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Gene Dmel\aly

General Information
Symbol	Dmel\aly	Species	D. melanogaster
Name	always early	Annotation symbol	CG2075
Feature type	protein_coding_gene	FlyBase ID	FBgn0004372
Gene Model Status	Current	Stock availability	6 publicly available
Genomic Location
Chromosome (arm)	3L	Recombination map	3-4.4
Cytogenetic map	63A3-63A3	Sequence location	3L:3,024,129..3,026,521 [-]
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 always early is referred to in FlyBase by the symbol Dmel\aly (CG2075, FBgn0004372). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding. There is experimental evidence that it is involved in the biological process: male meiosis I; positive regulation of transcription from RNA polymerase II promoter; spermatid differentiation; regulation of gene expression; positive regulation of transcription during meiosis; spermatogenesis. 18 alleles are reported. The phenotypes of these alleles are annotated with: testis; spermatocyte. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: DIRP. 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 in adult male stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Comments on Affy2 ProbeSet: ProbeSet 1627064_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of aly. Gene sequence location is 3L:3024129..3026521.
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.
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 63A3-63A3   Limits computationally determined from genome sequence between P{PZ}Spn06911 and P{PZ}l(3)0680306803
Experimentally Determined Cytological Location
Cytogenetic map Notes References 63A3-63A4   (determined by in situ hybridisation)   (White-Cooper, 2000.8.7)
Experimentally Determined Recombination Data
Location	3-4.4   3-4.4 +/- 0.9 (Lin et al., 1996)
Left of (cM)	h (Lin et al., 1996)
Right of (cM)	ru (Lin et al., 1996)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\aly 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 5.45
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) aly-RA FBtr0073006  NM_080118   2267   568 aly-RB FBtr0332086  NM_001274419   1777   568
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 aly-PA   FBpp0072876   65.9   568   8.50     NP_524857   AAF47702 aly-PB   FBpp0304396   65.9   568   8.50     NP_001261348   AGB94043
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • DIRP (IPR010561)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014296 AAF47702   AE014296 AGB94043   AI531556   AJ277307 CAB86720   BF496466   BG634700   BI161847   BI366886   BT011102   DQ316007 ABC48754   DQ316008 ABC48755   DQ316009 ABC48756   DQ316010 ABC48757   DQ316011 ABC48758   DQ316012 ABC48759   DQ316013 ABC48760   DQ316014 ABC48761   DQ316015 ABC48762   DQ316016 ABC48763   DQ316017 ABC48764   DQ316018 ABC48765   DQ316019 ABC48766   DQ316020 ABC48767   DQ316021 ABC48768   DQ316022 ABC48769   DQ316023 ABC48770   DQ316024 ABC48771   DQ316025 ABC48772   DQ316026 ABC48773   DQ316027 ABC48774   DQ316028 ABC48775   DQ316029 ABC48776   DQ316030 ABC48777
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VZW3 Q2PNP3 Q2PNN6 Q2PNP0 Q2PNP6 Q2PNM9 Q2PNP8 Q2PNN2 Q2PNN1 Q2PNQ1 Q2PNN3 Q2PNQ2 Q2PNN0 Q2PNP9 Q2PNP7 Q2PNN5 Q2PNN4 Q2PNP1 Q2PNP5 Q9NFM3 Q2PNP4
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
immunolocalization Stage Tissue/Position (including subcellular localization) Reference adult stage | male   spermatocyte   • spindle (Wang and Mann, 2003) Comment:meiotic metaphase spermatocyte   • nucleus (Wang and Mann, 2003) Comment:NOT meiotic metaphase adult stage   spermatid   • nucleus (Wang and Mann, 2003) in situ Stage Tissue/Position (including subcellular localization) Reference spermatogenesis & adult stage | male   primary spermatocyte   • nucleus (Perezgasga et al., 2004) primary spermatocyte   • chromatin (Perezgasga et al., 2004) primary spermatocyte   • nucleoplasm (Perezgasga et al., 2004)
