• Home
• Tools
  • Tools Overview
  • Query Tools

    
    • QuickSearch
    • QueryBuilder
    • TermLink
    • CytoSearch
    • RNA-Seq Search
    • Interactions Browser
    • ImageBrowse
    • Find A Person
    • Google™ FlyBase
  • Genomic/Map Tools

    
    • BLAST
    • GBrowse
    • GBrowse 2 Beta
    • CytoSearch
    • Feature Mapper
    • Aberrations Maps
    • Chromosome Maps
    • Coordinates Converter
  • Retrieve/Convert

    
    • Batch Download
    • Coordinates Converter
    • ID Converter
  • Data Submission

    
    • Fast-Track Your Paper
    • Submit Personal Comm
    • Add A New Person
    • Update Person Info
  • People

    
    • Find A Person
    • Add A New Person
    • Update Person Info
• Files
  • Files Overview
  • Current release
  • Archived releases
  • Map Conversion
  • FTP site:
  • Releases (FTP)
  • Genomes (FTP)
• Species
  • Phylogeny
  • Sequenced Species
  • Synteny Table
  • Color Illustrations
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All Resources
  • Model Organisms
  • Stock Collections
  • Vectors & Constructs
  • Other links:
  • BDGP
  • DGRC
  • DIS by issue
  • FlyExpress
  • Interactive Fly
  • modENCODE
  • Textpresso for Fly
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • FlyBase Guides
  • Video Tutorials
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Contact FlyBase
• Archives
  • Prior Release
  • Other Archives
  • Coordinate Converter

Gene Dmel\squ

General Information
Symbol	Dmel\squ	Species	D. melanogaster
Name	squash	Annotation symbol	CG4711
Feature type	protein_coding_gene	FlyBase ID	FBgn0002652
Gene Model Status	Current	Stock availability	5 publicly available
Genomic Location
Chromosome (arm)	2L	Recombination map	2-54
Cytogenetic map	36A10-36A10	Sequence location	2L:16,680,054..16,681,653 [+]
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 squash is referred to in FlyBase by the symbol Dmel\squ (CG4711, FBgn0002652). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: gene silencing by RNA; oogenesis; dorsal appendage formation. 9 alleles are reported. The phenotypes of these alleles are annotated with: egg; oocyte; karyosome; dorsal appendage. It has 3 annotated transcripts and 3 annotated polypeptides. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult ovary, adult testis. Comments on Affy2 ProbeSet: ProbeSet 1641317_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of squ. Gene sequence location is 2L:16680054..16681653.
User Contributed Data
	Beta version, feedback welcome
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.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
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 36A10-36A10   Limits computationally determined from genome sequence between P{PZ}dacP and P{EP}grpEP921&P{lacW}l(2)k13905k13905
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	2-54 (Schupbach and Wieschaus, 1989)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\squ 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 5.47 Shares 5' UTR with downstream gene.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) squ-RA FBtr0080887  NM_206000   1372   241 squ-RB FBtr0305565  NM_001259115   1029   241 squ-RC FBtr0335140  NM_001273578   1171   241
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein squ-PA   FBpp0099829   27.6   241   5.45     NP_995722   AAS64715 squ-PB   FBpp0294016   27.6   241   5.45     NP_001246044   AFH03718 squ-PC   FBpp0307139   27.6   241   5.45     NP_001260507   AGB93042
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014134 AAS64715   AE014134 AFH03718   AE014134 AGB93042   AI512687   AQ024988   BI215533   BI357728   BI358364   BI361474   BI361479   BI362925   BI363073   BI366554   BI369248   BI370380   BI582504   BP555421   BQ103439   BT089046   CO262001   CO291056   CO298343   CO315611   EC070593   EC196953   EC231387   EC231472   EC238367   EC245583   GH751978   GH755609   GH775832   GH798796   GH816187   GH842209   GH844227   GH852665   GH889627   GH894705   GH913662   GH933937   GH942055   GH944818   GH945632   GH947910   GH948101   GH950177   GH950385   GH951216   GH951284   GH951411   GH954076   GH960926   GH962915   GH963060   GH963092   GH965756   GH965823   GH966444   GH967192   GH967242   GH974368   GH979470   GH979833   GH980988   GH982452   GH984034
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q7KT57
