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Gene Dmel\Nipped-A

General Information
Symbol	Dmel\Nipped-A	Species	D. melanogaster
Name	Nipped-A	Annotation symbol	CG33554
Feature type	protein_coding_gene	FlyBase ID	FBgn0053554
Gene Model Status	Current	Stock availability	13 publicly available
Also Known As	tra1, TRRAP, CG2905, dTra1, 41Ah, l(2)41Ah, dmTRRAP, GroupV, dTRRAP
Genomic Location
Chromosome (arm)	2R	Recombination map	2-55.1
Cytogenetic map	41E1-41E3	Sequence location	2R:1,065,470..1,138,527 [-]
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 Nipped-A is referred to in FlyBase by the symbol Dmel\Nipped-A (CG33554, FBgn0053554). It is a protein_coding_gene from Drosophila melanogaster. It is reported to have molecular function: protein kinase activity. There is experimental evidence that it is involved in the biological process: regulation of transcription, DNA-dependent; cytokinesis; positive regulation of Notch signaling pathway; wing disc pattern formation; phagocytosis, engulfment. 74 alleles are reported. The phenotypes of these alleles are annotated with: trichogen cell; ocellus; mesothoracic tergum; wing. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: Armadillo-like helical; Armadillo-type fold; PIK-related kinase; PIK-related kinase, FAT; PIK-related kinase, FATC; Phosphatidylinositol 3-/4-kinase, catalytic domain; Protein kinase-like domain. 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 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at high levels in the following post-embryonic organs or tissues: larval central nervous system. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult central nervous system, adult crop, larval/adult hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval carcass. Gene sequence location is 2R:1065470..1138527.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
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 41E1-41E3
Experimentally Determined Cytological Location
Cytogenetic map Notes References 41A-41A     (Dorsett, 1999.3.3)
Experimentally Determined Recombination Data
Location	2- (Rollins et al., 1998, Rollins et al., 1997) 2-55.1
Left of (cM)	stw (Dorsett, 1999.3.3)
Right of (cM)	RpL38 (Dorsett, 1999.3.3)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Nipped-A for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Low-frequency RNA-Seq exon junction(s) not annotated. Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters. Gene model reviewed during 5.47
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Nipped-A-RA FBtr0091528  NM_001014499   11554   3803 Nipped-A-RE FBtr0303293  NM_001103722   11515   3790
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 Nipped-A-PA   FBpp0085431   436.5   3803   7.81     NP_001014499   AAF57342 Nipped-A-PE   FBpp0292385   435.3   3790   7.79     NP_001097192   ABV53702
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Phosphatidylinositol 3-/4-kinase, catalytic domain (IPR000403) PIK-related kinase, FAT (IPR003151) PIK-related kinase, FATC (IPR003152) PIK-related kinase (IPR014009) Armadillo-type fold (IPR016024) Protein kinase-like domain (IPR011009) Armadillo-like helical (IPR011989)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA141515   AA699085   AA803518   AE013599 AAF57342   AE013599 ABV53702   AI404310   AI520585   AI532154   AI534313   AI542305   AW941980   AW943533   AY094769 AAM11122   AY142217 AAN52145   BG640949   BG640970   BI173238   BI486858   BI566006   BI581561   BI581709   BI581710   BI582444   BI591096   BI591131   BI607529   BI611641   BI613041   BI621401   BI625936   BP559637   BP559638   CK659679   CK661131   CK661551   CO153428   CO176952   CO177045   CO177216   CO177851   CO178291   CO178335   CO178623   CO178806   CO178998   CO185786   CO187215   CO189011   CO189811   CO191125   CO194645   CO196246   CO196589   CO261825   CO261985   CO262220   CO262491   CO263186   CO264809   CO265600   CO268395   CO269566   CO269909   CO270570   CO274890   CO274942   CO278075   CO278824   CO279273   CO280255   CO281199   CO283225   CO284922   CO285276   CO286740   CO286883   CO286920   CO287019   CO287150   CO287963   CO288430   CO288547   CO289595   CO289953   CO291356   CO292691   CO293149   CO297590   CO299703   CO300497   CO300627   CO300790   