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Gene Dmel\Rx

General Information
Symbol	Dmel\Rx	Species	D. melanogaster
Name	Retinal Homeobox	Annotation symbol	CG10052
Feature type	protein_coding_gene	FlyBase ID	FBgn0020617
Gene Model Status	Current	Stock availability	4 publicly available
Also Known As	drx, E97, bk50, PPH17
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	57B4-57B4	Sequence location	2R:16,804,258..16,824,535 [+]
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 Retinal Homeobox is referred to in FlyBase by the symbol Dmel\Rx (CG10052, FBgn0020617). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: neurogenesis. 7 alleles are reported. The phenotypes of these alleles are annotated with: trichogen cell; mesothoracic tergum. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: Homeobox, conserved site; Homeodomain; Homeodomain-like; OAR domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 06-24 hour embryonic stages, during early larval stages, during early pupal stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Comments on Affy2 ProbeSet: ProbeSet 1632237_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of Rx. Gene sequence location is 2R:16804285..16824537.
User Contributed Data
	Beta version, feedback welcome
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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FB2013_03	Polypeptides Rx-PB Transcripts Rx-RB
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 57B4-57B4   Limits computationally determined from genome sequence between P{lacW}l(2)k06409k06409&P{PZ}insc05475 and P{PZ}l(2)0780607806
Experimentally Determined Cytological Location
Cytogenetic map Notes References 57B-57B     (Walldorf, 1998.1.28) 56D5-56D6     (Mathers, 1997.6.24) 57B-57B   (determined by in situ hybridisation)   (Eggert et al., 1998) 57B5-57B6   (determined by in situ hybridisation)   (Noll, 1996.3.2) 57B5-57B6   (determined by in situ hybridisation)   (Dalton et al., 1989)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Rx for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Mutation in sequenced strain: single base deletion in first exon (2R:16804601) resulting in frameshift. Gene model reviewed during 5.51
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Rx-RB FBtr0342783     3267   904
Additional Transcript Data & Comments
Reported size (kB)	3.2 (longest cDNA) (Eggert et al., 1998)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Rx-PB   FBpp0309625   95.8   904   6.87
Additional Polypeptide Data & Comments
Reported size (kDa)	902, 772 (aa); 96 (kD predicted) (Eggert et al., 1998)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeodomain (IPR001356) OAR domain (IPR003654) Homeodomain-like (IPR009057)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AF001910   AJ223300 CAA11241   AY118390 AAM48419   AY433196   BI241835   CO272806   CO332356   CO343525   EC067807   EC243775   EC259568   FE426484   FE426499   FE862650   FE862670   FE862748   FE863192   FE863242   FE863307   GH738881   GH740676   GH741062   GH741302   GH741430   GH742717   GH743801   GH744057   GH744377   GH745484   GH745991   GH746203   GH746352   GH761508   GH762972   GH763451   GH764018   GH766979   GH767927   GH768981   GH769467   GO254426
UniProtKB/Swiss-Prot	Q9W2Q1
UniProtKB/TrEMBL
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 4 -- 6   central brain anlage in statu nascendi   (Fisher et al., 2012) visual anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi antennal anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi dorsal head epidermis anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi embryonic stage 7 -- 8   central brain anlage   (Fisher et al., 2012) embryonic stage 8 -- 17   labral segment   (Eggert et al., 1998) embryonic procephalic segment   (Eggert et al., 1998) embryonic stage 9 -- 10   central brain primordium   (Fisher et al., 2012) embryonic stage 10 -- 11   eye-antennal disc primordium   (Mathers et al., 1997) embryonic stage 11 -- 12   central brain primordium   (Fisher et al., 2012) clypeo-labral primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 11 -- 17   presumptive embryonic/larval central nervous system   (Eggert et al., 1998) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic dorsal epidermis   (Fisher et al., 2012) embryonic/larval dorsal vessel   (Fisher et al., 2012) embryonic/larval nervous system   (Fisher et al., 2012) embryonic/larval oenocyte   (Fisher et al., 2012) embryonic/larval pericardial cell   (Fisher et al., 2012) labral segment   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012) embryonic stage 13 -- 17   antenno-maxillary complex   (Eggert et al., 1998)
Additional Descriptive Data