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
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
P granule inferred from direct assay (Pane et al., 2007)
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: Expression at moderate levels in the following post-embryonic organs or tissues: adult ovary, adult testis. [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    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    68.9 Larval Midgut    6 Larval Hindgut    6.9 Larval Malpighian Tubules    1.7 Larval Fat Body    55.8 Larval Salivary Gland    21.7 Larval Trachea    42.2 Larval Carcass    9.8 Adult Head    1.3 Adult Eye    1.325 Adult Brain    1.4 Adult Thoracic-Abdominal Ganglion    1.7 Adult Crop    5.9 Adult Midgut    4.2 Adult Hindgut    2.4 Adult Malpighian Tubules    7.5 Adult Fat Body    61.4 Adult Salivary Gland    48.1 Adult Heart    19.125 Adult VirginFemale Spermatheca    24.9 Adult InseminatedFemale Spermatheca    19.3 Adult Ovary    375.4 Adult Testis    317.5 Adult Male Accessory Gland    13.1 Adult Carcass    34.9 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    1.3   NA  Eye    1.325   NA  Brain    1.4   68.9  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    1.7   NA  Crop    5.9   6  Midgut    4.2   6.9  Hindgut    2.4   1.7  Malpighian Tubules    7.5   no informative data  Fat Body    61.4   21.7  Salivary Gland    48.1   NA  Heart    19.125   42.2  Trachea    NA   NA  VirginFemale Spermatheca    24.9   NA  InseminatedFemale Spermatheca    19.3   NA  Ovary    375.4   NA  Testis    317.5   NA  Male Accessory Gland    no informative data   9.8  Carcass    no informative data 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    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female    101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (33) central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female  (101) ovary, mated 4-day female  (93) testis, mated 4-day male  (38) accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female  101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 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    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female    101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female    101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (33) central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female  (101) ovary, mated 4-day female  (93) testis, mated 4-day male  (38) accessory gland, mated 4-day male    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female  101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 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    33 central nervous system, larvae L3    10 central nervous system, pupae P8    4 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    1 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    3 salivary gland, white prepupae    6 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    6 digestive system, 20-day adult    3 fat body, larvae L3 wandering    2 fat body, white prepupae    8 fat body, pupae P8    9 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    7 carcass, 20-day adult    7 ovary, virgin 4-day female    101 ovary, mated 4-day female    93 testis, mated 4-day male    38 accessory gland, mated 4-day male    7 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 moderately high expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages, in adult female 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    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (41) embryo 02-04hr  (29) embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day  (31) adult female 30day  (28) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 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    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (41) embryo 02-04hr  29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day  31 adult female 30day  28 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 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    41 embryo 02-04hr    29 embryo 04-06hr    17 embryo 06-08hr    15 embryo 08-10hr    17 embryo 10-12hr    11 embryo 12-14hr    12 embryo 14-16hr    6 embryo 16-18hr    7 embryo 18-20hr    3 embryo 20-22hr    8 embryo 22-24hr    10 larva L1    1 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    