CO300901   CO302568   CO307720   CO307995   CO309048   CO310667   CO313564   CO314877   CO315285   CO317363   CO318414   CO318456   CO318722   CO321906   CO322487   CO324928   CO325308   CO325661   CO326573   CO327986   CO328447   CO330991   CO331421   CO332092   CO332134   CO332318   CO333006   CO333106   CO333541   CO333663   CO338498   CO340164   CO341552   CO343746   CO344557   CO344804   CO344959   CO345299   DQ352451   EC051715   EC053224   EC053701   EC054719   EC056491   EC057200   EC057703   EC061114   EC065524   EC069811   EC070739   EC073829   EC076655   EC077626   EC077749   EC078785   EC079037   EC081558   EC198558   EC204811   EC208542   EC211679   EC215136   EC220804   EC221652   EC229062   EC229639   EC231244   EC233839   EC234103   EC234328   EC235639   EC235786   EC239808   EC245341   EC246809   EC250125   EC266233   EV584124   EV595703   GH941972   GH942806   GH943742   GH943867   GH945718   GH945842   GH946490   GH946769   GH947625   GH949344   GH949570   GH950490   GH950837   GH951596   GH952622   GH953162   GH953833   GH954210   GH954587   GH955129   GH955599   GH956071   GH956343   GH956915   GH957447   GH960109   GH962016   GH965335   GH966119   GH967424   GH968562   GH968599   GH969085   GH970796   GH972128   GH972963   GH973109   GH976772   GH977084   GH977442   GH979534   GH981761   GH981834   GH984007
UniProtKB/Swiss-Prot	Q8I8U7
UniProtKB/TrEMBL	A8DY44 Q2EZ47
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
mass spectroscopy Stage Tissue/Position (including subcellular localization) Reference day 5 of adulthood & male -- day 7 of adulthood & male   spermatozoon   (Wasbrough et al., 2010) day 7 of adulthood -- day 49 of adulthood   adult heart   (Cammarato et al., 2011)
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
cytoplasm inferred from direct assay (Gause et al., 2006) histone acetyltransferase complex inferred from direct assay (assigned by UniProtKB) (Kusch et al., 2003) inferred from physical interaction with pont (Kusch et al., 2004) microtubule associated complex inferred from direct assay (Hughes et al., 2008) nucleus inferred from direct assay (Gause et al., 2006, Kusch et al., 2004, Weake et al., 2011, Guelman et al., 2006) polytene chromosome inferred from direct assay (Gause et al., 2006) polytene chromosome puff inferred from direct assay (Gause et al., 2006) SAGA complex inferred from direct assay (Weake et al., 2011, Guelman et al., 2006)
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: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at high levels in the following post-embryonic organs or tissues: larval central nervous system. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult central nervous system, adult crop, larval/adult hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female  (29) ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female  29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    22 central nervous system, pupae P8    19 head, virgin 1-day female    4 head, virgin 4-day female    3 head, virgin 20-day female    3 head, mated 1-day female    3 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    4 head, mated 4-day male    7 head, mated 20-day male    6 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    2 fat body, larvae L3 wandering    1 fat body, white prepupae    4 fat body, pupae P8    3 carcass, larvae L3 wandering    9 carcass, 1-day adult    2 carcass, 4-day adult    3 carcass, 20-day adult    2 ovary, virgin 4-day female    29 ovary, mated 4-day female    13 testis, mated 4-day male    1 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic 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    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 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    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 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    7 embryo 02-04hr    11 embryo 04-06hr    24 embryo 06-08hr    9 embryo 08-10hr    11 embryo 10-12hr    5 embryo 12-14hr    14 embryo 14-16hr    3 embryo 16-18hr    5 embryo 18-20hr    2 embryo 20-22hr    2 embryo 22-24hr    4 larva L1    2 larva L2    4 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    10 white prepupae new    11 white prepupae 12hr    10 white