	Rx transcripts are first observed at embryonic stage 8 in two dorsolateral spots in the procephalic region. At the end of stage 8, additional staining is seen in the dorsal region that will give rise to the clypeolabrum. The head region expression becomes more pronounced by stage 9 and additional staining appears in the CNS. Later expression is observed in the antenno-maxillary complex. Staining at the medial edges of the two brain lobes, in the clypeolabrum, and in the antenno-maxillary complex persists until the end of embryogenesis. (Eggert et al., 1998) Rx transcripts are detected by in situ hybridization during early embryogenesis in the eye disc primordia. They are also observed in a patch of cells in the anterior of the embryo corresponding to the clypeolabrum, in a region that gives rise to the epiphysis. (Mathers et al., 1997)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 13   adult clypeo-labral primordium   (Davis et al., 2003) embryonic brain | medial & restricted   (Davis et al., 2003) third instar larval stage   clypeo-labral disc | restricted   (Davis et al., 2003) embryonic/larval brain | medial & restricted   (Davis et al., 2003) adult stage   brain | dorsal & posterior & restricted   (Davis et al., 2003)
Additional Descriptive Data
	Protein is detected in stage 13 embryos in a restricted pattern in the central nervous system with staining in the embryonic brain hemispheres near the midline. Protein is expressed in larval central nervous system in several cell clusters near the midline. Additional expression in larvae is observed in a subset of cells in the clypeo-labral disc. Expression is detected in dorsal and posterior regions of the adult brain. (Davis et al., 2003)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
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) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    40.825 Larval Midgut    2 Larval Hindgut    1.1 Larval Malpighian Tubules    4.2 Larval Fat Body    4.6 Larval Salivary Gland    1 Larval Trachea    1.475 Larval Carcass    2.675 Adult Head    6.7 Adult Eye    1.1 Adult Brain    42.4 Adult Thoracic-Abdominal Ganglion    4.6 Adult Crop    1.9 Adult Midgut    3.3 Adult Hindgut    2 Adult Malpighian Tubules    1.9 Adult Fat Body    5.4 Adult Salivary Gland    7.6 Adult Heart    1.3 Adult VirginFemale Spermatheca    0.8 Adult InseminatedFemale Spermatheca    2.6 Adult Ovary    1.6 Adult Testis    5.5 Adult Male Accessory Gland    2 Adult Carcass    2.8 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    6.7   NA  Eye    1.1   NA  Brain    42.4   40.825  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    4.6   NA  Crop    1.9   2  Midgut    3.3   1.1  Hindgut    2   4.2  Malpighian Tubules    1.9   4.6  Fat Body    5.4   1  Salivary Gland    7.6   NA  Heart    1.3   1.475  Trachea    NA   NA  VirginFemale Spermatheca    0.8   NA  InseminatedFemale Spermatheca    2.6   NA  Ovary    1.6   NA  Testis    5.5   NA  Male Accessory Gland    2   2.675  Carcass    2.8 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    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    1 central nervous system, larvae L3    5 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    0 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 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    0 fat body, pupae P8    1 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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 moderate expression to a trough of extremely low expression. Peak expression observed within 06-24 hour embryonic stages, during early larval stages, during early pupal 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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    1 embryo 04-06hr    3 embryo 06-08hr    9 embryo 08-10hr    9 embryo 10-12hr    14 embryo 12-14hr    11 embryo 14-16hr    16 embryo 16-18hr    12 embryo 18-20hr    15 embryo 20-22hr    8 embryo 22-24hr    7 larva L1    7 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    6 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    1 adult male 05day    1 adult male 30day    1 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 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 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_11 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • RE39020 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0020617 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG10052-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Rx Stages(s) 1-3 Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal RxGD4076 partially lethal - majority die | pupal stage, with Scer\GAL4pnr-MD237 RxGD4076 Other Phenotypes Allele neuroanatomy defective | larval stage RxGD4076 visible, with Scer\GAL4pnr-MD237 RxGD4076 Phenotype manifest in Allele ganglion mother cell | larval stage RxGD4076 mesothoracic tergum, with Scer\GAL4pnr-MD237 RxGD4076 trichogen cell, with Scer\GAL4pnr-MD237 RxGD4076
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Rx Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Rx Class Mutagen Stocks Known lesion RxGD4076 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes RxJF03089 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes RxKK102142 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Rx+m.BSKK in vitro construct - minigene 0 Yes RxNIG.10052R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes RxScer\UAS.cDa in vitro construct - regulatory fusion 0 Yes Rxt7BBH in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)E2 (Davis et al., 2003) Df(2R)ex8 (Davis et al., 2003) Df(2R)Exel6071 (Ryder, 2004.4.26) Df(2R)Exel7166 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4076} NA P{KK102142} NA P{NIG.10052R} NA P{TRiP.JF03089} NA P{UAS-Rx.D} NA characterization construct P{Act57B.t7BBH} NA P{Rx.BSKK} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}3A2 No
Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
Terms Based on Experimental Evidence ( 1 term )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
neurogenesis inferred from mutant phenotype (Neumüller et al., 2011)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding inferred from electronic annotation with InterPro:IPR001356, InterPro:IPR017970 (FlyBase Curators et al., 2004-) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with EMBL:AF001911 (FlyBase, 1992-)
Biological Process
CV term Evidence References
brain development non-traceable author statement (Swiss-Prot Project Members, 2001.8.20) regulation of transcription from RNA polymerase II promoter inferred from sequence or structural similarity with EMBL:AF001911 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with EMBL:AF001911 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 2001.8.20)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
RNA-protein
Interacting group Assay References
Rx - B52 electrophoretic mobility shift assay, autoradiography, systematic evolution of ligands by exponential enrichment, full identification by DNA sequencing (Kim et al., 2003)
protein-protein
Interacting group Assay References
Rx - 14-3-3ζ anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - CG15735 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - Hel25E anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - RpL7-like anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - RpLP0 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - kst anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rx - mRpL44 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 Rx allele Gene References
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0020617 DroID - A comprehensive database of gene and protein interactions. • FBgn0020617 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 37367
Orthologs
OrthoDB Orthologs (45) - 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 EOG65HSH2 Dipteran inclusive ortholog search EOG6WH8W3 Insect inclusive ortholog search EOG63BKKX Arthropod inclusive ortholog search EOG659ZZK Metazoa inclusive ortholog search EOG6SNDGQ
Orthologs in Drosophila Species (EOG65HSH2)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Rx     Drosophila simulans   Dsim\GD11547 Y   Drosophila sechellia   Dsec\GM15784 Y   Drosophila erecta   Dere\GG22067 Y   Drosophila yakuba   Dyak\GE12148 Y   Drosophila ananassae   Dana\GF12207 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA10035 Y   Drosophila persimilis   Dper\GL17060 Y   Drosophila willistoni   Dwil\GK23335 Y   Drosophila virilis   Dvir\GJ17468 Y   Drosophila mojavensis   Dmoj\GI19710 Y   Drosophila grimshawi   Dgri\GH22006 Y
Orthologs in non-Drosophila Dipterans (EOG6WH8W3)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001689 Y Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001696 Y Anopheles gambiae Malaria mosquito  Agam\AGAP005311 Y Anopheles gambiae Malaria mosquito  Agam\AGAP005096 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ016464 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ015160 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ016463 Y
Orthologs in non-Dipteran Insects (EOG63BKKX)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\Rx   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG007405   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH20740   Atta cephalotes Leafcutter ant  Acep\ACEP27607   Atta cephalotes Leafcutter ant  Acep\ACEP27609   Camponotus floridanus Florida carpenter ant  Cflo\CFLO15626   Camponotus floridanus Florida carpenter ant  Cflo\CFLO26923   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL12223   Linepithema humile Argentine ant  Lhum\LH14722   Linepithema humile Argentine ant  Lhum\LH14726   Pogonomyrmex barbatus Red harvester ant  Pbar\PB10270   Pogonomyrmex barbatus Red harvester ant  Pbar\PB21876   Solenopsis invicta Red fire ant  Sinv\SINV20595   Acyrthosiphon pisum Pea aphid  Apim\ACYPI000963   Bombyx mori Silkmoth  Bmor\BGIBMGA013941   Pediculus humanus Human body louse  Phum\PHUM121710   Pediculus humanus Human body louse  Phum\PHUM121700   Tribolium castaneum Red flour beetle  Tcas\Rx
Orthologs in non-Insect Arthropods (EOG659ZZK)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\hba1   Ixodes scapularis Deer tick  Isca\ISCW014108
Orthologs in non-Arthropod Metazoa (EOG6SNDGQ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\ceh-8   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_014289gn   Danio rerio Zebrafish  Drer\rx1   Danio rerio Zebrafish  Drer\rx2   Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000031298   Gallus gallus Domestic chicken  Ggal\RX1
