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Gene Dmel\l(1)sc

General Information
Symbol	Dmel\l(1)sc	Species	D. melanogaster
Name	lethal of scute	Annotation symbol	CG3839
Feature type	protein_coding_gene	FlyBase ID	FBgn0002561
Gene Model Status	Current	Stock availability	6 publicly available
Also Known As	L'Sc, T3, AS-C T3, EG:198A6.2, lsc
Genomic Location
Chromosome (arm)	X	Recombination map	1-0.0
Cytogenetic map	1B1-1B1	Sequence location	X:303,756..304,850 [+]
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 lethal of scute is referred to in FlyBase by the symbol Dmel\l(1)sc (CG3839, FBgn0002561). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II regulatory region sequence-specific DNA binding; sequence-specific DNA binding transcription factor activity; sequence-specific DNA binding; protein heterodimerization activity. There is experimental evidence that it is involved in the biological process: positive regulation of transcription from RNA polymerase II promoter; epithelial cell proliferation involved in Malpighian tubule morphogenesis; positive regulation of transcription, DNA-dependent; Malpighian tubule tip cell differentiation; neurogenesis. 20 alleles are reported. The phenotypes of these alleles are annotated with: multicellular structure; sense organ; portion of tissue; anatomical structure; adult segment; organ system; organ system subdivision; adult; epithelium; larval head segment; ventral nerve cord primordium. It has one annotated transcript and one annotated polypeptide. Protein features are: Achaete-scute transcription factor-related; Myc-type, basic helix-loop-helix (bHLH) domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Comments on Affy2 ProbeSet: ProbeSet 1627194_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of l(1)sc. Gene sequence location is X:303756..304850.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	l(1)sc: lethal at scute Deficiency from which existence of l(1)sc inferred, i.e., In(1)sc4Lsc9R, embryonic lethal. Volume of embryonic ventral nerve cord slightly reduced; posterior commisures thinner than in wild type; longitudinal connectives virtually lacking. Concomitant deletions for scα or scα and ac cause more severe CNS disruptions, although by themselves these deletions have no observable CNS effects; simultaneous deletion of the sc/ region also enchances the CNS disruptions (Jimenez and Campos-Ortega). Transiently expressed at periphery of syncytial blastoderm; late blastoderm shows paired dorsolateral and ventrolateral longitudinal stripes of expression, the latter being coincident with the presumptive neurogenic ectoderm. During germ-band expression, l(1)sc expression seen in many cell clusters over most of the ectoderm; segmental distribution becomes apparent both internally and externally. l(1)sc expression seen in many foci in the head region and in the posterior midgut rudiment (Romani, Campuzano, and Modolell, 1987, EMBO J. 6: 2085-92; Cabrera, Martinez-Arias, and Bate, 1987, Cell 50: 425-33). Little if any expression in later stages, except in the central nervous system (Romani, Campuzano, Macagno, and Modolell, 1989, Genes Dev. 3: 997-1007).
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 1B1-1B1   Limits computationally determined from genome sequence between P{EP}CG17896EP1320&P{EP}EP1398 and P{EP}svrEP356&P{EP}argEP452
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	1-0.0
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\l(1)sc 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 5.51
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) l(1)sc-RA FBtr0070074  NM_057275   1095   257
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 l(1)sc-PA   FBpp0070073   29.0   257   6.34     NP_476623   AAF45500
Additional Polypeptide Data & Comments
Reported size (kDa)	258 (aa); 29 (kD) (Alonso and Cabrera, 1988) 257 (aa) (Martin-Bermudo et al., 1993)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Myc-type, basic helix-loop-helix (bHLH) domain (IPR011598) Achaete-scute transcription factor-related (IPR015660)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014298 AAF45500   AL024453 CAA19656   AY121693 AAM52020   BI357070   BI371474   BI372386   BI372472   EC221886   X12549 CAA31065   X71806 CAA50680
UniProtKB/Swiss-Prot	P09774
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References protein binding site FBsf0000160814 X:303,123..303,143 bound_moiety=HLHm5-XP evidence=experimental bound_moiety=E(spl)-XP (Oellers et al., 1994, Bergman et al., 2005)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage   procephalic segment   (Romani et al., 1987) ventral midline   (Romani et al., 1987) posterior embryonic/larval midgut   (Romani et al., 1987) labral segment   (Romani et al., 1987) central nervous system   (Romani et al., 1987) epidermoblast   (Cabrera, 1990) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   Malpighian tubule   (Romani et al., 1987) neuroblast   (Cabrera, 1990) ectoderm   (Romani et al., 1987) cephalic furrow   (Romani et al., 1987) organism | pair rule expression pattern   (Cabrera, 1990) optic lobe   (Romani et al., 1987) stomodeum   (Romani et al., 1987) embryonic stage 4 -- 6   anlage in statu nascendi   (Fisher et al., 2012) central brain anlage in statu nascendi   (Fisher et al., 2012) ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi ventral ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi antennal anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi dorsal head epidermis anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi visual anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi embryonic stage 7 -- 8   antennal anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage central brain anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage dorsal head epidermis anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage visual anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage hindgut anlage   (Fisher et al., 2012) posterior endoderm   