prepupae 24hr    11 pupae 2d postWPP    7 pupae 3d postWPP    3 pupae 4d postWPP    1 adult male 01day    2 adult male 05day    2 adult male 30day    1 adult female 01day    3 adult female 05day    9 adult female 30day    6 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+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (33) Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2  (37) embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2  (39) wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3  (28) eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2  (29) ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 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+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (33) Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2  (37) embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2  (39) wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3  28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2  29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 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+    33 Schneider line 2 Sg4    8 embryonic 1182-4H    6 embryonic GM2    37 embryonic Kc167    15 embryonic S1    7 embryonic S3    25 leg disc CME L1    6 wing disc CME-W2    39 wing disc ML-DmD8    22 wing disc ML-DmD9    4 wing disc ML-DmD16-c3    11 wing disc ML-DmD21    5 wing disc ML-DmD32    6 haltere disc ML-DmD17-c3    28 eye-antennal disc ML-DmD11    15 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    4 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    9 tumorous blood cells mbn2    29 ovary fGS/OSS    7 ovary OSC    14 ovary OSS    7 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    8 Cadmium 50 mM 48 hrs, 4-day adult    5 Cadmium 100 mM 48 hrs, 4-day adult    12 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    12 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    5 Ethanol 2.5% 3 hrs, larvae L3    7 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    8 Paraquat 10 mM 48 hrs, 4-day adult    5 Rotenone 2 μg 12 hrs, larvae L3    4 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. (Graveley et al., 2011) mE1_20_mRNA_expression_cluster_07
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0053554 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CT29602;CG2905-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal Nipped-AGD9847 Nipped-AGD15595 lethal | embryonic stage | recessive Nipped-A2 Nipped-AC25 lethal | larval stage | recessive Nipped-A222.3 Nipped-A323 Nipped-A394.2 lethal | partially | recessive Nipped-A22 lethal | pupal stage, with Scer\GAL4pnr-MD237 Nipped-AGD15595 lethal | recessive Nipped-A1 Nipped-A8 Nipped-A226.1 Nipped-A357.2 Nipped-AIR5 Nipped-AIR6 Nipped-AIR17 Nipped-AIR43 Nipped-ANC106 Nipped-ANC116 Nipped-ANC186 lethal | second instar larval stage (with Df(2R)Nipped-E43) Nipped-ANC105 Nipped-ANC106 Nipped-ANC194 Other Phenotypes Allele increased cell death | third instar larval stage Nipped-ANC96 neuroanatomy defective | larval stage Nipped-AGD9847 visible, with Scer\GAL4pnr-MD237 Nipped-AGD15595 Phenotype manifest in Allele embryonic/larval brain | larval stage Nipped-AGD15595 embryonic/larval neuroblast | larval stage Nipped-AGD9847 ganglion mother cell | larval stage Nipped-AGD9847 imaginal disc | third instar larval stage Nipped-ANC96 mesothoracic tergum, with Scer\GAL4pnr-MD237 Nipped-AGD15595 ocellus Nipped-A12 Nipped-A3 trichogen cell, with Scer\GAL4pnr-MD237 Nipped-AGD15595 wing Nipped-A12 Nipped-A8
Classical Alleles ( 68 )
For All Classical Alleles Show
Allele of Nipped-A Class Mutagen Stocks Known lesion Nipped-AKG10162 1 -- Nipped-AMI00364 1 -- Nipped-AMI04079 1 -- Nipped-ANC116 ethyl methanesulfonate 1 Yes Nipped-ANC186 ethyl methanesulfonate 1 Yes Nipped-A10 ethyl methanesulfonate 0 Yes Nipped-A11 0 Yes Nipped-A12 ethyl methanesulfonate 0 Yes Nipped-A13 ethyl methanesulfonate 0 Yes Nipped-A14 ethyl methanesulfonate 0 Yes Nipped-A15 ethyl methanesulfonate 0 Yes Nipped-A16 ethyl methanesulfonate 0 Yes Nipped-A17 ethyl methanesulfonate 0 Yes Nipped-A18 ethyl methanesulfonate 0 Yes Nipped-A19 ethyl methanesulfonate 0 Yes Nipped-A1 ethyl methanesulfonate 0 Yes Nipped-A20 ethyl methanesulfonate 0 Yes Nipped-A21 ethyl methanesulfonate 0 Yes