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Gene Dmel\rn

General Information
Symbol	Dmel\rn	Species	D. melanogaster
Name	rotund	Annotation symbol	CG42277
Feature type	protein_coding_gene	FlyBase ID	FBgn0259172
Gene Model Status	Current	Stock availability	101 publicly available
Also Known As	roe, CG10040, P5.3
Genomic Location
Chromosome (arm)	3R	Recombination map	3-47.6
Cytogenetic map	84D3-84D3	Sequence location	3R:3,098,339..3,135,351 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents Beta	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene rotund is referred to in FlyBase by the symbol Dmel\rn (CG42277, FBgn0259172). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: compound eye development; negative regulation of transcription from RNA polymerase II promoter; imaginal disc-derived leg morphogenesis; negative regulation of transcription, DNA-dependent. 77 alleles are reported. The phenotypes of these alleles are annotated with: adult segment; organ system subdivision; organ system; external compound sense organ; thoracic segment; appendage segment; imaginal precursor; epithelial furrow; metatarsus; peripheral nervous system. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: Zinc finger C2H2-type/integrase DNA-binding domain; Zinc finger, C2H2; Zinc finger, C2H2-like. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of low expression to a trough of no expression detected. Peak expression observed within 12-24 hour embryonic stages, during late larval stages, at stages throughout the pupal period, in adult male stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Gene sequence location is 3R:3098339..3135351.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	rn: rotund (S. Kerridge) rn: rotund From Bridges and Brehme, 1944, Carnegie Inst. Washington Publ. No. 552: 159. All alleles are viable as homozygotes. Both males and females are sterile; sterility is not germ line dependent. Two transcripts from the rotund region of Drosophila show similar positional specificities in imaginal disc tissues. Adult defects are restricted to homologous distal parts of the appendages, i.e., the antennae, legs, wings, halteres, and proboscis. In the antenna the basal capsule is missing and the third antennal segment is reduced in size; all other antennal and eye disc derivatives are normal. In all three pairs of legs abnormalities caused by the lack of rn+ product are localized specifically in the tarsus; instead of five individual tarsal segments, a single tarsus-like segment differentiates. The distal claw and proximal leg articulations (tibia, femur, trochanter, and coxa) are unaffected. Incomplete and duplicated joints seen at the presumptive positions of the tarsus 1-2 and 4-5 joints; intermediate joints virtually absent (Held, Duarte, and Derakhshanian, 1986, Wilhelm Roux's Arch. Dev Biol. 195: 145-57). Of the wing disc derivatives, the medial and distal costa are fused and the corresponding region in the posterior wing, the alula, is smaller, making the wing as a whole appear shorter; distal wing and mesonotum are formed as in wild type. Vein L5 and to a lesser extent L2 interrupted (rn3). Specific and localized deficiencies of labial and haltere disc derivatives are also evident. Genital and abdominal patterns are indistinguishable from wild-type patterns; however, seminal receptacles shorter than in wild-type females. Examination of the imaginal discs from third-instar rn larvae shows localized cell death in regions determined from fate maps to give rise to distal appendage parts (Cavallin). rnD: rotund-Dominant Dominant mutation with complete penetrance and high expressivity. In Dipr/+ flies the distal wing blade reduced to two-thirds normal length; triple row replaced by two to three rows of irregularly sized bristles resembling those found on costa; occasionally these bristles may be bracted as are those of proximal costa. Posterior row of marginal bristles absent distally. Venation in proximal portion of wing irregular and crowded but more nearly normal distally. Trichomes of wing blade organized into whorls. Capitellum of haltere covered with small adventitious bristles and sometimes pedicellar-like sensilla. Pleura, coxa, trochanter, femur, tibia, and fifth tarsal segment unaffected; other tarsal segments reduced; tarsal segments two to four variably fused; ectopic sex combs form on second tarsal segment in 70-90% of forelegs. Basal cylinder of antenna reduced or missing; replaced by bristle elements at third-segment-arista junction resembling those on third segment. Proboscis contains five to seven rows of pseudotracheae rather than normal twelve; replaced by bristles laterally. Kerridge suggests transformation of distal into more proximal appendage elements. Homozygotes survive and are more extreme. roe: roughened eye Produces a slight roughening of the eye owing to the irregular disposition of the facets; interommatidial bristles lost from posterior portion of the eye. Extreme expression in mutant/deficiency heterozygotes and more so in deficiency homozygotes; enhanced roughening and posterior loss of ommatidial bristles; in addition the eye is reduced in size and remaining interommatidial bristles are clumped. RK1.