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) Comment:reported as ventral nerve cord anlage embryonic stage 9 -- 10   antennal primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium central brain primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium visual primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium inclusive hindgut primordium   (Fisher et al., 2012) posterior endoderm   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   central brain primordium   (Fisher et al., 2012) embryonic neuroblast of ventral nerve cord primordium   (Fisher et al., 2012) hindgut proper primordium   (Fisher et al., 2012) lateral cord   (Fisher et al., 2012) midline primordium   (Fisher et al., 2012) midline ventral glial cell   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) procephalic neuroblast   (Fisher et al., 2012) somatic muscle primordium   (Fisher et al., 2012) stomatogastric nervous system primordium   (Fisher et al., 2012) ventral sensory complex anlage   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic central brain   (Fisher et al., 2012) embryonic stomatogastric nervous system   (Fisher et al., 2012) embryonic/larval nervous system   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012) radioisotope in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   procephalic neuroblast   (Cabrera et al., 1987) neuroblast   (Cabrera et al., 1987) presumptive embryonic/larval peripheral nervous system   (Cabrera et al., 1987) embryonic/larval optic lobe | presumptive   (Cabrera et al., 1987) epidermoblast   (Cabrera et al., 1987) procephalic neurogenic region   (Cabrera et al., 1987) neurogenic region   (Cabrera et al., 1987) embryonic stomatogastric nervous system   (Cabrera et al., 1987) posterior embryonic/larval midgut   (Cabrera et al., 1987) embryonic stage | early   organism | ubiquitous   (Cabrera et al., 1987) embryonic stage 11 -- 12   embryonic ganglion mother cell   (Cabrera et al., 1987)
Additional Descriptive Data
	At cellular blastoderm, l(1)sc transcripts are expressed in 12 dorsolateral stripes of alternating intensity which are interrupted by a narrow lateral nonexpressing strip and dorsal and ventral nonexpressing regions. At gastrulation, the weaker stripes increase in intensity. At germ band extension, the pattern of expression evolves into a "circle" pattern and subsequently into the "double stripe" pattern. The mRNA level appears constant throughout. (Cabrera, 1990) l(1)sc transcripts are uniformly distributed in early embryos. In the cellular blastoderm, transcripts are localized within stripes in the presumptive neurectoderm. By early gastrula, there is one stripe per metameric unit and transcripts are also detected in the procephalic neurogenic region. Between stages 8 and 9, the pattern changes to two stripes per metamere. l(1)sc is expressed in the segregating neuroblasts as well as in the cells that remain ectodermal. l(1)sc transcripts are also observed in cephalic neuroblasts and in the posterior midgut. In stages 11 and 12, l(1)sc is expressed by some ganglion mother cells. It then appears to be expressed in PNS precursors. Later expression appears to be restricted to the stomatogastric nervous system and the optic lobes. (Cabrera et al., 1987) l(1)sc transcripts are detected in a dynamic pattern from syncytial blastoderm through stage 11 embryos and are expressed in most neurogenic regions. In blastoderm embryos, l(1)sc is expressed in pairs of longitudinal bands located ventro- and dorso-laterally. Later, expression is seen in clusters of cells over most of the ectoderm. After stage 10 some clusters of expressing cells are found internally near the mesoderm. Expression is also seen along the midline and cephalic regions. (Romani et al., 1987)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage   epidermoblast   (Cabrera, 1990) embryonic stage 8 -- 11   procephalic neurogenic region | restricted   (Urbach et al., 2003) procephalic neuroblast | subset   (Urbach et al., 2003) embryonic stage 9 -- 11   protocerebral neuroblast | subset   (Urbach and Technau, 2003) tritocerebral neuroblast | subset   (Urbach and Technau, 2003) deuterocerebral neuroblast | subset   (Urbach and Technau, 2003)
Additional Descriptive Data
	Significant l(1)sc protein accumulation begins well after RNA accumulation, from mid-stage 8 onwards. At the onset of the first wave of neuroblast segregation, only a subset of cells that express RNA also express protein. These l(1)sc protein-expressing cells are thought to be the segregating neuroblasts. In N and Dl mutants, l(1)sc protein expression is not limited to the neuroblasts, but occurs in all cells that accumulate RNA. (Cabrera, 1990) In stages 8-11 ac and l(1)sc proteins are expressed in a dynamic pattern in the procephalic neurectoderm in a largely complementary pattern. By stage 8 l(1)sc protein is detected in a large central domain and as development proceeds the area of protein expression increases. The first proto and deuterocerebral neuroblasts develop from this area. About 60% of all neuroblasts formed until stage 11 express l(1)sc. In stage 8 ac expression is detected in a small dorsal ocular and antennal group of cells. In stage 9 ac expression expands to several large domains in the neuroectoderm. (Urbach et al., 2003) Expression in procephalic neuroblasts stage 9-11: tritocerebrum - d1-d4, d6, d7, v3; deuterocerebrum - d1, d3, d6, d7, v2, v4-v6, v8; protocerebrum - ad1, ad3, ad5, ad7-10, ad13-15, ad17, av1, cd2, cd3, cd5, cd6, cd8-10, cd14-17, cd19-21, cv1-9, pd3, pd5, pd8-11, pd13, pd15, pd17, pd18, pv1-3 (Urbach and Technau, 2003)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
transcription factor complex inferred from physical interaction with da (Cabrera and Alonso, 1991)