7 white prepupae new    8 white prepupae 12hr    12 white prepupae 24hr    12 pupae 2d postWPP    10 pupae 3d postWPP    5 pupae 4d postWPP    3 adult male 01day    6 adult male 05day    8 adult male 30day    6 adult female 01day    8 adult female 05day    31 adult female 30day    28 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+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (27) Schneider line 2 Sg4  (27) embryonic 1182-4H  (30) embryonic GM2  (33) embryonic Kc167  (38) embryonic S1  (47) embryonic S3  (62) leg disc CME L1  (28) wing disc CME-W2  (41) wing disc ML-DmD8  (29) wing disc ML-DmD9    20 wing disc ML-DmD16-c3  (39) wing disc ML-DmD21    8 wing disc ML-DmD32  (32) haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11  (34) antennal disc ML-DmD20-c5  (53) mixed discs ML-DmD4-c1  (40) CNS ML-DmBG1-c1  (43) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2  (60) ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 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+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  27 Schneider line 2 Sg4  27 embryonic 1182-4H  30 embryonic GM2  (33) embryonic Kc167  (38) embryonic S1  (47) embryonic S3  (62) leg disc CME L1  28 wing disc CME-W2  (41) wing disc ML-DmD8  29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3  (39) wing disc ML-DmD21    8 wing disc ML-DmD32  32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11  (34) antennal disc ML-DmD20-c5  (53) mixed discs ML-DmD4-c1  (40) CNS ML-DmBG1-c1  (43) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2  (60) ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 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+    27 Schneider line 2 Sg4    27 embryonic 1182-4H    30 embryonic GM2    33 embryonic Kc167    38 embryonic S1    47 embryonic S3    62 leg disc CME L1    28 wing disc CME-W2    41 wing disc ML-DmD8    29 wing disc ML-DmD9    20 wing disc ML-DmD16-c3    39 wing disc ML-DmD21    8 wing disc ML-DmD32    32 haltere disc ML-DmD17-c3    20 eye-antennal disc ML-DmD11    34 antennal disc ML-DmD20-c5    53 mixed discs ML-DmD4-c1    40 CNS ML-DmBG1-c1    43 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    60 ovary fGS/OSS    12 ovary OSC    23 ovary OSS    12 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    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult  (60) Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult  (69) Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3  (34) Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (51) Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult  (38) Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 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    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult  (60) Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult  (69) Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3  (34) Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (51) Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult  (38) Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 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    10 cold shock, 4-day adult    8 heat shock, 4-day adult    21 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    20 Cadmium 100 mM 48 hrs, 4-day adult    60 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    69 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    24 Ethanol 2.5% 3 hrs, larvae L3    34 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    51 Caffeine 25 mg/ml 48 hrs, 4-day adult    19 Paraquat 5 mM 48 hrs, 4-day adult    38 Paraquat 10 mM 48 hrs, 4-day adult    19 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    2 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_01 mE1_20_mRNA_expression_cluster_05
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002652 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • HDC02844
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage | maternal effect | recessive squHK35 viable, with Scer\GAL4pnr-MD237 squGD16229 Sterility Allele female sterile squHE47 squHK35 squPP32 female sterile | recessive squHK35 Phenotype manifest in Allele dorsal appendage (with squHE47) squPP32 dorsal appendage (with squPP32) squHE47 egg (with squHE47) squPP32 egg (with squPP32) squHE47 embryonic/first instar larval cuticle | maternal effect squHK35 embryonic head | maternal effect squHK35 embryonic segment | maternal effect squHK35 karyosome squunspecified oocyte squunspecified stage 5 embryo | maternal effect squHK35
