538 EK303908 EK306155 EK306950 EN06737 EN07841 GM08264
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0259938 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44669
Antibody Information
	polyclonal (Richier et al., 2008)
Other Information
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
Relationship to Other Genes
Source for database identity 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 "stich1S143702" 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}stich1S143702 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 "stich1D233" 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
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_080036 RefSeq (Proteins) • NP_524775 DDBJ / EMBL / GenBank • AA696211 AAF24476 AAF54527 AF175947 AF175948 AF203477 Entrez Gene - A searchable database of RefSeq genes. • 44669 UniProtKB/TrEMBL • Q9U450 Q9VGZ5
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Orange subgroup (IPR018352) Orange (IPR003650) Helix-loop-helix DNA-binding (IPR011598)
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0259938 DRSC - Results from 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 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0259938 FlyReactome - A curated knowledgebase of Drosophila melanogaster pathways • 432599 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44669 InParanoid A subset of ortholog calls from InParanoid. • XP_001121958.1 Apis mellifera (honey bee) 103107 Branchiostoma floridae (lancelet) BGIBMGA010929-PA Bombyx mori (silk worm) 196737 Capitella spl (polychaete worm) ENSP00000242728 Homo sapiens (human) ISCW004855-PA Ixodes scapularis (deer tick) ENSMODP00000020661 Monodelphis domestica (gray opossum) ENSMUSP00000032386 Mus musculus (house mouse) PHUM006980-PA Pediculus humanus (human body louse) ENSPTRP00000008155 Pan troglodytes (chimpanzee) XP_001812240.1 Tribolium castaneum (red flour beetle) ENSTRUP00000037143 Takifugu rubripes (pufferfish Takifugu) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /genebrief/clockwkorange.htm modMine - Data generated by the modENCODE project. • FBgn0259938
Synonyms & Secondary IDs ( 11 )
Reported As
Symbol Synonym	AAF24476.1 (Ledent and Vervoort, 2001) bHLHe49 (Stevens et al., 2008) CG17100 (Matsumoto et al., 2007, Lim et al., 2007, Kadener et al., 2007, Stevens et al., 2008, Stevens et al., 2008, Perkins et al., 2009.3.31, Keleman et al., 2009.8.5, Perkins et al., 2009, Shafer et al., 2006, Nagoshi et al., 2010, Ellis and Carney, 2011) cwo (Matsumoto et al., 2007, Lim et al., 2007, Kadener et al., 2007, Kadener et al., 2009, Yang et al., 2008, Richier et al., 2008, Kula-Eversole et al., 2010, Nagoshi et al., 2010, Duncan and Dearden, 2010, Ellis and Carney, 2011, Fathallah-Shaykh et al., 2009, Wasbrough et al., 2010, Fathallah-Shaykh, 2010) CWO (Lim et al., 2011) GM05287 (Prokopenko et al., 2000) mel_cwo (Paquet et al., 2008) unnamed (Durand et al., 2000)
Name Synonym	CG17100   clockwork orange (Lim et al., 2007, Matsumoto et al., 2007, Kadener et al., 2007) clockworkorange (Kadener et al., 2009) Stich (Cao et al., 2008)
Secondary FlyBase IDs
	FBgn0011718 FBgn0016941 FBgn0037813 FBgn0259894
References ( 40 )
Generate a list of	All references relating to this gene ( 40 )
List References by type	Research paper  ( 22 ) Supplementary material  ( 4 ) Personal communication to FlyBase  ( 9 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Computer file  ( 2 ) Automatic genome annotation  ( 1 )
Recent research papers ( 7 )
	Ellis and Carney, 2011, Genetics 187(1): 157--169 Socially-Responsive Gene Expression in Male Drosophila melanogaster Is Influenced by the Sex of the Interacting Partner. [FBrf0212780] Goda et al., 2011, PLoS Genet. 7(7): e1002167 Adult Circadian Behavior in Drosophila Requires Developmental Expression of cycle, But Not period. [FBrf0214302] Lim et al., 2011, Nature 470(7334): 399--403 The novel gene twenty-four defines a critical translational step in the Drosophila clock. [FBrf0213059] Duncan and Dearden, 2010, Genome Res. 20(7): 917--928 Evolution of a genomic regulatory domain: the role of gene co-option and gene duplication in the Enhancer of split complex. [FBrf0211195] Fathallah-Shaykh, 2010, PLoS ONE 5(10): e11207 Dynamics of the Drosophila circadian clock: theoretical anti-jitter network and controlled chaos. [FBrf0212140] Kula-Eversole et al., 2010, Proc. Natl. Acad. Sci. U.S.A. 107(30): 13497--13502 Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila. [FBrf0211416] Nagoshi et al., 2010, Nat. Neurosci. 13(1): 60--68 Dissecting differential gene expression within the circadian neuronal circuit of Drosophila. [FBrf0209632] Show all research papers ...