Nipped-A222.3 loss of function allele gamma ray 0 -- Nipped-A226.1 loss of function allele gamma ray 0 -- Nipped-A22 ethyl methanesulfonate 0 Yes Nipped-A23 ethyl methanesulfonate 0 Yes Nipped-A24 ethyl methanesulfonate 0 Yes Nipped-A25 ethyl methanesulfonate 0 Yes Nipped-A26 ethyl methanesulfonate 0 Yes Nipped-A27 ethyl methanesulfonate 0 Yes Nipped-A28 ethyl methanesulfonate 0 Yes Nipped-A29 ethyl methanesulfonate 0 Yes Nipped-A2 loss of function allele ethyl methanesulfonate 0 Yes Nipped-A30 ethyl methanesulfonate 0 Yes Nipped-A31 0 -- Nipped-A323 loss of function allele gamma ray 0 -- Nipped-A32 0 -- Nipped-A33 spontaneous 0 -- Nipped-A357.2 loss of function allele gamma ray 0 Yes Nipped-A394.2 loss of function allele gamma ray 0 -- Nipped-A3 ethyl methanesulfonate 0 Yes Nipped-A4 ethyl methanesulfonate 0 Yes Nipped-A5 ethyl methanesulfonate 0 Yes Nipped-A6 ethyl methanesulfonate 0 Yes Nipped-A7 ethyl methanesulfonate 0 Yes Nipped-A8 ethyl methanesulfonate 0 Yes Nipped-A9 ethyl methanesulfonate 0 Yes Nipped-Aa9 0 -- Nipped-AC25 hypomorphic allele - genetic evidence gamma ray 0 -- Nipped-AIR17 IR-hybrid dysgenesis 0 -- Nipped-AIR43 IR-hybrid dysgenesis 0 -- Nipped-AIR5 IR-hybrid dysgenesis 0 -- Nipped-AIR6 IR-hybrid dysgenesis 0 -- Nipped-ANC102 ethyl methanesulfonate 0 -- Nipped-ANC105 ethyl methanesulfonate 0 Yes Nipped-ANC106 ethyl methanesulfonate 0 Yes Nipped-ANC111 ethyl methanesulfonate 0 -- Nipped-ANC119 ethyl methanesulfonate 0 -- Nipped-ANC120 ethyl methanesulfonate 0 -- Nipped-ANC169 ethyl methanesulfonate 0 -- Nipped-ANC194 ethyl methanesulfonate 0 Yes Nipped-ANC212 ethyl methanesulfonate 0 -- Nipped-ANC220 ethyl methanesulfonate 0 -- Nipped-ANC22 ethyl methanesulfonate 0 -- Nipped-ANC26 ethyl methanesulfonate 0 -- Nipped-ANC36 ethyl methanesulfonate 0 -- Nipped-ANC3 ethyl methanesulfonate 0 -- Nipped-ANC44 ethyl methanesulfonate 0 -- Nipped-ANC55 ethyl methanesulfonate 0 -- Nipped-ANC57 ethyl methanesulfonate 0 -- Nipped-ANC82 ethyl methanesulfonate 0 -- Nipped-ANC96 ethyl methanesulfonate 0 Yes
Alleles Carried on Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Nipped-A Class Mutagen Stocks Known lesion Nipped-AGD15595 in vitro construct - RNAi in vitro construct - regulatory fusion 3 Yes Nipped-AGD9847 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Nipped-AGL00432 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Nipped-AHMS00167 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Nipped-AJF01196 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Nipped-ANIG.2905R 0 --
Aneuploid Aberrations
Disrupted in	Df(2R)Exel9021 (Ryder, 2004.4.26) Df(2R)M41A4 (Hilliker, 1976, Ganetzky, 1977, Eberl et al., 1993, Duffy et al., 1996, Koryakov and Zhimulev, 1996) Df(2R)M41A8 (Rollins et al., 1999, Myster et al., 2004, Myster et al., 2004, Koryakov and Zhimulev, 1996, Gambetta and Mueller, 2009.8.18) Df(2R)M41A10 (Rollins et al., 1999, Myster et al., 2004, Myster et al., 2004, Hilliker, 1976, Ganetzky, 1977, Sharp et al., 1985, Eberl et al., 1993, Duffy et al., 1996, Koryakov and Zhimulev, 1996, Gambetta and Mueller, 2009.8.18) Df(2R)nap1 (Myster et al., 2004, Gambetta and Mueller, 2009.8.18) Df(2R)nap4 (Gambetta and Mueller, 2009.8.18) Df(2R)nap8 (Gambetta and Mueller, 2009.8.18) Df(2R)NC13 (Myster and Peifer, 2003.9.11, Myster et al., 2004) Df(2R)NC31 (Sinclair et al., 2009) Df(2R)NC50 (Myster et al., 2004) Df(2R)NC68 (Myster et al., 2004) Df(2R)NC125 (Myster et al., 2004) Df(2R)NC167 (Myster et al., 2004) Df(2R)NC191 (Myster et al., 2004) Df(2R)NC202 (Myster et al., 2004) Df(2R)NC218 (Myster et al., 2004) Df(2R)NC228 (Myster and Peifer, 2003.9.11, Myster et al., 2004) Df(2R)Nipped-C160.1 (Rollins et al., 1999) Df(2R)Nipped-D (Myster et al., 2004, Myster et al., 2004) Df(2R)Nipped-D263.3 (Rollins et al., 1999) Df(2R)Nipped-D341.1 (Rollins et al., 1999) Df(2R)Nipped-E43 (Rollins et al., 1999, Gause et al., 2006) Df(2R)Nipped-E299.1 (Rollins et al., 1999) Df(2R)Nipped-E338 (Rollins et al., 1999) T(2;3)Nipped-A394.2 (Rollins et al., 1999) T(2;3)Nipped-C138.2 (Rollins et al., 1999)