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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FB2013_03	Alleles rn[MI07760] rn[MI05987]
FB2013_02
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 84D3-84D3   Limits computationally determined from genome sequence between P{EP}EP3060EP3060 and P{PZ}grn05930
Experimentally Determined Cytological Location
Cytogenetic map Notes References 84D-84E   (determined by in situ hybridisation)   (Shilkova et al., 2000) 84D3-84D4   (determined by in situ hybridisation)   (Agnel et al., 1989)
Experimentally Determined Recombination Data
Location	3-47.6 (Puro and Nygren, 1975) 3-47.7 +/- 1.1 (Carlson, 1956)
Left of (cM)
Right of (cM)	Antp (Lewis et al., 1980)
Notes	Mapping based on rn3. (Puro and Nygren, 1975)
Gene Model & Products
Please see the GBrowse view of Dmel\rn for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.43 Gene model reviewed during 5.44 Gene model reviewed during 5.49 gene_with_stop_codon_read_through ; SO:0000697 Stop-codon suppression (UAG) postulated; FBrf0216884. Due to an oversight in the implementation of gene annotation merges, the symbols for some of the transcripts and polypeptides of this gene were changed to non-unique designations in r5.8. Although there were no conflicts within a given release, the same symbols were used for different isoforms in different releases. The affected gene product symbols have now been changed to symbols not used previously in the database; see individual transcript reports for details.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) rn-RC FBtr0299637  NM_206456   3565   692 rn-RE FBtr0300518  NM_141458   5014   946 rn-RF FBtr0299639  NM_001144549   4270   927 rn-RG FBtr0330140  NM_001275414   5014   952
Additional Transcript Data & Comments
Reported size (kB)	5.3, 1.7 (northern blot) (Agnel et al., 1989) 1.7 (unknown) (Agnel et al., 1992)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein rn-PC   FBpp0288912   75.8   692   9.40     NP_996178   AAS65102 rn-PE   FBpp0289745   100.9   946   8.24     NP_649715   AAF54032 rn-PF   FBpp0288914   99.6   927   8.23     NP_001138021   ACL83480 rn-PG   FBpp0303173   101.6   952   8.23     NP_001262343   AGB95726
Additional Polypeptide Data & Comments
Reported size (kDa)	384 (aa); 44 (kD) (Agnel et al., 1992) 384, 383 (aa) (Hoemann et al., 1996)
Comments	It is unclear which ATG is used for translation initiation. If the downstream ATG is the actual initation site, the protein is 362aa and 41kD. (Agnel et al., 1992) form 1 (FlyBase, 1992-) form 2 (FlyBase, 1992-)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger C2H2-type/integrase DNA-binding domain (IPR013087) Zinc finger, C2H2-like (IPR015880) Zinc finger, C2H2 (IPR007087)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF54032   AE014297 AAS65102   AC008029   AE014297 ACL83480   AF395904 AAL59598   AF395905 AAL59599   AE014297 AGB95726   AY118393   BT022161   BT024401   CO264055   CO271450   CO271622   CO271633   CO306975   CO308502   CO328597   CO343248   CZ484348   CZ484349   CZ485563   CZ485564   CZ488326   EC060086   EC077472   EC079461   EC090461   EC203755   EC217919   EC220206   EC221217   EC226155   EC232126   EC232129   EL872987   EL872988   EL873163   EL873259   EL873260
UniProtKB/Swiss-Prot	Q9VI93
UniProtKB/TrEMBL	B7Z0U8 B7Z0U9
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
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference pupal stage | early   imaginal disc   (Agnel et al., 1992) pupal stage & spermatogenesis & adult stage   spermatocyte   (Agnel et al., 1992) spermatogenesis & adult stage   testis   (Agnel et al., 1992, Hoemann et al., 1996) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic labial sensory complex   (Fisher et al., 2012) embryonic maxillary sensory complex   (Fisher et al., 2012) labral sensory complex   (Fisher et al., 2012) prepupal stage P1 -- P2   adepithelial cell of wing disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF antennal disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF wing disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF haltere disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF genital disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF labial disc   (Agnel et al., 1989) Comment:reference states 0-2 hr APF ventral thoracic disc   (Agnel et al., 1989) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage -- pupal stage     (Agnel et al., 1989) larval stage & pupal stage     (Agnel et al., 