Additional Descriptive Data
	aly protein is concentrated on the chromatin and distributed in the nucleoplasm in the nuclei of primary spermatocytes. (Perezgasga et al., 2004)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
chromatin inferred from direct assay (White-Cooper et al., 2000) cytoplasm inferred from direct assay (White-Cooper et al., 2000) nuclear chromatin inferred from direct assay (Jiang et al., 2007) nucleus inferred from direct assay (Jiang and White-Cooper, 2003) inferred from direct assay AND inferred from sequence or structural similarity (White-Cooper et al., 2000)
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    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    1.4 Larval Midgut    3.6 Larval Hindgut    1.1 Larval Malpighian Tubules    2 Larval Fat Body    9.5 Larval Salivary Gland    5.3 Larval Trachea    3.225 Larval Carcass    0.975 Adult Head    1 Adult Eye    1.525 Adult Brain    1.7 Adult Thoracic-Abdominal Ganglion    2.4 Adult Crop    2.4 Adult Midgut    4.1 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    3.4 Adult Salivary Gland    5.4 Adult Heart    5.1 Adult VirginFemale Spermatheca    1.5 Adult InseminatedFemale Spermatheca    3.3 Adult Ovary    1 Adult Testis    26.8 Adult Male Accessory Gland    2.3 Adult Carcass    3 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   NA  Eye    1.525   NA  Brain    1.7   1.4  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    2.4   NA  Crop    2.4   3.6  Midgut    4.1   1.1  Hindgut    1.2   2  Malpighian Tubules    3.3   9.5  Fat Body    3.4   5.3  Salivary Gland    5.4   NA  Heart    5.1   3.225  Trachea    NA   NA  VirginFemale Spermatheca    1.5   NA  InseminatedFemale Spermatheca    3.3   NA  Ovary    1   NA  Testis    26.8   NA  Male Accessory Gland    2.3   0.975  Carcass    3 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    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 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    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 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    8 central nervous system, larvae L3    0 central nervous system, pupae P8    0 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 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    1 fat body, pupae P8    1 carcass, larvae L3 wandering    0 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    20 accessory gland, mated 4-day male    2 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 in adult male stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    1 embryo 04-06hr    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 embryo 06-08hr    0 embryo 08-10hr    0 embryo 10-12hr    0 embryo 12-14hr    0 embryo 14-16hr    0 embryo 16-18hr    0 embryo 18-20hr    0 embryo 20-22hr    0 embryo 22-24hr    0 larva L1    0 larva L2    0 larva L3 12hr old    1 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    2 white prepupae new    2 white prepupae 12hr    3 white prepupae 24hr    4 pupae 2d postWPP    3 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    3 adult male 05day    6 adult male 30day    4 adult female 01day    0 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    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 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    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    1 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    1 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_28 mE1_20_mRNA_expression_cluster_08
External Data & Images