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    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    94.7 Larval Midgut    1.1 Larval Hindgut    1.7 Larval Malpighian Tubules    1.5 Larval Fat Body    2.1 Larval Salivary Gland    6.4 Larval Trachea    1.925 Larval Carcass    0.925 Adult Head    2.2 Adult Eye    1.425 Adult Brain    1.5 Adult Thoracic-Abdominal Ganglion    0.9 Adult Crop    2.3 Adult Midgut    0.7 Adult Hindgut    2.5 Adult Malpighian Tubules    2.5 Adult Fat Body    8 Adult Salivary Gland    6.6 Adult Heart    0.35 Adult VirginFemale Spermatheca    3.4 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary    0.3 Adult Testis    0.4 Adult Male Accessory Gland    2.1 Adult Carcass    1.9 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    2.2   NA  Eye    1.425   NA  Brain    1.5   94.7  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    0.9   NA  Crop    2.3   1.1  Midgut    0.7   1.7  Hindgut    2.5   1.5  Malpighian Tubules    2.5   2.1  Fat Body    8   6.4  Salivary Gland    6.6   NA  Heart    0.35   1.925  Trachea    NA   NA  VirginFemale Spermatheca    3.4   NA  InseminatedFemale Spermatheca    4.6   NA  Ovary    0.3   NA  Testis    0.4   NA  Male Accessory Gland    2.1   0.925  Carcass    1.9 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    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    4 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    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    0 carcass, 4-day adult    0 carcass, 20-day adult    0 ovary, virgin 4-day female    0 ovary, mated 4-day female    1 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of no expression detected. 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    48 embryo 04-06hr    180 embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr  (48) embryo 04-06hr  (180) embryo 06-08hr  (98) embryo 08-10hr  (39) embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    48 embryo 04-06hr  (180) embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    48 embryo 04-06hr    180 embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    48 embryo 04-06hr    180 embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr  (48) embryo 04-06hr  (180) embryo 06-08hr  (98) embryo 08-10hr  (39) embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    48 embryo 04-06hr  (180) embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    7 embryo 02-04hr    48 embryo 04-06hr    180 embryo 06-08hr    98 embryo 08-10hr    39 embryo 10-12hr    7 embryo 12-14hr    4 embryo 14-16hr    1 embryo 16-18hr    1 embryo 18-20hr    1 embryo 20-22hr    0 embryo 22-24hr    1 larva L1    0 larva L2    0 larva L3 12hr old    0 larva L3 puffstage 1-2    1 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    0 white prepupae 12hr    0 white prepupae 24hr    0 pupae 2d postWPP    0 pupae 3d postWPP    0 pupae 4d postWPP    0 adult male 01day    0 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    0 cold shock, 4-day adult    0 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    0 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    1 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    0 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    0 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_31 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • RE59335 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002561 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG3839-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for l(1)sc Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal l(1)scGD16279 lethal | embryonic stage, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa viable, with Scer\GAL4pnr-MD237 l(1)scGD4368 Other Phenotypes Allele neuroanatomy defective | larval stage l(1)scGD16279 visible, with Scer\GAL4455.2 l(1)scScer\UAS.cHa visible, with Scer\GAL4ptc-559.1 l(1)scScer\UAS.cHa visible, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa Phenotype manifest in Allele embryonic/larval maxillary chordotonal organ with two scolopidia, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa embryonic/larval somatic muscle, with Scer\GAL4how-24B, Scer\GAL4twi.PG l(1)scScer\UAS.cCa embryonic/larval somatic muscle, with Scer\GAL4W381 l(1)scScer\UAS.cCa embryonic cardioblast, with Scer\GAL4Mef2.PR l(1)scNIG.3839R ganglion mother cell | larval stage l(1)scGD16279 intermediate ventral neurectoderm, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa lateral ventral neurectoderm, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa macrochaeta, with Scer\GAL4hs.PB l(1)scScer\UAS.cBa macrochaeta & abdominal sternite 1, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & abdominal sternite 2, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & abdominal sternite 3, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & abdominal sternite 4, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & abdominal sternite 5, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & abdominal sternite 6, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa macrochaeta & mesothoracic laterotergite, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa macrochaeta & metathoracic laterotergite, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa macrochaeta & pronotum, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa macrochaeta & scutellum, with Scer\GAL4455.2 l(1)scScer\UAS.cHa macrochaeta & scutum, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa macrochaeta & wing, with Scer\GAL4564.2 l(1)scScer\UAS.cHa macrochaeta | ectopic, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cHa medial ventral neurectoderm, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa microchaeta, with Scer\GAL4527.3 l(1)scScer\UAS.cHa microchaeta, with Scer\GAL4hs.PB l(1)scScer\UAS.cBa microchaeta & mesothoracic laterotergite, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa microchaeta & metathoracic laterotergite, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa microchaeta & pronotum, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa microchaeta & scutum, with Scer\GAL4h-540.3 l(1)scScer\UAS.cHa microchaeta | ectopic, with Scer\GAL4ptc-559.1 l(1)scScer\UAS.cHa monoscolopidial chordotonal organ, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa scutellar bristle, with Scer\GAL4455.2 l(1)scScer\UAS.cHa scutellar bristle | ectopic, with Scer\GAL4455.2 l(1)scScer\UAS.cHa scutellar bristle | ectopic, with Scer\GAL4ptc-559.1 l(1)scScer\UAS.cHa scutellum & microchaeta, with Scer\GAL4ptc-559.1 l(1)scScer\UAS.cHa sense organ, with Scer\GAL4hs.PB l(1)scScer\UAS.cBa sense organ, with Scer\GAL4sca-537.4 l(1)scScer\UAS.cCa sensory mother cell & dorsal mesothoracic disc, with Scer\GAL4ap-md544 l(1)scScer\UAS.cHa stage 1 neuroblast, with Scer\GAL4da.G32 l(1)scScer\UAS.cHa wing vein, with Scer\GAL4527.3 l(1)scScer\UAS.cHa
