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Gene Dmel\ci

General Information
Symbol	Dmel\ci	Species	D. melanogaster
Name	cubitus interruptus	Annotation symbol	CG2125
Feature type	protein_coding_gene	FlyBase ID	FBgn0004859
Gene Model Status	Current	Stock availability	127 publicly available
Also Known As	CID, ciD, l(4)17, l(4)13, Gli, ci155, ci-D, Ce, Ci/GLI
Genomic Location
Chromosome (arm)	4	Recombination map	4-0.0
Cytogenetic map	102A1-102A3	Sequence location	4:68,336..77,667 [-]
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 cubitus interruptus is referred to in FlyBase by the symbol Dmel\ci (CG2125, FBgn0004859). 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; protein binding; transcription regulatory region DNA binding; RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription. There is experimental evidence for 17 unique biological process terms, many of which group under: single-organism developmental process; system development; biological regulation; multicellular organismal development; regionalization; neuron differentiation; cellular component organization or biogenesis; positive regulation of biological process; sensory organ development; open tracheal system development; cellular process; multicellular organism reproduction. 197 alleles are reported. The phenotypes of these alleles are annotated with: organ system; organ system subdivision; adult segment; thoracic segment; external compound sense organ; imaginal precursor; integumentary specialisation; portion of tissue; peripheral nervous system; dorsal branch primordium; keyhole structure; larval abdominal segment; larval head segment; spiracle. It has 3 annotated transcripts and 3 annotated polypeptides. Protein features are: Zinc finger C2H2-type/integrase DNA-binding domain; Zinc finger, C2H2; Zinc finger, C2H2-like. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed within 00-12 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: larval trachea. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, larval central nervous system, adult crop, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, adult spermathecae, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1623144_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of ci. Gene sequence location is 4:68336..77667.
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	Ce: Cell Ocelli reduced or absent; ocellar and scutellar bristles absent; interocellar microchaetae disrupted but frontals normal; postverticals short, thick, often with an adventitious pair between the normally placed postvertical bristles. Wing veins L3 and L4 converge, giving wing phenotype much like fu although wing phenotype variable. Homozygous lethal; lethality occurs during embryonic period (Hochman). Shown to be a segment polarity gene; homozygous embryos exhibit loss of the naked cuticle in the posterior half of each segment plus the anterior margin of the adjacent segment; most dorsal pattern elements also eliminated, leaving a lawn of fine hairs. Engrailed-antibody staining fails to detect a subset of CNS neurons in Ce homozygotes that are normally stained in wild-type embryos (Patel, Schafer, Goodman, and Holmgren, 1989, Genes Dev. 3: 890-904). No maternal requirement of Ce+ for either oogenesis or embryonic phenotype (Orenic, Chidsey, and Holmgrern, 1987, Dev. Biol. 124: 50-56). Lethal phenotype of Ce not complemented by l(4)17 or by induced revertants of the wing phenotype of ciD (Orenic et al.); pupal lethal in combination with ciD [Hochman, 1976, The Genetics and Biology of Drosophila (Ashburner and Novitski, eds.). Academic Press, London, New York, San Francisco, Vol. 1b, pp. 902-28]. RK3. ci: cubitus interruptus ci: cubitus interruptus Wings showing from no interruption (extreme left) to complete absence (extreme right) of the cubital vein. From Stern and Kodani, 1955, Genetics 40: 343-73. Vein L4 shows one or more gaps both distal and proximal to posterior crossvein, generally nonterminal. Anterior crossvein shortened or absent. Other gaps and scattered branch veins in region of crossveins. At 19, nearly all flies have a mutant phenotype; at 25, there is slight overlap with wild type; at 30, virtually all flies are wild type. Dosage effect such that ci/0 haplo-4's are more extreme than ci/ci diplo-4's, which are more extreme than ci/ci/ci triplo-4's. Suppressed by su(Hw)2 (Kotarski). For interactions of ci with en, H, ve, and cg, see House (1953, Genetics 38: 199-214, 309-27; 1955, Anat. Record 122: 471; 1959, Genetics, 44: 516; 1961, Genetics, 46: 871). Expression of ci sensitive to genetic background; selection possible for more and less extreme phenotypes (House and Yeatts, 1962, Genetics 47: 960); contribution of chromosome 2 more important than that of 3 (House and Pernaveau, 1971, Genetics 68: s29). Phenotypic effect visible in prepupa by absence of the longer longitudinal vein. RK1 at 19 and higher rank with higher temperatures. *ci+2: cubitus interruptus-wild-type isoallele Homozygote wild type at 14 and 26. ci+2/Df(4)M wild type at 26; shows some thinning and interruption of L4 at 14. ci+2/ci wild type at 26; at 14, fewer flies show thinning or interruption of L4 than ci+C/ci. ci+2/ciW shows significantly greater amount of thinning and interruption of L4 than ci+C/ciW. RK3. ciD: cubitus interruptus-Dominant Wings show interruptions of L4 in two places: proximal to and distal to anterior crossvein. L5 also shows distal interruption. L3 and L5 thick. Considerable plexus effect and knotting of veins. Wings broader, warped or concave upward, regularly extended, and bent backward. Alula