Not disrupted in	Df(2R)244 (Myster et al., 2004) Df(2R)247 (Myster et al., 2004) Df(2R)B (Hilliker, 1976, Ganetzky, 1977) Df(2R)Dark2 (Myster et al., 2004) Df(2R)M41A2 (Myster et al., 2004, Myster et al., 2004) Df(2R)nap11 (Gambetta and Mueller, 2009.8.18) Df(2R)NC32 (Myster et al., 2004, Gambetta and Mueller, 2009.8.18) Df(2R)NC73 (Myster et al., 2004) Df(2R)NC98 (Myster et al., 2004) Df(2R)NC168 (Myster et al., 2004) Df(2R)NC195 (Myster et al., 2004) Df(2R)NC207 (Myster et al., 2004) Df(2R)NC219 (Myster et al., 2004) Df(2R)NC1198 (Myster et al., 2004) Df(2R)PR50 (Eberl et al., 1993) Df(2R)PRB (Eberl et al., 1993) Df(2R)PRF (Eberl et al., 1993) Df(2R)rl-1G (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-2J (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-4J (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-5B (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-6C (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-9B (Hilliker, 1976) Df(2R)rl-10G (Rollins et al., 1999, Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-12E (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-13D (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-14C (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-18C (Hilliker, 1976) Df(2R)rl-B (Hilliker, 1976) Df(2R)rl-D (Hilliker, 1976) Df(2R)rl-F (Hilliker, 1976, Ganetzky, 1977) Df(2R)rl-I (Hilliker, 1976) Df(2R)Rsp1 (Ganetzky, 1977) Df(2R)Rsp11 (Ganetzky, 1977) Df(2R)Rsp31 (Ganetzky, 1977) T(Y;2)B (Dimitri, 1991) Ts(Y;2Lt)C+Ts(Y;2Rt)A (Dimitri, 1991)
Partially disrupted in	Df(2R)Nipped-AC25 (Rollins et al., 1999)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD9847} NA P{GD15595} NA P{TRiP.GL00432} NA P{TRiP.HMS00167} NA P{TRiP.JF01196} NA characterization construct P{NIG.2905R} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions Mi{MIC}Nipped-AMI00364 NA Mi{MIC}Nipped-AMI04079 NA P{SUPor-P}Nipped-AKG10162 NA
Gene Ontology: Function, Process & Cellular Component ( 14 unique terms )
Terms Based on Experimental Evidence ( 12 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
cytokinesis inferred from mutant phenotype (Echard et al., 2004) phagocytosis, engulfment inferred from mutant phenotype (Stroschein-Stevenson et al., 2006) positive regulation of Notch signaling pathway inferred from genetic interaction with mam (Gause et al., 2006) inferred from genetic interaction with N (Gause et al., 2006) regulation of transcription, DNA-dependent inferred from direct assay (assigned by UniProtKB) (Kusch et al., 2003) wing disc pattern formation inferred from genetic interaction with mam (Gause et al., 2006) inferred from genetic interaction with N (Gause et al., 2006)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Gause et al., 2006) histone acetyltransferase complex inferred from direct assay (assigned by UniProtKB) (Kusch et al., 2003) inferred from physical interaction with pont (Kusch et al., 2004) microtubule associated complex inferred from direct assay (Hughes et al., 2008) nucleus inferred from direct assay (Gause et al., 2006, Kusch et al., 2004, Weake et al., 2011, Guelman et al., 2006) polytene chromosome inferred from direct assay (Gause et al., 2006) polytene chromosome puff inferred from direct assay (Gause et al., 2006) SAGA complex inferred from direct assay (Weake et al., 2011, Guelman et al., 2006)
Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term Evidence References
phosphotransferase activity, alcohol group as acceptor inferred from electronic annotation with InterPro:IPR000403 (FlyBase Curators et al., 2004-) protein kinase activity non-traceable author statement (Manning, 2002.11.16)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
SAGA complex non-traceable author statement (Kusch, 2002.8.16)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Nipped-A - CG15118 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Nipped-A - His2Av anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Nipped-A allele Gene References Nipped-A1 run (Duffy et al., 1996) Nipped-A2 ct (Rollins et al., 1999) mam (Rollins et al., 1999) Nipped-A222.3 Chi (Rollins et al., 1999) ct (Rollins et al., 1999) mam (Rollins et al., 1999) N (Rollins et al., 1999) vg (Rollins et al., 1999) Nipped-A226.1 ct (Rollins et al., 1999) Nipped-A323 ct (Rollins et al., 1999) mam (Rollins et al., 1999) N (Rollins et al., 1999) vg (Rollins et al., 1999) Nipped-A394.2 Chi (Rollins et al., 1999) mam (Rollins et al., 1999) vg (Rollins et al., 1999) unspecified ct (Rollins et al., 1999) eve (Duffy et al., 1996) Kr (Duffy et al., 1996)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 61398 DroID - A comprehensive database of gene and protein interactions. • FBgn0053554 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35483 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • Q8I8U7