1989) pcr Stage Tissue/Position (including subcellular localization) Reference adult stage | female     (Hoemann et al., 1996) adult stage | male     (Hoemann et al., 1996) oogenesis & adult stage | female   ovary   (Hoemann et al., 1996) spermatogenesis & adult stage   testis   (Hoemann et al., 1996)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (del Alamo and Mlodzik, 2008)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. [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 (>999.999) 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 Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    25 central nervous system, larvae L3    17 central nervous system, pupae P8    7 head, virgin 1-day female    3 head, virgin 4-day female    4 head, virgin 20-day female    3 head, mated 1-day female    4 head, mated 4-day female    3 head, mated 20-day female    2 head, mated 1-day male    6 head, mated 4-day male    6 head, mated 20-day male    5 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    2 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    3 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression 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 low expression to a trough of no expression detected. Peak expression observed within 12-24 hour embryonic stages, during late larval stages, at stages throughout the pupal period, in adult male stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    0 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    1 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    4 larva L3 puffstage 7-9    4 white prepupae new    4 white prepupae 12hr    4 white prepupae 24hr    4 pupae 2d postWPP    4 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    2 adult male 30day    2 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  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     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Cell Line Expression Data (modENCODE_mRNA-Seq_cell.A) (modENCODE_mRNA-Seq_cell.B)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1  (30) wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1  30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    22 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    0 embryonic S1    0 embryonic S3    0 leg disc CME L1    30 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    3 cold shock, 4-day adult    3 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_04 mE1_20_mRNA_expression_cluster_13
External Data & Images
Linkouts	BDGP expression data • IP01358 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0259172 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG32467-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal (with Df(3R)Scx4) rnroe-KE80 rnroe-KE350 rnroe-KE409 rnroe-KX316 lethal | pupal stage, with Scer\GAL4pnr-MD237 rnGD10678 viable rn1-5 rn2-1 rn2 rn89 rnf01856 rnroe-SC1 viable (with Df(3R)Scx4) rnroe-KE17 rnroe-KE18 rnroe-KE27 rnroe-KE55 rnroe-KE89 rnroe-KE100 rnroe-KE113 rnroe-KE345 rnroe-KE380 rnroe-KE399 rnroe-KE405 rnroe-KEK2 rnroe-KX314 Sterility Allele female sterile | partially | recessive rn2 female sterile | recessive rn13-1 rn89300-2 rn89386 rn920017 rn921314 rn921503 fertile rn89 rnf01856 male sterile | recessive rn2 rn13-1 rn89300-2 rn89386 rn920017 rn921314 rn921503 sterile rn4 rn7 rn8 rn10 rn16 rn21 rn23 rnX49 Other Phenotypes Allele locomotor behavior defective | recessive rn13-1 short lived | recessive rn13-1 visible rnroe-1 rnroe-2 rnroe-3 rnroe-4 rnroe-SC1 rnΔ2-2 visible, with Scer\GAL4GMR.PF rnroe.Scer\UAS rnScer\UAS.cSPa visible, with Scer\GAL4rn-GAL4-5 rnroe.Scer\UAS visible (with Df(3R)rn20) rn5 rn16 rn19 rnGAL4-5 rnroe-SC1 rnΔ2-2 visible (with Df(3R)Scx4) rnroe-KE17 rnroe-KE18 rnroe-KE27 rnroe-KE55 rnroe-KE89 rnroe-KE100 rnroe-KE113 rnroe-KE345 rnroe-KE380 rnroe-KE399 rnroe-KE405 rnroe-KEK2 rnroe-KX314 visible (with rn5) rnroe-SC1 visible (with rnroe-SC1) rn5 visible | recessive rn3 rn13-1 rn89300-2 rn89386 rn920017 rn921314 rn921503 rnDipr rnroe-2 rnroe-3 Phenotype manifest in Allele alula rn3 rnDipr antenna rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 rni13 costal cell rn3 rnDipr egg chamber rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 eye rn10 rn13-1 rn16 rn21 rn23 rn4 rn7 rn8 rn89386 rn920017 rn921314 rn921503 rnX49 rnroe-1 rnroe-2 rnroe-3 rnroe-4 rnroe-KE350 rnroe-KE409 rnroe-KE80 rnroe-KX316 rnroe-SC1 eye, with Scer\GAL4GMR.PF rnScer\UAS.cSPa rnroe.Scer\UAS eye (with Df(3R)rn20) rn16 rnroe-SC1 