Classical Alleles ( 5 )
For All Classical Alleles Show
Allele of squ Class Mutagen Stocks Known lesion squPP32 ethyl methanesulfonate 1 Yes squEP921 P-element activity 0 Yes squHE47 ethyl methanesulfonate 0 Yes squHK35 ethyl methanesulfonate 0 Yes squunspecified 0 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of squ Class Mutagen Stocks Known lesion squGD16229 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes squGL00116 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes squKK106571 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes squScer\UAS.P\T.T:Ivir\HA1 0 Yes
Aneuploid Aberrations
Not disrupted in	Df(2L)OD15 (Digilio et al., 1996) Df(2L)TW50 (Butler, 2001) Df(2L)TW65 (Butler, 2001) Df(2L)γ244 (Digilio et al., 1996)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD16229} NA P{KK106571} NA P{TRiP.GL00116} NA P{UASp-HA-squ} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}grpEP921 NA
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
Terms Based on Experimental Evidence ( 4 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
dorsal appendage formation inferred from mutant phenotype (Schupbach and Wieschaus, 1991) gene silencing by RNA inferred from mutant phenotype (Pane et al., 2007) oogenesis inferred from mutant phenotype (Schupbach and Wieschaus, 1991)
Cellular Component
CV term Evidence References
P granule inferred from direct assay (Pane et al., 2007)
Terms Based on Predictions or Assertions ( 1 term )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
oogenesis traceable author statement (van Eeden and St. Johnston, 1999)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	gene_with_dicistronic_primary_transcript (FlyBase Genome Annotators, 2004) nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions squ allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 77769 DroID - A comprehensive database of gene and protein interactions. • FBgn0002652 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 2768920
Orthologs
OrthoDB Orthologs (13) - 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 EOG644M5M 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 (EOG644M5M)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\squ     Drosophila simulans   Dsim\GD24068 Y   Drosophila sechellia   Dsec\GM17192 Y   Drosophila erecta   Dere\GG22758 Y   Drosophila yakuba   Dyak\GE12753 Y   Drosophila ananassae   Dana\GF14004 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA13764 Y   Drosophila persimilis   Dper\GL19649     Drosophila persimilis   Dper\GL12351 Y   Drosophila willistoni   Dwil\GK18923 Y   Drosophila virilis   Dvir\GJ22736 Y   Drosophila mojavensis   Dmoj\GI17267 Y   Drosophila grimshawi   Dgri\GH25198 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 (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD24068 Drosophila sechellia Dsec\GM17192 Drosophila erecta Dere\GG22758 Drosophila yakuba Dyak\GE12753 Drosophila ananassae Dana\GF14004 Drosophila pseudoobscura pseudoobscura Dpse\GA13764 Drosophila persimilis Dper\GL12351 Drosophila willistoni Dwil\GK18923 Drosophila virilis Dvir\GJ22736 Drosophila mojavensis Dmoj\GI17267 Drosophila grimshawi Dgri\GH25198
Stocks & Reagents
Stocks Listed in FlyBase ( 5 )
Bloomington	5114 squPP32 cn1 bw1/CyO, l(2)DTS5131 35574 y1 sc* v1; P{TRiP.GL00116}attP2/TM3, Sb1
VDRC	v101017 P{KK106571}VIE-260B v47103 w1118; P{GD16229}v47103/TM3 v47104 w1118; P{GD16229}v47104/TM3
Genomic Clones ( 1 )
	BACR26O03 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 62 )
	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	RE53210
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	LD44630 RE22056 RE44277 RE45115 RE45702 RE45708 RE47618 RE47794 RE52119 RE55370 RE56877 RH20726
Other clones	48538 158698 CK01.98B.D3 CK01.107C.D6 CK01.110B.C6 EK076014 EK083543 EK172815 EK262023 FGM235B10 RP003033220 RP003127983 RP003167717 RP003173515 RP003212025 RP003223092 RP003514570 RP003555173 RP003559211 RP003584282 RP003611986 RP003632037 RP004120056 RP004159172 RP004161378 RP004166151 RP004174537 RP004175589 RP004201531 RP004203086 RP004204123 RP004220916 RP004228296 RP004235999 RP004236071 RP004245158 RP004250456 RP004259851 RP004365350 RP004470184 RP004471569 RP004479870 RP004487479 RP004488069 RP004518054 RP004518756 RP004520143 RP004540961 UUGC0844