Linkouts	BDGP expression data • RE01333 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004372 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2075-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | recessive aly3 viable alyPL00002 alyz3-1393 alyz3-3504 alyz3-4302 alyz3-4307 viable, with Scer\GAL4pnr-MD237 alyGD4261 viable (with aly2) aly3 viable (with aly3) aly2 Sterility Allele fertile alyPL00002 male sterile aly1 alyz3-1393 alyz3-3504 alyz3-4302 alyz3-4307 male sterile (with aly2) aly3 male sterile (with aly3) aly2 male sterile | recessive aly1 aly2 aly4 aly5 aly6 aly7 aly8 male sterile | recessive | heat sensitive aly1 Other Phenotypes Allele meiotic cell cycle defective | recessive aly1 aly2 aly4 aly5 aly6 aly7 aly8 meiotic cell cycle defective | recessive | heat sensitive aly1 Phenotype manifest in Allele nuclear chromosome & primary spermatocyte aly5 spermatocyte aly2 aly4 aly5 aly6 aly7 aly8 spermatocyte (with aly2) aly3 spermatocyte (with aly3) aly2 spermatocyte | heat sensitive aly1 testis aly2 aly4 aly5 aly6 aly7 aly8 testis (with aly2) aly3 testis (with aly3) aly2 testis | heat sensitive aly1
Classical Alleles ( 14 )
For All Classical Alleles Show
Allele of aly Class Mutagen Stocks Known lesion aly1 P-element activity 2 -- alyPL00002 P-element activity 1 -- aly2 ethyl methanesulfonate 0 Yes aly3 ethyl methanesulfonate 0 -- aly4 Delta2-3 0 Yes aly5 Delta2-3 0 Yes aly6 Delta2-3 0 Yes aly7 Delta2-3 0 Yes aly8 Delta2-3 0 Yes alyunspecified 0 -- alyz3-1393 ethyl methanesulfonate 0 Yes alyz3-3504 ethyl methanesulfonate 0 Yes alyz3-4302 ethyl methanesulfonate 0 Yes alyz3-4307 ethyl methanesulfonate 0 Yes
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of aly Class Mutagen Stocks Known lesion alyGD4261 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes alyHMS01614 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes alyKK106416 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes alyScer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Not disrupted in	Df(3L)aly+ (White-Cooper et al., 2000) Df(3L)HR218 (Lin et al., 1996)
Disrupted in	Df(3L)BSC23 (Deal et al., 2002.11.12) Df(3L)BSC428 (Christensen et al., 2008.4.15) Df(3L)BSC671 (Christensen et al., 2008.12.28) Df(3L)Exel6092 (Ryder, 2004.4.26) Df(3L)HR370 (Lin et al., 1996)
Not duplicated in	Dp(3;3)pdp7 (Lin et al., 1996)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4261} NA P{KK106416} NA P{TRiP.HMS01614} NA P{UAS-eGFP-aly} NA characterization construct P{aly-SCEI.HEG-1} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap binary system PBac{GAL4D,EYFP}alyPL00002 No miscellaneous insertions H{}aly5 NA P{}aly4 NA P{}aly6 NA P{}aly7 NA P{}aly8 NA
Gene Ontology: Function, Process & Cellular Component ( 15 unique terms )
Terms Based on Experimental Evidence ( 11 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with tomb (Jiang et al., 2007) inferred from physical interaction with wuc (Doggett et al., 2011)
Biological Process
CV term Evidence References
male meiosis I inferred from mutant phenotype (Lin et al., 1996) positive regulation of transcription during meiosis inferred from mutant phenotype (Jiang et al., 2007) positive regulation of transcription from RNA polymerase II promoter inferred from mutant phenotype (Doggett et al., 2011) regulation of gene expression inferred from mutant phenotype (White-Cooper et al., 1998) spermatid differentiation inferred from mutant phenotype (White-Cooper et al., 1998) spermatogenesis inferred from expression pattern (White-Cooper et al., 2000) inferred from mutant phenotype (Lin et al., 1996)
Cellular Component
CV term Evidence References
chromatin inferred from direct assay (White-Cooper et al., 2000) cytoplasm inferred from direct assay (White-Cooper et al., 2000) nuclear chromatin inferred from direct assay (Jiang et al., 2007) nucleus inferred from direct assay (Jiang and White-Cooper, 2003) inferred from direct assay AND inferred from sequence or structural similarity (White-Cooper et al., 2000)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