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD11547 Drosophila sechellia Dsec\GM15784 Drosophila erecta Dere\GG22067 Drosophila yakuba Dyak\GE12148 Drosophila ananassae Dana\GF12207 Drosophila pseudoobscura pseudoobscura Dpse\GA10035 Drosophila persimilis Dper\GL17060 Drosophila willistoni Dwil\GK23335 Drosophila virilis Dvir\GJ17468 Drosophila mojavensis Dmoj\GI19710 Drosophila grimshawi Dgri\GH22006
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
Bloomington	28674 y1 v1; P{TRiP.JF03089}attP2
VDRC	v106185 P{KK102142}VIE-260B v44716 w1118; P{GD4076}v44716 v44717 w1118; P{GD4076}v44717
Genomic Clones ( 3 )
	BACR04E05 BACR10P11 BACR10P16 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 38 )
	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	RE39020
Other clones	DPiM_RE39020
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	9552 214503.60 275421 EK108437 EK303235 EP16961 RM05016 RM05116 RM05216 RM05516 RM06116 RM06316 RM06416 RM06516 RP01484 RP01546 RP01562 RP001002738 RP001004881 RP001006594 RP001008156 RP001008803 RP001013240 RP001013819 RP001016961 RP001019591 RP001020637 RP001023331 RP001034207 RP001035712 RP001037587 RP001039590 RP001040740 RP001045381 RP001048702 RP001051859
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0020617 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 37367
Antibody Information
	polyclonal (Davis et al., 2003)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: Rx E97 wom (McGinnis, 2000.3.15)
Additional comments	Although extensive DNA sequence for "E97" has not been determined, no sequence overlapping that of the homeodomain of "PPH17" has been identified. Cross hybridization analysis suggests that "E97" and "PPH17" represent different homeodomain genes at 57B. (McGinnis, 1996.3.4)
Other Comments
	Rx is isolated in an attempt to analyse the 5' region of otp. (Eggert et al., 1998) Rx is cloned and sequenced and the gene structure and expression pattern determined. (Eggert et al., 1998) Rx encodes a prd-type homeodomain that is distinct from hbn or otp. (Noll, 1996.3.2) 57B is one of several locations where pairs of distinct homeodomains, in this case hbn and Rx, are found. (Dessain and McGinnis, 1993) One of the homeodomain loci identified in a screen for genes encoding DNA binding proteins capable of binding to a consensus Engrailed binding site. (Kalionis and O'Farrell, 1993) Identified on the basis of similarity to the eve homeobox sequence. (Dalton et al., 1989)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AAF46639 AAM48419 AF001910 AJ223300 AY118390 BI241835 CAA11241 Entrez Gene - A searchable database of RefSeq genes. • 37367 UniProtKB/Swiss-Prot • Q9W2Q1
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeodomain (IPR001356) OAR domain (IPR003654) Homeodomain-like (IPR009057) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE39020
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0020617 DroID - A comprehensive database of gene and protein interactions. • FBgn0020617 DRSC - Results from RNAi screens. • FBgn0020617 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0020617 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG10052-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0020617 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 37367 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /hjmuller/rx1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 37367 modMine - Data generated by the modENCODE project. • FBgn0020617
Synonyms & Secondary IDs ( 13 )
Reported As
Symbol Synonym	bk50 (Kalionis, 1996.5.7, Kalionis and O'Farrell, 1993) CG10052 (Whitfield, 2002.7.24, Davis, 2000.10.25, Keleman et al., 2009.8.5, Perkins et al., 2009) drx (Davis et al., 2003, Davis and Mardon, 2001, Kaspar et al., 2005) DRx (Walldorf, 1998.1.28, Treisman, 1999, Kammermeier et al., 1999, Eggert et al., 1998, Walldorf et al., 1998) Drx (Galliot et al., 1999, Mathers et al., 1997) E97 (McGinnis, 1996.3.4, Dessain and McGinnis, 1993, Dalton et al., 1989, ) PPH17 (McGinnis, 1996.3.4, Noll, 1996.3.2) Rx (Davis et al., 2005, Junion et al., 2007, Copley, 2005, de Velasco et al., 2007, Neumüller et al., 2011, Japanese National Institute of Genetics, 2012.5.21, Kunz et al., 2012) W60 (Eggert et al., 1998) wom
Name Synonym	Drosophila Rx (Eggert et al., 1998) Retinal Homeobox (Davis et al., 2003) wombat
Secondary FlyBase IDs
	FBgn0000530 FBgn0003998 FBgn0005641
References ( 54 )
Generate a list of	All references relating to this gene ( 54 )
List References by type	Research paper  ( 17 ) Supplementary material  ( 4 ) Review  ( 3 ) Personal communication to FlyBase  ( 14 ) Abstract  ( 7 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 2 ) Stock list  ( 1 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 ) Conference report  ( 1 )
Recent research papers ( 2 )
	Kunz et al., 2012, Development 139(14): 2510--2522 Origin of Drosophila mushroom body neuroblasts and generation of divergent embryonic lineages. [FBrf0218649] Neumüller et al., 2011, Cell Stem Cell 8(5): 580--593 Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi. [FBrf0213621] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...