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of l(1)sc Class Mutagen Stocks Known lesion l(1)scunspecified 0 --
Alleles Carried on Transgenic Constructs ( 19 )
For All Alleles Carried on Transgenic Constructs Show
Allele of l(1)sc Class Mutagen Stocks Known lesion l(1)scGD16279 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes l(1)scGD4368 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes l(1)scJF02399 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes l(1)scKK103581 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes l(1)scAct5C.PO in vitro construct - regulatory fusion 0 Yes l(1)schb.PP in vitro construct - regulatory fusion 0 Yes l(1)scNIG.3839R in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes l(1)scScer\UAS.cBa in vitro construct - regulatory fusion 0 Yes l(1)scScer\UAS.cCa in vitro construct - regulatory fusion 0 Yes l(1)scScer\UAS.cHa in vitro construct - regulatory fusion 0 Yes l(1)scScer\UAS.cHb in vitro construct - regulatory fusion 0 Yes l(1)scScer\UAS.cPa in vitro construct - regulatory fusion 0 Yes l(1)scYA.Scer\UAS in vitro construct - amino acid replacement 0 Yes l(1)scΔB.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes l(1)scΔC1.Scer\UAS in vitro construct - deletion 0 Yes l(1)scΔC2.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes l(1)scΔHLH.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes l(1)scΔN.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes l(1)scΔNΔC2.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(1)260-1 (Duffy and Gergen, 1991, Ray and Rodrigues, 1994, Giebel et al., 1997) Df(1)sc19 (Dambly-Chaudiere and Ghysen, 1987, Alonso and Cabrera, 1988, Duffy and Gergen, 1991, Ray and Rodrigues, 1994, Kunisch et al., 1994) Df(1)sc-B57 (Heitzler et al., 1996, Rudolph et al., 1997) In(1)sc4Lsc9R (Campuzano et al., 1985, Alonso and Cabrera, 1988, Cabrera and Alonso, 1991) In(1)sc8Lsc9R   In(1)scL8Lsc9R   In(1)scS1Lsc9R   In(1)y3PLsc9R   In(1)y4Lsc9R   Ts(1Rt;3Rt)Hw49c-rv1 (Balcells et al., 1988) Ts(1Rt;4Rt)scH (Dambly-Chaudiere and Ghysen, 1987, Heitzler et al., 1996)
Duplicated in	Dp(1;2)sc19 (Dambly-Chaudiere and Ghysen, 1987, Jimenez and Campos-Ortega, 1990) Dp(1;2)sc+ip2 (Heitzler et al., 1996) Dp(1;3)sc+ip3 (Heitzler et al., 1996) In(1)wm4Lsc4R   Ts(1Lt;4Lt)scH (Dambly-Chaudiere and Ghysen, 1987)
Not disrupted in	Df(1)ase-1 (Campuzano et al., 1985, Alonso and Cabrera, 1988, Gonzalez et al., 1989) In(1)sc8Lsc4R (Alonso and Cabrera, 1988, Ray and Rodrigues, 1994) In(1)scV2 (Campuzano et al., 1985) In(1)y3PLsc4R   In(1)y3PLsc8R (Alonso and Cabrera, 1988, Ray and Rodrigues, 1994) In(1)y3PLscS1R   Ts(1Rt;2Lt)Hw49c-rv4 (Balcells et al., 1988)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4368} NA P{GD16279} NA P{KK103581} NA P{TRiP.JF02399} NA P{UAS-l'sc} NA P{UAS-l(1)sc.B} NA P{UAS-l(1)sc.C} NA P{UAS-l(1)sc.H} NA P{UAS-l(1)sc.LSC} NA P{UAS-l(1)sc.YA} NA P{UAS-l(1)sc.ΔB} NA P{UAS-l(1)sc.ΔC1} NA P{UAS-l(1)sc.ΔC2} NA P{UAS-l(1)sc.ΔHLH} NA P{UAS-l(1)sc.ΔN} NA P{UAS-l(1)sc.ΔNΔC2} NA characterization construct P{hb-l(1)sc} NA P{NIG.3839R} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 17 unique terms )
Terms Based on Experimental Evidence ( 10 terms )
Molecular Function
CV term Evidence References
protein heterodimerization activity inferred from physical interaction with da (Cabrera et al., 1994, Jennings et al., 1999, van Doren et al., 1991, Cabrera and Alonso, 1991, Jarman et al., 1993) contributes_to RNA polymerase II regulatory region sequence-specific DNA binding inferred from physical interaction with da (Jarman et al., 1993) sequence-specific DNA binding inferred from direct assay (Cabrera et al., 1994, Jennings et al., 1999) contributes_to sequence-specific DNA binding inferred from direct assay (van Doren et al., 1991) inferred from physical interaction with da (Cabrera and Alonso, 1991) contributes_to sequence-specific DNA binding transcription factor activity inferred from direct assay (Cabrera and Alonso, 1991)
Biological Process
CV term Evidence References
epithelial cell proliferation involved in Malpighian tubule morphogenesis inferred from mutant phenotype (Sudarsan et al., 2002) Malpighian tubule tip cell differentiation inferred from mutant phenotype (Hoch et al., 1994) neurogenesis inferred from mutant phenotype (Neumüller et al., 2011) positive regulation of transcription, DNA-dependent inferred from direct assay (Cabrera and Alonso, 1991) positive regulation of transcription from RNA polymerase II promoter inferred from mutant phenotype (Jarman et al., 1993)
Cellular Component
CV term Evidence References
transcription factor complex inferred from physical interaction with da (Cabrera and Alonso, 1991)
Terms Based on Predictions or Assertions ( 8 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:P50553 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1989.3.1)
Biological Process
CV term Evidence References