Orthologs
OrthoDB Orthologs (49) - 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 EOG6J6S94 Dipteran inclusive ortholog search EOG6XWG5P Insect inclusive ortholog search EOG6RR5C4, EOG6D7X25 Arthropod inclusive ortholog search EOG64QRFQ, EOG6JSXNJ Metazoa inclusive ortholog search EOG6GBKZS
Orthologs in Drosophila Species (EOG6J6S94)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Nipped-A     Drosophila simulans   Dsim\GD10365 Y   Drosophila sechellia   Dsec\GM11096 Y   Drosophila erecta   Dere\GG10869 Y   Drosophila yakuba   Dyak\GE11256 Y   Drosophila ananassae   Dana\GF19759     Drosophila ananassae   Dana\GF19760     Drosophila pseudoobscura pseudoobscura   Dpse\GA24014     Drosophila persimilis   Dper\GL14099     Drosophila persimilis   Dper\GL14100     Drosophila willistoni   Dwil\GK21939 Y   Drosophila virilis   Dvir\GJ20435 Y   Drosophila mojavensis   Dmoj\GI20685 Y   Drosophila grimshawi   Dgri\GH20167 Y
Orthologs in non-Drosophila Dipterans (EOG6XWG5P)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL012951   Anopheles gambiae Malaria mosquito  Agam\AGAP005533   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ013348
Orthologs in non-Dipteran Insects (EOG6RR5C4, EOG6D7X25)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\Nipped-A   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG003925   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH18219   Atta cephalotes Leafcutter ant  Acep\ACEP19519   Camponotus floridanus Florida carpenter ant  Cflo\CFLO21204   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL20096   Linepithema humile Argentine ant  Lhum\LH18374   Pogonomyrmex barbatus Red harvester ant  Pbar\PB18943   Solenopsis invicta Red fire ant  Sinv\SINV14762   Acyrthosiphon pisum Pea aphid  Apim\ACYPI001469   Acyrthosiphon pisum Pea aphid  Apim\ACYPI002974   Acyrthosiphon pisum Pea aphid  Apim\ACYPI53390   Acyrthosiphon pisum Pea aphid  Apim\ACYPI087019   Bombyx mori Silkmoth  Bmor\BGIBMGA006169   Pediculus humanus Human body louse  Phum\PHUM249010   Tribolium castaneum Red flour beetle  Tcas\GLEAN_15434   Tribolium castaneum Red flour beetle  Tcas\GLEAN_15435
Orthologs in non-Insect Arthropods (EOG64QRFQ, EOG6JSXNJ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\MAGEA3   Ixodes scapularis Deer tick  Isca\ISCW009654   Ixodes scapularis Deer tick  Isca\ISCW001767
Orthologs in non-Arthropod Metazoa (EOG6GBKZS)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\trr-1   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_028482gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_001401gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_022766gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_013559gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_000865gn   Danio rerio Zebrafish  Drer\ENSDARG00000090442   Xenopus tropicalis Western clawed frog  Xtro\trrap   Gallus gallus Domestic chicken  Ggal\TRRAP   Mus musculus House mouse  Mmus\Trrap   Rattus norvegicus Norway rat  Rnor\Trrap   Homo sapiens Human  Hsap\TRRAP
Human Orthologs (1)
Gene OMIM HGNC Hsap\TRRAP
AAA Orthologs (8) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD10365 Drosophila sechellia Dsec\GM11096 Drosophila erecta Dere\GG10869 Drosophila yakuba Dyak\GE11256 Drosophila willistoni Dwil\GK21939 Drosophila virilis Dvir\GJ20435 Drosophila mojavensis Dmoj\GI20685 Drosophila grimshawi Dgri\GH20167
Stocks & Reagents
Stocks Listed in FlyBase ( 13 )
Bloomington	31255 y1 v1; P{TRiP.JF01196}attP2 16514 y1; P{SUPor-P}Nipped-AKG10162/CyO 35595 y1 sc* v1; P{TRiP.GL00432}attP2 34849 y1 sc* v1; P{TRiP.HMS00167}attP2 30971 y1 w*; Mi{MIC}Nipped-AMI00364/CyO 37234 y1 w*; Mi{MIC}Nipped-AMI04079/SM6a 7187 Nipped-ANC186 cn1 bw1/CyO, P{GAL4-Kr.C}DC3, P{UAS-GFP.S65T}DC7
VDRC	v52486 w1118 P{GD9847}v52486 v52487 w1118; P{GD9847}v52487/TM3 v40789 w1118; P{GD15595}v40789/TM3 v40790 w1118; P{GD15595}v40790/CyO v44781 w1118; P{GD15595}v44781/TM3
	More stocks available...