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0002652 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 2768920
Antibody Information
	monoclonal (Kibanov et al., 2011) polyclonal (Haase et al., 2010)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: squ CG4711 (Wehr and Schupbach, 2005)
Additional comments	Annotation CG4711 has been restored as a distinct annotation from CG17161 in release 3.2 of the genome annotation. In addition, release 3.2 annotations CG17161 (which corresponds to grp) and CG4711 encode alternative transcripts which share untranslated sequences, but encode non-overlapping open reading frames. (FlyBase Genome Annotators, 2004) Release 1 annotation CG4711 (which was eliminated in release 2 of the genome annotation) has been merged with CG17161 in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
Other Comments
	squ is required for rasiRNA production in the female germline. (Pane et al., 2007) Mutants affect normal oogenesis. (Digilio et al., 1996) Mutations at the squ locus cause defects in midoogenesis. (Schupbach and Wieschaus, 1991) Mutant embryos exhibit variable cellularization defects: embryos form cuticles with holes, variable head defects and segment fusions. (Schupbach and Wieschaus, 1989)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_206000 NM_001259115 NM_001273578 RefSeq (Proteins) • NP_995722 NP_001246044 NP_001260507 DDBJ / EMBL / GenBank • AAS64715 AAS64715.1 AFH03718 AGB93042 AQ024988 Entrez Gene - A searchable database of RefSeq genes. • 2768920 UniProtKB/TrEMBL • Q7KT57
Other Crossreferences
Linkouts
	BioGRID - A database of protein and genetic interactions • 77769 DroID - A comprehensive database of gene and protein interactions. • FBgn0002652 DRSC - Results from RNAi screens. • FBgn0002652 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002652 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • HDC02844 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0002652 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 2768920 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 2768920 modMine - Data generated by the modENCODE project. • FBgn0002652
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	CG4711 (Wehr and Schupbach, 2005, Pane et al., 2007, Keleman et al., 2009.8.5, Ni et al., 2011.7.19) mat(2)cell-A   mat(2)cellHK35 (Schupbach and Wieschaus, 1989, ) squ (Georlette et al., 2007, Pane et al., 2007, Buchon et al., 2009, Malone et al., 2009, Chambeyron et al., 2008, Todeschini et al., 2010, Haase et al., 2010, Nagao et al., 2010, Becalska et al., 2011, Rouget et al., 2010) SQU (Kolaczkowski et al., 2011, Janic et al., 2010)
Name Synonym	Squash (Wehr and Schupbach, 2001, Becalska et al., 2011, Janic et al., 2010, Rouget et al., 2010, Felix et al., 2012) squash (Castillo et al., 2011, Pane et al., 2007, Malone et al., 2009, Robine et al., 2009, Todeschini et al., 2010, Olivieri et al., 2010, Haase et al., 2010)
Secondary FlyBase IDs
	FBgn0032594 FBgn0069054
References ( 40 )
Generate a list of	All references relating to this gene ( 40 )
List References by type	Research paper  ( 23 ) Supplementary material  ( 4 ) Review  ( 4 ) Personal communication to FlyBase  ( 3 ) Abstract  ( 3 ) FlyBase analysis  ( 2 )
Recent research papers ( 6 )
	Felix et al., 2012, Genetics 191(3): 989--1002 Age-Specific Variation in Immune Response in Drosophila melanogaster Has a Genetic Basis. [FBrf0218944] Lee and Langley, 2012, Genetics 192(4): 1411--1432 Long-term and short-term evolutionary impacts of transposable elements on Drosophila. [FBrf0220133] Becalska et al., 2011, Dev. Biol. 349(1): 46--52 Aubergine is a component of a nanos mRNA localization complex. [FBrf0212348] Castillo et al., 2011, BMC Evol. Biol. 11: 258 Molecular evolution under increasing transposable element burden in Drosophila: A speed limit on the evolutionary arms race. [FBrf0216257] Kibanov et al., 2011, Mol. Biol. Cell 22(18): 3410--3419 A novel organelle, the piNG-body, in the nuage of Drosophila male germ cells is associated with piRNA-mediated gene silencing. [FBrf0215572] Kolaczkowski et al., 2011, Mol. Biol. Evol. 28(2): 1033--1042 Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. [FBrf0212798] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...