central nervous system development non-traceable author statement (Skaer et al., 2002, Swiss-Prot Project Members, 1989.3.1) myoblast cell fate determination traceable author statement (Bate et al., 1999) neuroblast fate determination non-traceable author statement (Swiss-Prot Project Members, 1989.3.1) traceable author statement (Skeath and Thor, 2003) peripheral nervous system development non-traceable author statement (Skaer et al., 2002, Swiss-Prot Project Members, 1989.3.1) regulation of transcription from RNA polymerase II promoter inferred from sequence or structural similarity with UniProtKB:P50553 (FlyBase, 1992-) ventral cord development traceable author statement (Skeath and Thor, 2003)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:P50553 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions l(1)sc allele Gene References l(1)schb.PP h (Parkhurst et al., 1993) l(1)scScer\UAS.cHa Acsl (Rottgen et al., 1998) da (Rottgen et al., 1998, Hoch and Jackle, 1998) Dl (Rottgen et al., 1998) E(spl)m8-HLH (Giebel and Campos-Ortega, 1997, Rottgen et al., 1998) eIF-4a (Rottgen et al., 1998) emc (Rottgen et al., 1998) H (Rottgen et al., 1998) h (Rottgen et al., 1998) Hr46 (Rottgen et al., 1998) Hrb27C (Rottgen et al., 1998) jumu (Rottgen et al., 1998) mam (Rottgen et al., 1998) ptc (Rottgen et al., 1998) unspecified N (Rottgen et al., 1998)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 57556 DroID - A comprehensive database of gene and protein interactions. • FBgn0002561 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 30983
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 EOG6WDDZJ Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6WDDZJ)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\l(1)sc     Drosophila simulans   Dsim\l(1)sc Y   Drosophila sechellia   Dsec\GM19063 Y   Drosophila erecta   Dere\l(1)sc Y   Drosophila yakuba   Dyak\l(1)sc Y   Drosophila ananassae   Dana\GF21451 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA17723 Y   Drosophila persimilis   Dper\GL20379 Y   Drosophila willistoni   Dwil\GK25271 Y   Drosophila virilis   Dvir\GJ15597 Y   Drosophila mojavensis   Dmoj\GI10999 Y   Drosophila grimshawi   Dgri\GH24341 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\l(1)sc Drosophila sechellia Dsec\GM19063 Drosophila erecta Dere\l(1)sc Drosophila yakuba Dyak\l(1)sc Drosophila ananassae Dana\GF21451 Drosophila pseudoobscura pseudoobscura Dpse\GA17723 Drosophila persimilis Dper\GL20379 Drosophila willistoni Dwil\GK25271 Drosophila virilis Dvir\GJ15597 Drosophila mojavensis Dmoj\GI10999 Drosophila grimshawi Dgri\GH24341
Stocks & Reagents
Stocks Listed in FlyBase ( 6 )
Bloomington	27058 y1 v1; P{TRiP.JF02399}attP2
VDRC	v104691 P{KK103581}VIE-260B v12703 w1118; P{GD4368}v12703 v12704 w1118; P{GD4368}v12704 v47122 w1118; P{GD16279}v47122 v47123 w1118; P{GD16279}v47123
Genomic Clones ( 2 )
	BACR08O05 BACR13J02 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	RE59335
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE43421 RE58372 RE59441
Other clones	34948
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0002561 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 30983
Antibody Information
	polyclonal (Cabrera, 1990, Stagg et al., 2011)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: l(1)sc CG3839 (Nusskern, 1999.11)
Source for database merge of
Additional comments
Other Comments
	In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes. (Kliman and Eyre-Walker, 1998) Analysis of the function of l(1)sc. (Giebel et al., 1997) tll expression in brain neuroblasts is examined and it is demonstrated that the expression is not detectably regulated by btd, oc, l(1)sc or tll itself. (Rudolph et al., 1997) The bHLH domains of the gene products encoded by the E(spl)-C and AS-C differ in their ability to form homo- and/or heterodimers. The interactions established through the bHLH link the products of the two complexes in a single interaction network which may function to ensure that a given cell retains the capacity to choose between epidermoblast and neuroblast fates until the cell becomes definitively determined. (Gigliani et al., 1996) ac-sc mutants are epistatic over E(spl)-C mutants. (Heitzler et al., 1996) All proneural proteins are similarly able to promote the segregation of a neural precursor at the MP2 neuroblast position but show distinct capacities in its specification. (Parras et al., 1996) The function of l(1)sc is not interchangable with that of ac or sc within the MP2, specification of MP2 is similar in embryos lacking ac/sc compared with those lacking ac/sc plus ectopic l(1)sc expression. (Skeath and Doe, 1996) The expression pattern of proneural genes of the AS-C and neurogenic genes of the E(spl)-C are examined in the procephlon and a map of the cells is constructed. (Younossi-Hartenstein et al., 1996) Loss of function and over-expression phenotypes indicate a role for l(1)sc in the segregation of muscle progenitors and the formation of the muscle pattern. (Carmena et al., 1995) Overexpression of da using the GAL4 system, but not the ectopic expression of the AS-C genes l(1)sc or sc, leads to the formation of ectopic neural cells in embryonic tissue without neural competence. This effect os strongly enhanced by coexpressing l(1)sc or sc. Expression of da and/or l(1)sc is not sufficient to overcome the lateral inhibition in the analgen of the embryonic nervous system. (Giebel et al., 1995) Neurogenic genes principally regulate l(1)sc expression at the transcriptional level without affecting the domains of proneural gene expression. N and neur are required for the establishment of the mesectodermal fate, Dl and members of the E(spl) complex may be involved in the same process. (Martin-Bermudo et al., 1995) Giant fibre growth studies in cells where l(1)sc has been ablated suggest l(1)sc is normally required to repel the growth cone of the giant fibre. (Moffat et al., 1995) Ectopic expression does not affect the viability of either sex, but it does rescue the female lethality caused by ectopic expression of h. (Shoop and Parkhurst, 1995) emc forms heterodimers with the ac, sc, l(1)sc, and da products. emc inhibits DNA-binding of ac, sc and l(1)sc/da heterodimers and da homodimers. (Cabrera et al., 1994) The proneural function of l(1)sc is independent of ac, sc and ase. Deletion analysis of l(1)sc demonstrates the basic helix-loop-helix domain is necessary and sufficient to mediate the proneural function of l(1)sc to activate neurogenic genes, E(spl), Dl and HLHm5, and to allow lateral inhibition. (Hinz et al., 1994) The gene products of ac, sc and