eye (with Df(3R)Scx4) rnroe-KE100 rnroe-KE113 rnroe-KE17 rnroe-KE18 rnroe-KE27 rnroe-KE345 rnroe-KE380 rnroe-KE399 rnroe-KE405 rnroe-KE55 rnroe-KE89 rnroe-KEK2 rnroe-KX314 eye disc (with Df(3R)rn20) rn16 eye photoreceptor cell rnroe-SC1 eye photoreceptor cell (with Df(3R)rn20) rn16 female genitalia rn89300-2 rn89386 rn920017 rn921314 rn921503 fourth segment of antenna rn89300-2 rn89386 rn920017 rn921314 rn921503 haltere rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 interommatidial bristle, with Scer\GAL4GMR.PF rnroe.Scer\UAS leg rn13-1 rni13 leg (with Df(3R)rn20) rnroe-SC1 leg (with rn5) rnroe-SC1 leg (with rnroe-SC1) rn5 leg | distal rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 male genitalia rn89300-2 rn89386 rn920017 rn921314 rn921503 metatarsus (with Df(3R)rn20) rn16 morphogenetic furrow (with Df(3R)rn20) rn16 ommatidium rn13-1 rnroe-1 rnroe-2 rnroe-3 rnroe-KE350 rnroe-KE409 rnroe-KE80 rnroe-KX316 ommatidium (with Df(3R)Scx4) rnroe-KE100 rnroe-KE113 rnroe-KE17 rnroe-KE18 rnroe-KE27 rnroe-KE345 rnroe-KE380 rnroe-KE399 rnroe-KE405 rnroe-KE55 rnroe-KE89 rnroe-KEK2 rnroe-KX314 oocyte rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 ovary rn10 rn13-1 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 pigment cell, with Scer\GAL4GMR.PF rnroe.Scer\UAS posterior crossvein rn89386 rn920017 rn921314 rn921503 pretarsus (with Df(3R)rn20) rn16 proboscis rn10 rn16 rn21 rn23 rn4 rn7 rn8 rnX49 seminal receptacle rn18 rn19 rn5 rnX49 sex comb rn1 rn10 rn13-1 rn16 rn21 rn23 rn4 rn7 rn8 rn89386 rn920017 rn921314 rn921503 rnX49 rni13 sex comb (with Df(3R)rn20) rn16 tarsal segment rn13-1 rn2 rn89300-2 rn89386 rn920017 rn921314 rn921503 rnroe-SC1 tarsal segment 2 rn3 tarsal segment 2 (with Df(3R)rn20) rn16 rn5 tarsal segment 3 rn3 tarsal segment 3 (with Df(3R)rn20) rn16 rn5 tarsal segment 4 rn3 tarsal segment 4 (with Df(3R)rn20) rn16 rn5 tarsal segment, with Scer\GAL4rn-GAL4-5 rnroe.Scer\UAS tarsal segment (with Df(3R)rn20) rnΔ2-2 rn19 rnGAL4-5 wing rn1 rn13-1 rn3 rn89300-2 rn89386 rn920017 rn921314 rn921503 rni13 wing (with Df(3R)rn20) rnroe-SC1 wing (with rn5) rnroe-SC1 wing (with rnroe-SC1) rn5 wing | distal rnroe-SC1 wing | proximal rn10 rn16 rn21 rn23 rn3 rn4 rn7 rn8 rnDipr rnX49 wing hinge rnΔ2-2 wing vein L2 rn13-1 rn2 rn3 rn89300-2 rn89386 rn920017 rn921314 rn921503 wing vein L5 rn13-1 rn3 rn89386 rn920017 rn921314 rn921503
Classical Alleles ( 72 )
For All Classical Alleles Show
Allele of rn Class Mutagen Stocks Known lesion rnroe-1 hypomorphic allele - genetic evidence spontaneous 71 -- rn1 X ray 4 -- rn3 X ray 4 -- rn5 gamma ray X ray 2 -- rnf01856 piggyBac transposase 2 -- rn16 diepoxybutane 1 Yes rn19 diepoxybutane 1 Yes rn89 P-element activity 1 Yes rnf03006 piggyBac transposase 1 -- rnf05710 piggyBac transposase 1 -- rnGAL4-5 gene conversion P-element activity 1 Yes rnGAL4-DeltaS loss of function allele P-element activity 1 Yes rnMB03984 1 -- rnMB05313 1 -- rnMI01393 1 -- rnMI05987 1 -- rnroe-2 hypomorphic allele - genetic evidence ethyl methanesulfonate 1 -- rnroe-3 ethyl methanesulfonate 1 Yes rnΔ2-2 P-element activity 1 Yes rn1-5 P-element activity 0 Yes rn10 ethyl methanesulfonate 0 -- rn11 ethyl methanesulfonate 0 Yes rn13-1 hobo activity 0 -- rn14 ethyl methanesulfonate 0 -- rn15 ethyl methanesulfonate 0 -- rn18 hypomorphic allele - genetic evidence diepoxybutane 0 -- rn2-1 P-element activity 0 Yes rn21 diepoxybutane 0 -- rn23 diepoxybutane 0 -- rn2 spontaneous 0 -- rn4 ethyl methanesulfonate 0 -- rn6 X ray 0 -- rn7 ethyl methanesulfonate 0 -- rn89300-2 natural population 0 -- rn89386 natural population 0 -- rn8 ethyl methanesulfonate 0 -- rn920017 natural population 0 -- rn921314 natural population 0 -- rn921503 natural population 0 -- rnBM10 ethyl methanesulfonate 0 -- rnDipr X ray 0 Yes rnFC8 X ray 0 -- rnGAL4-13 gene conversion P-element activity 0 Yes rnGAL4-14 gene conversion P-element activity 0 Yes rni13 gamma ray 0 -- rnKK16 ethyl methanesulfonate 0 -- rnKM29 ethyl methanesulfonate 0 -- rnMI07760 0 -- rnroe-4 0 -- rnroe-KE100 ethyl methanesulfonate 0 -- rnroe-KE113 ethyl methanesulfonate 0 -- rnroe-KE17 ethyl methanesulfonate 0 -- rnroe-KE18 ethyl methanesulfonate 0 -- rnroe-KE27 ethyl methanesulfonate 0 -- rnroe-KE345 ethyl methanesulfonate 0 -- rnroe-KE350 ethyl methanesulfonate 0 -- rnroe-KE380 ethyl methanesulfonate 0 -- rnroe-KE399 ethyl methanesulfonate 0 -- rnroe-KE405 ethyl methanesulfonate 0 -- rnroe-KE409 ethyl methanesulfonate 0 -- rnroe-KE55 ethyl methanesulfonate 0 -- rnroe-KE80 ethyl methanesulfonate 0 -- rnroe-KE89 ethyl methanesulfonate 0 -- rnroe-KEK2 ethyl methanesulfonate 0 -- rnroe-KX314 X ray 0 -- rnroe-KX316 X ray 0 -- rnroe-P8 X ray 0 -- rnroe-SC1 ethyl methanesulfonate 0 -- rnSM8 ethyl methanesulfonate 0 -- rnunspecified 0 -- rnX130 X ray 0 -- rnX49 hypomorphic allele - genetic evidence X ray 0 --