chromatin organization non-traceable author statement (White-Cooper et al., 2000) DNA-dependent transcription, initiation traceable author statement (White-Cooper et al., 2000) meiosis traceable author statement (Fuller, 1998) spermatid development traceable author statement (White-Cooper et al., 2000, Fuller, 1998) spermatogenesis non-traceable author statement (White-Cooper, 2000.3.29)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
aly - wuc two hybrid (Doggett et al., 2011)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions aly allele Gene References unspecified comr (Jiang and White-Cooper, 2003)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 70019 DroID - A comprehensive database of gene and protein interactions. • FBgn0004372 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 45960
Orthologs
OrthoDB Orthologs (12) - 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 EOG6X0NCB Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search EOG6NP5ZC Arthropod inclusive ortholog search EOG62RBP6 Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6X0NCB)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\aly     Drosophila simulans   Dsim\aly Y   Drosophila sechellia   Dsec\GM14091 Y   Drosophila erecta   Dere\GG14487 Y   Drosophila yakuba   Dyak\GE21675 Y   Drosophila ananassae   Dana\GF10229 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA28313 Y   Drosophila persimilis   Dper\GL20762 Y   Drosophila willistoni   Dwil\GK16577 Y   Drosophila virilis   Dvir\GJ11265 Y   Drosophila mojavensis   Dmoj\GI11587 Y   Drosophila grimshawi   Dgri\GH16628 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\aly Drosophila sechellia Dsec\GM14091 Drosophila erecta Dere\GG14487 Drosophila yakuba Dyak\GE21675 Drosophila ananassae Dana\GF10229 Drosophila pseudoobscura pseudoobscura Dpse\GA28313 Drosophila persimilis Dper\GL20762 Drosophila willistoni Dwil\GK16577 Drosophila virilis Dvir\GJ11265 Drosophila mojavensis Dmoj\GI11587 Drosophila grimshawi Dgri\GH16628
Stocks & Reagents
Stocks Listed in FlyBase ( 6 )
Bloomington	36723 y1 sc* v1; P{TRiP.HMS01614}attP2 19586 w*; PBac{GAL4D,EYFP}alyPL00002 P{FRT(whs)}2A P{neoFRT}82B 1148 P{ry11}ry2, mwh1 aly1 ry506 e1/TM3, ryRK Sb1 Ser1
Kyoto	106225 P{ry11}ry2, mwh1 aly1 ry506 e1/TM3, ryRK Sb1 Ser1
VDRC	v104705 P{KK106416}VIE-260B v13673 w1118; P{GD4261}v13673
Genomic Clones ( 1 )
	BACR21A02 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 5 )
	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	RE01333
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT10387 AT31008 RE52520
Other clones	SD02648
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0004372 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 45960
Antibody Information
	polyclonal antibody (Perezgasga et al., 2004)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: aly CG2075 (FlyBase, 1996-)
Source for database merge of
Additional comments	Source for identity of aly CG2075 was sequence comparison (date:000414). (FlyBase, 1996-)
Other Comments
	comr and aly appear to have a mutually dependent role in transcriptional activation during spermatogenesis. (Jiang and White-Cooper, 2003) achi, vis, aly and comr proteins may exist in a complex. (Wang and Mann, 2003) aly may regulate cell cycle progression and terminal differentiation during male gametogenesis by regulating chromatin conformation in primary spermatocytes. (White-Cooper et al., 2000) aly is required for CycB and twe expression in primary spermatocytes. (White-Cooper et al., 1998) Wild type function of aly is required for cell-cycle progression through the G2/M transition of meiosis I in males and for onset of spermatid differentiation. (Lin et al., 1996) The phenotype of mutants is strikingly similar to the histopathological features of meiosis I maturation arrest infertility in human males, suggesting that the control point may be conserved from flies to man. (Lin et al., 1996) aly is required for both the progression of the male meiotic cell cycle and the onset of postmeiotic differentiation. (Lin et al., 1995) Mutations of aly affect the morphology and behaviour of