l(1)sc together with vnd act synergistically to specify the neuroectodermal E(spl) and HLHm5 expression. (Kramatschek and Campos-Ortega, 1994) Proneural gene products (ac, da and l(1)sc) activate transcription of Dl in the neuroectoderm by binding to specific sites within its promoter. This transcriptional activation enhances lateral inhibition and helps ensure that cells in the vicinity of prospective neuroblasts will themselves become epidermoblasts. (Kunisch et al., 1994) DNaseI footprinting analysis of bacterially expressed da and l(1)sc demonstrates that the gene products can bind as heterodimers to different E-box sequence upstream of the ac gene. (Oellers et al., 1994) vnd controls neuroblast formation, in part, through its regulation of the proneural genes of the ac-sc complex. vnd controls proneural gene expression at two distinct steps during neuroblast formation through separable regulatory regions. (Skeath et al., 1994) The l(1)sc gene has been cloned. A cluster of E boxes, upstream of the transcribed region, suggest regulation by helix-loop-helix gene products. (Martin-Bermudo et al., 1993) Ectopic expression shows that l(1)sc displays weak but significant feminizing activity. (Parkhurst et al., 1993) Analysis of deficiencies revealed that l(1)sc affects the level but not the spatial pattern of ac expression. (Skeath et al., 1992) In vitro DNA binding assays using gel retardation to an ac promoter region and hb zygotic promoter region target sequence demonstrates that da protein elicits a weak homodimeric binding and da/ac or da/sc heterodimers bind tightly. Single copy yeast promoters under the control of the GAL4 promoter were used to test whether ac, sc and da proteins could activate transcription of a Ecol\lacZ reporter gene in the yeast assay system, the l(1)sc gene does not induce Ecol\lacZ activity. Results suggest that da/l(1)sc heterodimers can function as transcriptional activators in direct proportion to their DNA-binding affinities. (Cabrera and Alonso, 1991) The expression of l(1)sc protein before and during neuroblast segregation in the embryo has been studied. (Martin-Bermudo et al., 1991) DNA sequence analysis reveals four E box binding sites, for the binding of hetero-oligomeric complexes composed of da or AS-C proteins, in the first 877 bp of the ac upstream region. Electrophoretic mobility shift assays demonstrate that the emc protein can specifically antagonise DNA binding of the da/AS-C complexes in vitro in a dose-dependent manner, h and E(spl) proteins fail to exhibit this inhibitory effect. (van Doren et al., 1991) A comparison of RNA and protein patterns suggests post-transcriptional regulation of l(1)sc. Protein accumulates in only a subset of the cells that express the RNA and these go on to become neuroblasts. The deployment of l(1)sc protein expression is one of the causal factors that assigns specific fates to the neuroblasts and a basis for the mechanism of lateral inhibition. (Cabrera, 1990) The function of ac, sc and l(1)sc are required for the normal development of the neuroblasts and absence of the genes causes neuroectodermal cells to enter the epidermal pathway of development. (Jimenez and Campos-Ortega, 1990) Ectopic expression of l(1)sc has no effect on sex determination. (Parkhurst et al., 1990) Wild-type embryos show the protein is present in the developing neuroblasts, whereas the corresponding RNA is found in the neural and epidermal lineages. A study of the protein product distribution in mutants and wild type demonstrated that mutants cause neural hyperplasia in embryos. (Simpson, 1990) Sequence analysis reveals that ac, sc and l(1)sc transcription units share highly conserved acidic and basic domains in their protein coding regions. The basic domain of the ac, sc and l(1)sc proteins show similarity to the vertebrate myc and MyoD proteins. (Alonso and Cabrera, 1988) Transcripts of ac, sc and l(1)sc accumulate at the blastoderm stage in periodic patterns within the neuroectoderm. Subsequent expression is in partially overlapping patterns that correlate with the segregation of the neuroblasts. (Cabrera et al., 1987) The patterns of expression of ac, sc and l(1)sc are complex and evolve rapidly, affecting most if not all the known neurogenic regions. Gene expression precedes and is concomitant with the histological appearance of precursors of neural cells. The achaete-scute complex plays a role in determination and early differentiation of embryonic neural cells. (Romani et al., 1987) Deficiencies for most regions of the achaete-scute complex are hemizygous and homozygous viable; however, deficiency for l(1)sc is lethal. (Garcia-Bellido, 1979) Inferred from the inviability of In(1)sc4Lsc9R <up>left break of In(1)sc9 in doubt</up>, except in the presence of Dp(1;2)sc19. No mutant recovered (Garcia-Bellido, 1979).   Deficiency from which existence of l(1)sc inferred, i.e., In(1)sc4Lsc9R, embryonic lethal. Volume of embryonic ventral nerve cord slightly reduced; posterior commissures thinner than in wild type; longitudinal connectives virtually lacking. Concomitant deletions for scα or scα and ac cause more severe CNS disruptions, although by themselves these deletions have no observable CNS effects; simultaneous deletion of the scγ region also enchances the CNS disruptions (Jimenez and Campos-Ortega, 1987). Transiently expressed at periphery of syncytial blastoderm; late blastoderm shows paired dorsolateral and ventrolateral longitudinal stripes of expression, the latter being coincident with the presumptive neurogenic ectoderm. During germ-band expression, l(1)sc expression seen in many cell clusters over most of the ectoderm; segmental distribution becomes apparent both internally and externally. l(1)sc expression seen in many foci in the head region and in the posterior midgut rudiment (Romani, Campuzano and Modolell, 1987; Cabrera, Martinez-Arias and Bate, 1987). Little if any expression in later stages, except in the central nervous system (Romani, Campuzano, Macagno and Modolell, 1989).