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of rn Class Mutagen Stocks Known lesion rnroe.Scer\UAS in vitro construct - regulatory fusion 2 Yes rnScer\UAS.cSPa in vitro construct - regulatory fusion 2 Yes rnGD10678 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes rnGD4587 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes rnKK102474 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes rnKK110545 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes rnΔ894.Scer\UAS in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)Antp1 (Lewis et al., 1980, Agnel et al., 1989) Df(3R)Antp17 (Duncan and Kaufman, 1975, Lewis et al., 1980, Wakimoto et al., 1984, Baker et al., 1991) Df(3R)D6 (Cavener et al., 1986, Baker et al., 1991) Df(3R)dsx2M (Cavener et al., 1986, Agnel et al., 1989, Baker et al., 1991) Df(3R)dsx10M (Sotillos and Campuzano, 2000, Cavener et al., 1986, Baker et al., 1991) Df(3R)dsx29 (Cavener et al., 1986, Agnel et al., 1989, Baker et al., 1991) Df(3R)ED5221 (Roote, 2004.7.20) Df(3R)Exel6146 (Ryder, 2004.4.26) Df(3R)F76 (Cavener et al., 1986) Df(3R)rn3 (Agnel et al., 1989) Df(3R)rn5 (Agnel et al., 1989) Df(3R)rn17 (Agnel et al., 1989) Df(3R)rn19 (Agnel et al., 1989) Df(3R)rn20 (Griffin-Shea, 1998.8.12, Agnel et al., 1989, Ma et al., 1996) Df(3R)rn22 (Agnel et al., 1989) Df(3R)Scx4 (Cavener et al., 1986, Agnel et al., 1989) In(3)rnXT130 (Agnel et al., 1989) In(3R)rnDipr+R1 (Agnel et al., 1989) In(3R)rnDipr+R2 (Agnel et al., 1989) In(3R)rnDipr+R5 (Agnel et al., 1989) In(3R)rnDipr+R7 (Agnel et al., 1989) In(3R)rnDipr+R9 (Agnel et al., 1989) In(3R)rnDipr (Kerridge, 1981, Agnel et al., 1989) T(2;3)P8 (Baker et al., 1991) T(2;3)rn (Agnel et al., 1989) Tp(3;1)FC8 (Agnel et al., 1989) Tp(3;3)Antp1 (Lewis et al., 1980)
Not disrupted in	Df(3R)Antp-A41 (Cavener et al., 1986) Df(3R)Antp-X1 (Cavener et al., 1986) Df(3R)D7 (Baker et al., 1991) Df(3R)dsx1 (Duncan and Kaufman, 1975) Df(3R)dsx2D (Duncan and Kaufman, 1975, Baker et al., 1991) Df(3R)dsx3 (Baker et al., 1991) Df(3R)dsx5 (Duncan and Kaufman, 1975) Df(3R)dsx10M (Cavener et al., 1986) Df(3R)dsx11 (Baker et al., 1991) Df(3R)dsx15 (Baker et al., 1991) Df(3R)dsx21 (Baker et al., 1991) Df(3R)dsx43 (Baker et al., 1991) Df(3R)p13 (Baker et al., 1991) Df(3R)p30 (Baker et al., 1991) Df(3R)p40 (Baker et al., 1991) Df(3R)Scr (Lewis et al., 1980, Wakimoto et al., 1984, Cavener et al., 1986) Df(3R)Scx2 (Wakimoto et al., 1984, Cavener et al., 1986) Df(3R)Tpl10 (Cavener et al., 1986) Df(3R)WIN3 (Cavener et al., 1986) In(3R)Antprv2 (Duncan and Kaufman, 1975, Lewis et al., 1980)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4587} NA P{KK102474} NA P{KK110545} NA P{UAS-rn.SP} NA P{UAS-rnΔ894} NA P{UAS-roe.SP} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions H{}rn13-1 NA Mi{MIC}rnMI01393 NA Mi{MIC}rnMI05987 NA Mi{MIC}rnMI07760 NA P{5'3'}rn1-5 NA P{5'3'}rn2-1 NA P{GawB.DeltaS}rnGAL4-DeltaS NA PBac{WH}rnf01856 NA PBac{WH}rnf03006 NA PBac{WH}rnf05710 NA insertion of enhancer trap P{lArB}rn89 No P{lArB}rnΔ2-2 No insertion of enhancer trap binary system Mi{ET1}rnMB03984 No Mi{ET1}rnMB05313 No P{GawB}rnGAL4-5 No P{GawB}rnGAL4-13 No P{GawB}rnGAL4-14 No
Gene Ontology: Function, Process & Cellular Component ( 10 unique terms )
Terms Based on Experimental Evidence ( 6 terms )
Molecular Function
CV term Evidence References
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity inferred from direct assay (del Alamo and Mlodzik, 2008)
Biological Process
CV term Evidence References
compound eye development inferred from mutant phenotype (St Pierre et al., 2002, del Alamo and Mlodzik, 2008) imaginal disc-derived leg morphogenesis inferred from mutant phenotype (St Pierre et al., 2002) negative regulation of transcription, DNA-dependent inferred from mutant phenotype (Dichtel-Danjoy et al., 2009) negative regulation of transcription from RNA polymerase II promoter inferred from mutant phenotype (del Alamo and Mlodzik, 2008)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (del Alamo and Mlodzik, 2008)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