the mitotic spindles of embryonic cleavage divisions to produce multipolar spindles in male meiosis and generate abnormal mitotic figures in larval neuroblasts. (Wilson and Fuller, 1991)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_080118 NM_001274419 RefSeq (Proteins) • NP_524857 NP_001261348 DDBJ / EMBL / GenBank • AAF47702 ABC48754 ABC48755 ABC48756 ABC48757 ABC48758 ABC48759 ABC48760 ABC48761 ABC48762 ABC48763 ABC48764 ABC48765 ABC48766 ABC48767 ABC48768 ABC48769 ABC48770 ABC48771 ABC48772 ABC48773 ABC48774 ABC48775 ABC48776 ABC48777 AGB94043 AJ277307 BI161847 CAB86720 DQ316007 DQ316008 DQ316009 DQ316010 DQ316011 DQ316012 DQ316013 DQ316014 DQ316015 DQ316016 DQ316017 DQ316018 DQ316019 DQ316020 DQ316021 DQ316022 DQ316023 DQ316024 DQ316025 DQ316026 DQ316027 DQ316028 DQ316029 DQ316030 Entrez Gene - A searchable database of RefSeq genes. • 45960 UniProtKB/TrEMBL • Q2PNM9 Q2PNN0 Q2PNN1 Q2PNN2 Q2PNN3 Q2PNN4 Q2PNN5 Q2PNN6 Q2PNP0 Q2PNP1 Q2PNP3 Q2PNP4 Q2PNP5 Q2PNP6 Q2PNP7 Q2PNP8 Q2PNP9 Q2PNQ1 Q2PNQ2 Q9NFM3 Q9VZW3
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • DIRP (IPR010561) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE01333
Linkouts
	BioGRID - A database of protein and genetic interactions • 70019 DroID - A comprehensive database of gene and protein interactions. • FBgn0004372 DRSC - Results from RNAi screens. • FBgn0004372 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004372 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2075-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004372 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 45960 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /polycomb/alwserly1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 45960 modMine - Data generated by the modENCODE project. • FBgn0004372
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	143450_at (Kristensen et al., 2005) aly (Mukai et al., 2006, Mikhaylova et al., 2006, Arya et al., 2006, Jiang et al., 2007, Doggett et al., 2007, Benson et al., 2007, Boutanaev et al., 2007, Kalmykova et al., 2005, Gan et al., 2010, Jiang et al., 2007, Christensen et al., 2008.4.15, Civetta et al., 2006, Metcalf and Wassarman, 2007, Morris et al., 2009, Christensen et al., 2008.12.28, Catron and Noor, 2008, Di Cara et al., 2010, Chan et al., 2011, Doggett et al., 2011, Zhao et al., 2010, Rincon-Arano et al., 2012) Aly (Beall et al., 2007, Franklin-Dumont et al., 2007, Jin et al., 2005) CG2075 (White-Cooper, 2000.8.7, Beall et al., 2007, Ni et al., 2011.7.19, Keleman et al., 2009.8.5) ms(3)2   ms(3)ry2
Name Synonym	always early (Mukai et al., 2006, Kalmykova et al., 2005, Civetta et al., 2006, Metcalf and Wassarman, 2007, Catron and Noor, 2008, Zhao et al., 2010) Always early (Doggett et al., 2011)
Secondary FlyBase IDs
	FBgn0013662 FBgn0014354 FBgn0035387
References ( 89 )
Generate a list of	All references relating to this gene ( 89 )
List References by type	Research paper  ( 37 ) Supplementary material  ( 4 ) Review  ( 3 ) Personal communication to FlyBase  ( 11 ) Abstract  ( 31 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 2 )
Recent research papers ( 4 )
	Rincon-Arano et al., 2012, Cell 151(6): 1214--1228 UpSET Recruits HDAC Complexes and Restricts Chromatin Accessibility and Acetylation at Promoter Regions. [FBrf0220189] Chan et al., 2011, Genetics 188(1): 33--44 Insect Population Control by Homing Endonuclease-Based Gene Drive: An Evaluation in Drosophila melanogaster. [FBrf0213627] Chen et al., 2011, Development 138(12): 2441--2450 Sequential changes at differentiation gene promoters as they become active in a stem cell lineage. [FBrf0213772] Doggett et al., 2011, Dev. Biol. 355(2): 381--393 Wake-up-call, a lin-52 paralogue, and Always early, a lin-9 homologue physically interact, but have opposing functions in regulating testis-specific gene expression. [FBrf0213964] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...