Genomic Clones ( 2 )
	BACR02D22 BACR07H20 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 205 )
	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	GM13382
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH23962 HL07440 LP17608 LP20301 LP21145 RE16017 RE70335 RH04810 RH04851 RH18014 RH19071 RH19246 RH19247 RH20526 RH35086 RH42109 RH52737 RH66446 RH74613 SD03536 SD07105 SD08579 SD12139 SD12166
Other clones	10576 15542 17461 20248 40460 43287 45871 52667 53023 59507 66991 72508 74528 107531 119091 153259 156760 157175 167294 189963 190283 194005 280539 572734 CK01.10D.D1 CK01.41A.F3 CK01.41D.F3 CK01.73D.C4 CK01.86D.C11 CK01.104D.E5 CK01.119D.H11 CK01889 Dmel_dig_007257_0652_3657 Dmel_neb_005202_0647_0916 EC38953 EC051715 EC053224 EC053701 EC054719 EC056491 EK002348 EK006334 EK012123 EK027315 EK042749 EK045227 EK050817 EK051735 EK052236 EK052904 EK054506 EK056328 EK056437 EK057219 EK057610 EK058142 EK063720 EK064152 EK064253 EK064631 EK065047 EK067428 EK068510 EK068844 EK071428 EK072655 EK077864 EK080119 EK083335 EK084721 EK085464 EK087719 EK091232 EK095016 EK096526 EK099335 EK115845 EK116011 EK128651 EK131764 EK133934 EK140359 EK143203 EK153512 EK156160 EK162632 EK167562 EK168649 EK170136 EK176351 EK178356 EK178831 EK179418 EK179625 EK184446 EK186754 EK188233 EK195157 EK196062 EK197042 EK200750 EK201931 EK222241 EK233432 EK238139 EK255411 EK256351 EK259961 EK260947 EK267816 EK272039 EK272206 EK273541 EK297142 EK299657 EK302509 EK302561 EK303132 EK305415 EK305720 EK307227 EK307606 EN01940 EN16942 EP04227 EP08363 EP09224 EP10131 EP12647 EP17944 EP19508 EP19924 EP21026 EP21759 FGM322A08 LD40782 RP004059150 RP004069165 RP004081521 RP004086079 RP004093845 RP004102876 RP004111340 RP004118373 RP004123495 RP004133827 RP004141467 RP004156435 RP004168326 RP004169476 RP004184447 RP004186812 RP004202931 RP004206528 RP004215948 RP004219349 RP004226231 RP004227765 RP004227952 RP004228127 RP004246384 RP004248092 RP004249369 RP004253924 RP004261040 RP004291330 RP004302496 RP004311463 RP004387944 RP004389484 RP004403459 RP004421823 RP004446196 RP004452222 RP004453555 RP004467477 RP004483120 RP004493527 RP004530103 RP004548824
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0053554 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35483
Antibody Information
	polyclonal (Gause et al., 2006)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: l(2)41Ah Nipped-A (Dorsett, 1999.3.3) Source for merge of: Nipped-A Tra1 (Myster et al., 2004) Source for merge of: Tra1 CG2905 CG10549 (FlyBase, 1996-)
Additional comments	Release 4.1 annotation CG33554 (which corresponds to Nipped-A) contains sequences corresponding to both release 3.2 annotation CG2905 and release 2 annotation CG10549. (FlyBase Genome Annotators, 2005) 'Nipped' mutations disrupt one or more of four recessive lethal complementation groups: l(2)41Ae, RpL38, Nipped-A and Nipped-B. (Rollins et al., 1999) Source for merge of Tra1 CG2905 CG10549 was sequence comparison (date:030120). (FlyBase, 1996-) Complementation map circular, with the majority of mutants falling into a single complementation group that is complemented by only three of the thirty alleles.
Other Comments
	dsRNA has been made from templates generated with primers directed against this gene. (Marr et al., 2006) S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells. (Stroschein-Stevenson et al., 2006) dsRNA directed against this gene causes defects in cytokinesis when tested in an RNAi screen in S2 cells. (Echard et al., 2004) CG10549 was eliminated in release 3 of the genome annotation, January 2003. (FlyBase Genome Annotators, 2002-2003) 'Nipped' mutations identify four essential complementation groups, l(2)41Ae, RpL38, Nipped-A and Nipped-B, that play distinct roles in regulating ct and N signalling. (Rollins et al., 1999) Nipped-A influences N receptor signalling or N expression during development of the wing margin and wing veins. (Rollins et al., 1999) The Nipped-group genes regulate ct and Ubx. (Rollins et al., 1997) Nipped-A acts as a dosage sensitive maternal modifier of run. (Duffy et al., 1996) Nipped-A locus exhibits high EMS mutability and the lethal alleles exhibit a complex interallelic complementation. (Hilliker, 1976)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_001014499 NM_001103722 RefSeq (Proteins) • NP_001014499 NP_001097192 DDBJ / EMBL / GenBank • AA803518 AAF57342 AAM11122 AAN52145 ABD22987 ABV53702 AI520585 AW941980 AW943533 AY094769 AY142217 DQ352451 Entrez Gene - A searchable database of RefSeq genes. • 35483 UniProtKB/Swiss-Prot • Q8I8U7 UniProtKB/TrEMBL • A8DY44 Q2EZ47