nucleic acid binding inferred from electronic annotation with InterPro:IPR013087 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with worm lin-29 (FlyBase Genome Annotators, 2002-2003) zinc ion binding inferred from electronic annotation with InterPro:IPR007087, InterPro:IPR015880 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
regulation of transcription, DNA-dependent inferred from sequence or structural similarity with worm lin-29 (FlyBase Genome Annotators, 2002-2003)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with worm lin-29 (FlyBase Genome Annotators, 2002-2003)
Sequence Ontology: Class of Gene
	gene_with_stop_codon_read_through (Jungreis et al., 2011) nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
rn - B52 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - CG11107 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - CG17768 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - CG6724 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - CG8728 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - CG9667 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Cbp80 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Cp1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Cypl anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Dp1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Elongin-B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Hsp68 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Imp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Prosβ6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - RpL7-like anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - Rpb8 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - SmD2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - SmD3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - SmG anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - U4-U6-60K anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - bsf anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - drk anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - eIF6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - kst anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - shrb anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - skpA anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) rn - εCOP anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions rn allele Gene References rnGAL4-5 Ser (St Pierre et al., 2002) rnGAL4-13 Ser (St Pierre et al., 2002) rnGAL4-14 Ser (St Pierre et al., 2002) rnroe-1 gl (Ma et al., 1996) rnroe-3 gl (Ma et al., 1996) rnroe-4 gl (Ma et al., 1996) rnroe-KE17 N (Brand and Campos-Ortega, 1990) rnroe-KE18 N (Brand and Campos-Ortega, 1990) rnroe-KE100 N (Brand and Campos-Ortega, 1990) rnroe-KE113 N (Brand and Campos-Ortega, 1990) rnroe-SC1 gl (Ma et al., 1996) unspecified N (Brand and Campos-Ortega, 1990) nej (Anderson et al., 2005)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 66073 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0259172 DroID - A comprehensive database of gene and protein interactions. • FBgn0259172 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40879
Orthologs
OrthoDB Orthologs (10) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6DRB06 Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6DRB06)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\rn     Drosophila simulans   Dsim\GD19488 Y   Drosophila sechellia   Dsec\GM10491 Y   Drosophila erecta   Dere\GG25249 Y   Drosophila yakuba   Dyak\GE25797     Drosophila ananassae   Dana\GF17309 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA26220 Y   Drosophila virilis   Dvir\GJ10241 Y   Drosophila mojavensis   Dmoj\GI23490 Y   Drosophila grimshawi   Dgri\GH19280 Y
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (10) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD19488 Drosophila sechellia Dsec\GM10491 Drosophila erecta Dere\GG25249 Drosophila ananassae Dana\GF17309 Drosophila pseudoobscura pseudoobscura Dpse\GA26220 Drosophila persimilis Dper\GL12186 Drosophila willistoni Dwil\GK11085 Drosophila virilis Dvir\GJ10241 Drosophila mojavensis Dmoj\GI23490 Drosophila grimshawi Dgri\GH19280
Stocks & Reagents
Stocks Listed in FlyBase ( 101 )
Bloomington	572 rnroe-1 pp 7403 w1118; P{UAS-rn.SP}1 7404 w1118; P{UAS-rn.SP}32 7401 w1118; P{UAS-roe.SP}18 7402 w1118; P{UAS-roe.SP}88 1708 T(2;3)rn, rn1/TM3, Sb1
Harvard	- PBac{WH}rnf01856 - PBac{WH}rnf03006 - PBac{WH}rnf05710
Kyoto	105986 rnroe-1 pp 106463 T(2;3)rn, rn1/TM3, Sb1
VDRC	v21603 w1118; P{GD10678}v21603
	More stocks available...