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057275 RefSeq (Proteins) • NP_476623 DDBJ / EMBL / GenBank • AAF45500 AAM52020 AL024453 AY121693 BI372386 CAA19656 CAA31065 CAA50680 X12549 X71806 Entrez Gene - A searchable database of RefSeq genes. • 30983 UniProtKB/Swiss-Prot • P09774
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Myc-type, basic helix-loop-helix (bHLH) domain (IPR011598) Achaete-scute transcription factor-related (IPR015660) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE59335
Linkouts
	BioGRID - A database of protein and genetic interactions • 57556 DroID - A comprehensive database of gene and protein interactions. • FBgn0002561 DRSC - Results from RNAi screens. • FBgn0002561 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002561 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG3839-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0002561 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 30983 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /neural/lethlscu.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 30983 modMine - Data generated by the modENCODE project. • FBgn0002561 REDfly - A database of transcriptional regulatory elements. • FBgn0002561
Synonyms & Secondary IDs ( 26 )
Reported As
Symbol Synonym	ASC-T3 (Roark et al., 1995) AS-C T3 (Abmayr et al., 1992, Wainwright and Ish-Horowicz, 1992, Vaessin et al., 1990, Murre et al., 1989) ascT3 (Johnson et al., 1990) AS-T3 (Nakachi et al., 1997) bHLHc28 (Stevens et al., 2008) CG3839 (Benos, 2000.12.13, Stevens et al., 2008, Stevens et al., 2008, Perkins et al., 2009.3.31, Keleman et al., 2009.8.5) EG:198A6.2 (Benos et al., 2001, Benos, 2000.12.13, ) L'Sc (Schnorrer and Dickson, 2004, Avedisov et al., 2001, Dworak and Sink, 2002, Wang et al., 2007) L'sc (Furlong, 2004, Buescher et al., 2002, Castanon et al., 2001, Caudy and Nakao, 2000, Bossing and Brand, 2006, Bolinger and Boekhoff-Falk, 2005, Boukhatmi et al., 2012, Wang et al., 2011) l'sc (Tien et al., 2005, Urbach and Technau, 2004, Bauer-DuMont et al., 2004, Belyaeva et al., 2003, Urbach and Technau, 2003, Zhimulev et al., 2003, Golovnin et al., 2003, Skeath and Thor, 2003, Overton et al., 2002, Skaer et al., 2002, Cripps and Olson, 2002, Carmena et al., 2002, Takano-Shimizu, 2001, Tapanes and Baylies, 2001, Ghazi and VijayRaghavan, 2000, Taylor, 2000, Sanchez Soriano and Russell, 2000, Stollewerk, 2000, Morgenstern and Atchley, 1999, Long et al., 2000, Wulbeck and Simpson, 2000, Huang et al., 2000, Zaffran and Frasch, 2000, Modolell, 1993.5.5, Takano-Shimizu, 1999, Skeath, 1999, Frasch, 1999, Apidianakis et al., 1999, Jazwinska et al., 1999, Wilson, 1999, Jennings et al., 1999, Crozatier and Vincent, 1999, Paululat et al., 1999, Chu et al., 1998, Carmena et al., 1998, Rottgen et al., 1997, Hoch and Jackle, 1998, Skeath, 1998, Jagla et al., 1998, Dumstrei et al., 1998, Takano, 1998, Lai and Posakony, 1998, Baylies et al., 1998, Buff et al., 1998, Campos-Ortega, 1998, Ruiz-Gomez, 1998, Modolell and Campuzano, 1998, Dambly-Chaudiere and Vervoort, 1998, Baylies et al., 1997, Rottgen et al., 1998, Nose et al., 1998, Carmena et al., 1998, Rudolph et al., 1997, Hartenstein, 1997, Klein and Campos-Ortega, 1997, Younossi-Hartenstein et al., 1997, Parras et al., 1996, Skeath and Doe, 1996, D'Alessio and Frasch, 1996, Biehs et al., 1996, Taylor, 1996, Gigliani et al., 1996, Younossi-Hartenstein et al., 1996, Hassan and Vassin, 1996, Michelson et al., 1996, Hartenstein et al., 1996, Carmena et al., 1995, Gomez-Skarmeta et al., 1995, Skeath et al., 1995, Wilkins, 1995, Jan and Jan, 1994, Brand et al., 1991, Kunisch et al., 1994, Ohsako et al., 1994, Francois et al., 1994, Tepass and Hartenstein, 1995, Skeath et al., 1994, Ray and Rodrigues, 1994, Jan and Jan, 1994, Martin-Bermudo et al., 1993, Abmayr et al., 1992, Skeath et al., 1992, Campuzano and Modolell, 1992, Campos-Ortega and Haenlin, 1992, Woods and Bryant, 1992, Merriam et al., 1991, Martin-Bermudo et al., 1991, Garrell and Campuzano, 1991, Hardy, 1990, Garrell and Modolell, 1990, Campuzano et al., 1985, Schlatter and Maier, 2005, Mari-Beffa