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Phosphatidylinositol 3-/4-kinase, catalytic domain (IPR000403) PIK-related kinase, FAT (IPR003151) PIK-related kinase, FATC (IPR003152) PIK-related kinase (IPR014009) Armadillo-type fold (IPR016024) Protein kinase-like domain (IPR011009) Armadillo-like helical (IPR011989)
Linkouts
	BioGRID - A database of protein and genetic interactions • 61398 DroID - A comprehensive database of gene and protein interactions. • FBgn0053554 DRSC - Results from RNAi screens. • FBgn0053554 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0053554 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CT29602;CG2905-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0053554 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35483 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /genebrief/nipped-a.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35483 modMine - Data generated by the modENCODE project. • FBgn0053554 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • Q8I8U7
Synonyms & Secondary IDs ( 23 )
Reported As
Symbol Synonym	41Ah (Dimitri et al., 2005, Cenci et al., 2003, Dimitri et al., 2003) CG2905 (Kusch et al., 2004, Bartolome and Maside, 2004, Dimitri et al., 2005, Song et al., 2004, Myster et al., 2004, Corradini et al., 2003, Hughes et al., 2008) CG10549   CG33554 (FlyBase Genome Annotators, 2005, Panhuis and Swanson, 2006, Ni et al., 2008, Ni et al., 2011.7.19, Cammarato et al., 2011) dmTRRAP (Lebedeva, 2005, Lebedeva et al., 2005) dTra1 (Raisner, 2006, Kusch et al., 2004, Kusch et al., 2004, Kusch et al., 2003, Jin, 2005, Latouche et al., 2007) dTRRAP (Kurshakova et al., 2007, Mohan et al., 2010) GroupV (Ganetzky, 1977, Hilliker, 1976) l(2)41Ah (Rollins et al., 1999, Corradini et al., 2003, Dimitri et al., 2003) l(2)C123   l(2)EMS34-12 (Eberl et al., 1993) NipA (Gause et al., 2006) Nip-A (Somma et al., 2008) NippedA (Yedvobnick et al., 2001) Nipped-A (Rossi et al., 2007, Roy et al., 2007, Yin et al., 2008, Yasuhara and Wakimoto, 2008, Sackton et al., 2009, Rees et al., 2011, Coulthard et al., 2010, Zhou et al., 2008, Zhang et al., 2010, Mourikis et al., 2010, Di Stefano et al., 2011, Roy et al., 2011, Wasbrough et al., 2010, Neumüller et al., 2011) Nipped A (Palomera-Sanchez et al., 2010) tra1 (Echard et al., 2004, Zhang et al., 2010) Tra-1 (Greil et al., 2003) Tra1 (Marr et al., 2006, Stroschein-Stevenson et al., 2006, Guelman et al., 2006, Gause et al., 2006, Weake et al., 2011, Weake et al., 2009, Yatsu et al., 2008, Spedale et al., 2012) TRRAP (Lebedeva, 2005, Lebedeva et al., 2005, Stadeli, 2006, Ullah et al., 2007, Gause et al., 2006, Lebedeva et al., 2007, Kurshakova et al., 2009)
Name Synonym	lethal(2)41Ah   Nipped (Rollins et al., 1997) Nipped-A (Roy et al., 2007, Gause et al., 2006, Yasuhara and Wakimoto, 2008, Bakal et al., 2008, Sathyanarayanan et al., 2008, Gambetta and Mueller, 2009.8.18, Mohan et al., 2010, Cammarato et al., 2011) NippedA (Somma et al., 2008)
Secondary FlyBase IDs
	FBan0002905 FBan0033554 FBgn0002067 FBgn0002172 FBgn0004661 FBgn0020393 FBgn0033013 FBgn0039989 FBtr0086095
References ( 101 )
Generate a list of	All references relating to this gene ( 101 )
List References by type	Research paper  ( 60 ) Supplementary material  ( 7 ) Review  ( 8 ) Personal communication to FlyBase  ( 13 ) Abstract  ( 4 ) FlyBase analysis  ( 5 ) DNA/RNA sequence record  ( 1 ) Curated genome annotation  ( 2 ) Book  ( 1 )
Recent research papers ( 7 )
	Baradaran-Heravi et al., 2012, Hum. Mol. Genet. 21(11): 2572--2587 Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. [FBrf0218299] Crawford et al., 2012, Cell Death Differ. 19(12): 2040--2048 Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. [FBrf0220233] Di Stefano et al., 2011, Genes Dev. 25(1): 17--28 Functional antagonism between histone H3K4 demethylases in vivo. [FBrf0212709] Neumüller et al., 2011, Cell Stem Cell 8(5): 580--593 Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi. [FBrf0213621] Rees et al., 2011, Mol. Cell. Proteomics 10(6): M110.002386 In Vivo Analysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry. [FBrf0213845] Roy et al., 2011, Mol. Genet. Genomics 285(2): 113--123 Lack of the Drosophila BEAF insulator proteins alters regulation of genes in the Antennapedia complex. [FBrf0212912] Weake et al., 2011, Genes Dev. 25(14): 1499--1509 Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation. [FBrf0214372] Show all research papers ...
Recent reviews ( 1 )
	Spedale et al., 2012, Genes Dev. 26(6): 527--541 ATAC-king the complexity of SAGA during evolution. [FBrf0219841] Show all reviews ...