Genomic Clones ( 2 )
	BACR01C11 BACR02B19 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 15 )
	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	IP01358 IP04909 RE47124
Other clones	DPiM_IP01358
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	EK103459 EK104057 EK104114 EK137260 EK252934 EK258530 EK290959 EP16406 IP04809 IP05009 IP05109
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0259172 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40879
Antibody Information
	polyclonal (Melicharek et al., 2008)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: rn CG10040 CG14600 CG14601 (Galindo et al., 2001, FlyBase, 1996-) Source for merge of: rn CG14603 (St Pierre et al., 2002) Source for merge of: rn CG32467 (FlyBase Genome Annotators, 2008)
Additional comments	Annotations CG32466 and CG32467 merged as CG42277 in release 5.8 of the genome annotation. (FlyBase Genome Annotators, 2008) Annotation CG14601 split into CG32467 and part of CG32466 (rn) in release 3 of the genome annotation. Release 3 annotation CG32466 contains sequences corresponding to release 2 annotations CG10040, CG14603, CG14600 and part of CG14601. (FlyBase Genome Annotators, 2002-2003) Source for merge of rn CG10040 CG14600 CG14601 was sequence comparison (date:020121). (Galindo et al., 2001, FlyBase, 1996-) The RacGAP84C gene is not responsible for the rn mutant phenotype. (St. Pierre et al., 2001) "rn" and "roe" may correspond to a single gene, since mutations which affect "rn" often also affect "roe", or they may be two closely linked genes. (Shilkova et al., 2000) "h-NC13" may correspond to "rn"; molecular lesions within the "h-NC13" transcription unit are found in the rnroe-1 and rnroe-2 alleles. (Phippen and Parkhurst, 1999) "rn" shares an intimate relationship with "roe", mutagenesis of one locus often results in simultaneous mutagenesis of the other. (Agnel et al., 1989)
Other Comments
	RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004) dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology. (Kiger et al., 2003) The rn locus encodes two different transcripts ("rotund" and "roughened eye") which are expressed in non-overlapping domains in the larval imaginal discs. The "rotund" and "roughened eye" proteins share a C-terminus but have unique N-termini. Each transcript can rescue only its corresponding mutation and they show negative effects when expressed in each other's domain of expression. The "rotund" and "roughened eye" phenotypes are genetically separable. In direction of increasing cytology: rn- RacGAP84C+ rn- (St Pierre et al., 2002) "rn" and "roe" functions of the rn gene are encoded by two transcripts which use different origins of transcription but share the same 3' exons. The proteins encoded by the two transcripts are functionally different; "UAS-rn" constructs can rescue the "rn" phenotype but not "roe", whereas "UAS-roe" constructs rescue "roe" phenotypes but not "rn". (Galindo et al., 2001) Expression of rn transcription in rn mutants suggests that the m5.3 transcript encodes rn morphogenetic function in the imaginal discs. Expression partitions all major imaginal discs into domains along the proximo-distal axis: two in the wing and haltere discs, and at least three in the leg and antennae discs. The m5.3 transcript is sex-regulated in the genital disc and is only expressed in the female, suggesting that this disc is organised similar to other imaginal discs. It is not yet clear whether rn function is required for establishment or maintainance of patterning in the proximo-distal axis. (Agnel et al., 1992) All alleles are viable as homozygotes. Both males and females are sterile; sterility is not germ line- dependent. Two transcripts from the rotund region of Drosophila show similar positional specificities in imaginal disc tissues. Adult defects are restricted to homologous distal parts of the appendages, i.e., the antennae, legs, wings, halteres and proboscis. In the antenna the basal capsule is missing and the third antennal segment is reduced in size; all other antennal and eye disc derivatives are normal. In all three pairs of legs abnormalities caused by the lack of rn+ product are localized specifically in the tarsus; instead of five individual tarsal segments, a single tarsus-like segment differentiates. The distal claw and proximal leg articulations (tibia, femur, trochanter, and coxa) are unaffected. Incomplete and duplicated joints seen at the presumptive positions of the tarsus 1-2 and 4-5 joints; intermediate joints virtually absent. Of the wing disc derivatives, the medial and distal costa are fused and the corresponding region in the posterior wing, the alula, is smaller, making the wing as a whole appear shorter; distal wing and mesonotum are formed as in wild type. Vein L5 and to a lesser extent L2 interrupted (rn3). Specific and localized deficiencies of labial and haltere disc derivatives are also evident. Genital and abdominal patterns are indistinguishable from wild-type patterns; however, seminal