et al., 1991, Zhao et al., 2007, Kaspar et al., 2008, Kunert et al., 2009, Schaaf et al., 2009, Lee et al., 1999, Cave et al., 2011, Grigorian et al., 2011, Egger et al., 2010, Kunz et al., 2012) l(1)1Ba   l(1)sc (Ko et al., 2006, Wheeler et al., 2006, Stark et al., 2005, Sun et al., 2012, Zhang et al., 2008, Yasugi et al., 2008, Brodsky et al., 2004, Kawamori et al., 2011, Duan et al., 2007, Takeuchi et al., 2007, Stagg et al., 2011, Gim et al., 2001, Ayyar et al., 2010, Watson et al., 2011, Kazemian et al., 2010, Yasugi et al., 2010, Venken et al., 2010, Busser et al., 2012) L(1)sc (Yasugi et al., 2008, Reddy et al., 2010) l1sc (Neumüller et al., 2011) lsc (Bush et al., 1996, Cabrera et al., 1994) l-sc   sc/T3   T3 (Cowden and Levine, 2002, Hemavathy et al., 1997, Hemavathy et al., 1997, Moffat et al., 1995, Shoop and Parkhurst, 1995, Ohsako et al., 1994, Francois et al., 1994, Gonzalez-Crespo and Levine, 1993, Parkhurst et al., 1993, Erickson and Cline, 1991, van Doren et al., 1991, Campos-Ortega and Knust, 1990, Campos-Ortega and Knust, 1990, Alonso and Cabrera, 1988, Campuzano et al., 1985, Mari-Beffa et al., 1991)
Name Synonym	achaete-scute proneural gene (Rebeiz et al., 2012) Lethal(1)scute (Reddy et al., 2010) lethal at scute (Lindsley and Zimm, 1992) Lethal of Scute (Carmena and Baylies, 2002, Carmena and Baylies, 2001, Bolinger and Boekhoff-Falk, 2005, Wang et al., 2007) lethal of scute (Wheeler et al., 2006, Schlatter and Maier, 2005, Zhang et al., 2008, Kawamori et al., 2011, Duan et al., 2007, Bardin et al., 2010, Lee et al., 1999, Watson et al., 2011) lethal of Scute (Bossing and Brand, 2006) Lethal of scute (Yasugi et al., 2008) Lethal-scute (Gim et al., 2001)
Secondary FlyBase IDs
References ( 273 )
Generate a list of	All references relating to this gene ( 273 )
List References by type	Research paper  ( 164 ) Supplementary material  ( 5 ) Review  ( 59 ) Personal communication to FlyBase  ( 5 ) Abstract  ( 28 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 3 ) Letter  ( 1 ) Book  ( 1 ) Curated genome annotation  ( 3 ) Protein sequence record  ( 1 ) Website  ( 1 )
Recent research papers ( 12 )
	Boukhatmi et al., 2012, Development 139(19): 3572--3582 Tup/Islet1 integrates time and position to specify muscle identity in Drosophila. [FBrf0219376] Busser et al., 2012, PLoS Genet. 8(3): e1002531 A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. [FBrf0217716] Kunz et al., 2012, Development 139(14): 2510--2522 Origin of Drosophila mushroom body neuroblasts and generation of divergent embryonic lineages. [FBrf0218649] Rebeiz et al., 2012, Dev. Biol. 362(2): 282--294 Ancestral and conserved cis-regulatory architectures in developmental control genes. [FBrf0217764] Sun et al., 2012, PLoS Genet. 8(2): e1002515 Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants. [FBrf0217508] Cave et al., 2011, Mol. Cell. Biol. 31(1): 22--29 Differential Regulation of Transcription through Distinct Suppressor of Hairless DNA Binding Site Architectures during Notch Signaling in Proneural Clusters. [FBrf0212524] Grigorian et al., 2011, Dev. Biol. 353(1): 105--118 The convergence of Notch and MAPK signaling specifies the blood progenitor fate in the Drosophila mesoderm. [FBrf0213410] Kawamori et al., 2011, Dev. Growth Differ. 53(5): 653--667 Fat / Hippo pathway regulates the progress of neural differentiation signaling in the Drosophila optic lobe. [FBrf0213932] 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] Stagg et al., 2011, Development 138(11): 2171--2183 Dual role for Drosophila lethal of scute in CNS midline precursor formation and dopaminergic neuron and motoneuron cell fate. [FBrf0213671] Wang et al., 2011, Dev. Biol. 350(2): 414--428 Notch signaling regulates neuroepithelial stem cell maintenance and neuroblast formation in Drosophila optic lobe development. [FBrf0212909] Watson et al., 2011, Development 138(7): 1285--1295 Drosophila hedgehog signaling and engrailed-runt mutual repression direct midline glia to alternative ensheathing and non-ensheathing fates. [FBrf0213237] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...