receptacles shorter than in wild-type females. Examination of the imaginal discs from third instar rn larvae shows localized cell death in regions determined from fate maps to give rise to distal appendage parts. (Lindsley and Zimm, 1992) rn mutants lack structures in the distal parts of all appendages. (Agnel et al., 1989) The abnormal rn phenotype is due to a developmental defect: late occurring defects. Adult eye is rough and slightly reduced, eye disc pattern appears normal. (Renfranz and Benzer, 1989) Clonal analysis demonstrates that the rn gene is required for normal morphogenesis of specific distal parts of the adult appendages. (Kerridge and Thomas-Cavallin, 1988)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_141458 NM_206456 NM_001144549 NM_001275414 RefSeq (Proteins) • NP_649715 NP_996178 NP_001138021 NP_001262343 DDBJ / EMBL / GenBank • AAF54032 AAL59598 AAL59599 AAS65102 AC008029 ACL83479 ACL83480 AF395904 AF395905 AGB95726 CZ484348 CZ484349 CZ485563 CZ485564 CZ488326 Entrez Gene - A searchable database of RefSeq genes. • 40879 UniProtKB/Swiss-Prot • Q9VI93 UniProtKB/TrEMBL • B7Z0U8 B7Z0U9
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger C2H2-type/integrase DNA-binding domain (IPR013087) Zinc finger, C2H2-like (IPR015880) Zinc finger, C2H2 (IPR007087) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • IP01358
Linkouts
	BioGRID - A database of protein and genetic interactions • 66073 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0259172 DroID - A comprehensive database of gene and protein interactions. • FBgn0259172 DRSC - Results from RNAi screens. • FBgn0259172 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0259172 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG32467-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0259172 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40879 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /hjmuller/rotund1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40879 modMine - Data generated by the modENCODE project. • FBgn0259172
Synonyms & Secondary IDs ( 16 )
Reported As
Symbol Synonym	5.3 (Raymond et al., 2001) CG10040 (Boutros et al., 2004, Thummel, 2001, ) CG14600   CG14601   CG14603   CG32466 (Keleman et al., 2009.8.5) CG32467 (Keleman et al., 2009.8.5) CG42277 (FlyBase Genome Annotators, 2008) Dipr   P5.3 (Agnel et al., 1989, Agnel et al., 1989) rn (Galindo et al., 2007, Hoskins et al., 2005, Christensen et al., 2008.4.15, Félix et al., 2007, Zecca and Struhl, 2007, Matta et al., 2011, Jungreis et al., 2011, del Alamo and Mlodzik, 2008, Pueyo and Couso, 2008, Melicharek et al., 2008, Terriente et al., 2008, Dichtel-Danjoy et al., 2009, Aerts et al., 2009, Dworkin et al., 2009, Firth and Baker, 2007, Bosch et al., 2010, Kertesz et al., 2007, Raymond et al., 2004, Reid et al., 2012) roe (Zhao et al., 2008, St. Pierre, 2001.6.28, St. Pierre et al., 2001, Phippen and Parkhurst, 1999, Vaisman and Zakharov, 1995, Ma et al., 1996, Vaisman and Zakharov, 1995, Weisman et al., 1995, Markowitz, 1963, Baker et al., 1991, Brand and Campos-Ortega, 1990, Agnel et al., 1989, Renfranz and Benzer, 1989, Kerridge and Thomas-Cavallin, 1988, Cavener et al., 1986, Wakimoto et al., 1984, Lewis et al., 1980, Duncan and Kaufman, 1975, del Alamo and Mlodzik, 2008, Melicharek et al., 2008, Herz et al., 2010)
Name Synonym	CG32467   CG42277 (FlyBase Genome Annotators, 2008) Distal-into-proximal   rotund (Galindo et al., 2007, Reig et al., 2007, Zecca and Struhl, 2007, Matta et al., 2011, Dichtel-Danjoy et al., 2009, Carpenter et al., 2009, Melicharek et al., 2008) Rotund (Reid et al., 2012) roughened eye (Zhao et al., 2008, Marenda et al., 2008, St. Pierre, 2001.6.28, del Alamo and Mlodzik, 2008, Melicharek et al., 2008, Herz et al., 2010)
Secondary FlyBase IDs
	FBgn0003263 FBgn0003269 FBgn0037494 FBgn0037495 FBgn0037496 FBgn0037497 FBgn0052466 FBgn0052467
References ( 120 )
Generate a list of	All references relating to this gene ( 120 )
List References by type	Research paper  ( 63 ) Supplementary material  ( 8 ) Review  ( 11 ) Personal communication to FlyBase  ( 18 ) Abstract  ( 10 ) FlyBase analysis  ( 4 ) DNA/RNA sequence record  ( 2 ) Book  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 4 )
	Natori et al., 2012, Dev. Biol. 361(2): 450--462 Progressive tarsal patterning in the Drosophila by temporally dynamic regulation of transcription factor genes. [FBrf0217059] Reid et al., 2012, Front. Cell. Infect. Microbiol. 2: 24 Identification of genetic modifiers of CagA-induced epithelial disruption in Drosophila. [FBrf0219288] Gabilondo et al., 2011, Mech. Dev. 128(3-4): 208--221 A targeted genetic screen identifies crucial players in the specification of the Drosophila abdominal Capaergic neurons. [FBrf0213290] Matta et al., 2011, Dev. Genes Evol. 221(1): 49--57 Getting real with real-time qPCR: a case study of reference gene selection for morphological variation in Drosophila melanogaster wings. [FBrf0213646] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...