fused with and in same plane as blade of wing. Black dried haemolymph from axillary spiracle. Slight scalloping of inner wing margin, with hairs and tufts. Direction and extent of temperature effects depends on genetic background (Scharloo). In general, no overlapping of wild type. Inviable in combination with Ax/Ax or Ax/Y (House and Lutes, 1975, Genetics 80: 542-43). H/+ inhibits scalloping of ciD but greatly enhances L4 interruption (House, 1959, Genetics 44: 516). Fully dominant in triplo-4's (Sturtevant, 1936, Genetics 21: 448). Two doses of ciD reduce survival of triplo-4 flies (Parker, 1969, Mutat. Res. 7: 393-407). Homozygotes lethal in embryo (Hochman, 1971, Genetics 67: 235-52). Embryonic segment polarity disrupted; anterior portions of segments with their denticle belts duplicated in mirror-image fashion; posterior portions missing; each segment almost entirely covered with denticles (Nusslein-Volhard and Wieschaus, 1980, Nature 287: 795-801). Fine hairs eliminated from dorsal abdominal segments; replaced with clear cuticle and socketed denticles (Orenic, Chidsey, and Holmgren, 1987, Dev. Biol. 124: 50-56). Embryonic CNS relatively normal (Patel, Schafer, Goodman, and Holmgren, 1989, Genes Dev. 3: 890-904). Genotype of oocyte with respect to ciD without effect on phenotype of progeny (Orenic et al.). ciD/l(4)102ABc dies as embryo, ciD/l(4)102ABb as embryo or larva; in ciD/Ce2 death usually delayed until pupal stage (Hochman, 1971). Survival of ci/ciD/Df(4)M101-63a argues for nonallelism or pseudoallelism of ci and ciD (Hochman, 1971). RK1. ciW: cubitus interruptus of Wallace Homozygote is extreme ci type. Wings sometimes almost twice normal width, arclike, and virtually lack veins. Often present is a well-organized pattern of venation in which the posterior crossvein flows smoothly into L5. Legs lumpy, sex combs larger than normal, antennae enlarged, eyes smaller, and extra bristles present. Heterozygote shows gap in L4 in 80% of flies. ciW enhanced by H, en, and Cy (House, 1953, Genetics 38: 669-70; 1959, Genetics 44: 516) and by Tp(4;Y) (Benner, 1972, Genetics 71: s4). Temperature effect described by House (1955, Genetics 40: 576). RK2.
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	Alleles ci[S849A.Scer\UAS] Transgenic Constructs P{UAS-ci.S849A}
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 102A1-102A3   Limits computationally determined from genome sequence between P{SUPor-P}KG01127&PBac{5HPw+}A173 and PBac{5HPw+}A437
Experimentally Determined Cytological Location
Cytogenetic map Notes References 101F2-102A5     (Schwartz, 1995.2.21) 101F-101F   (determined by in situ hybridisation)   (Eaton and Kornberg, 1990) 101F-101F   (determined by in situ hybridisation)   (Orenic et al., 1990) 102A3-102A3     (Tearle and Nusslein-Volhard, 1987)
Experimentally Determined Recombination Data
Location	4-0 (Tearle and Nusslein-Volhard, 1987, Mickey, 1952) 4- (Green, 1952) 4-0.0
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\ci 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 5.39 Low-frequency RNA-Seq exon junction(s) not annotated. Gene model reviewed during 5.46
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) ci-RA FBtr0089178  NM_079878   4941   1397 ci-RB FBtr0306168  NM_001258473   5191   1279 ci-RC FBtr0308074  NM_001258472   4874   572
Additional Transcript Data & Comments
Reported size (kB)	4.6 (northern blot) (Orenic et al., 1990)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein ci-PA   FBpp0088245   153.3   1397   7.21     NP_524617   AAF59373 ci-PB   FBpp0297298   140.6   1279   7.24     NP_001245402   AFH06762 ci-PC   FBpp0300417   61.8   572   7.85     NP_001245401   AFH06761
Additional Polypeptide Data & Comments
Reported size (kDa)	1282 (aa) (Orenic et al., 1990) 155 (kD) (Aza-Blanc et al., 1997)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, C2H2 (IPR007087) Zinc finger C2H2-type/integrase DNA-binding domain (IPR013087) Zinc finger, C2H2-like (IPR015880)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA264101   AA694817   AA699063   AE014135 AAF59373   AC010915   AC011250   AF242878   AF433680 AAM17953   AE014135 AFH06761   AE014135 AFH06762   AY231874   AY573706 AAS87249   BG637900   BI352516   BI352634   BI354809   BI368610   BP545426   BP545427   BP550455   BP550456   BT024198   BT100227   BT133159   BZ286250   CK131277   CO176910   CO178708   CO182831   CO184355   CO186051   CO188511   CO189398   CO190525   CO190695   CO190986   CO264191   CO265137   CO266576   CO267025   CO271181   CO274211   CO276521   CO277021   CO278143   CO280258   CO281036   CO284876   CO286215   CO286792   CO291839   CO295760   CO296667   CO301626   CO302219   CO302783   CO307592   CO308139   CO317923   CO322378   CO325415   CO328076   CO330585   CO332586   CO341038   CO341392   CO341432   CO344489   CO344532   CO345292   DN154337   EC057331   EC062542   EC064628   EC069543   EC069979   EC072054   EC074297   EC075028   EC075660   EC075744   EC080189   EC083815   EC084041   EC089069   EC195290   EC197727   EC198988   EC200560   EC200960   EC206238   EC209747   EC209863   EC210162   EC212318   EC213364   EC214521   EC218348   EC218349   EC220514   EC221398   EC221816   EC224675   EC226130   EC230006   EC232079   EC238050   EC244698   EC244907   EC245215   EC247442   EC250802   EC252184   EC252597   EC252701   EC255393   EC255913   EC257474   EC257510   EC258274   U21389   U21390 AAG15271   U66884 AAC47752   X54360 CAA38244
UniProtKB/Swiss-Prot	P19538
UniProtKB/TrEMBL	H9XVL6 H9XVL7 Q6J8P4
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 FBsf0000160578 4:80,673..80,681 bound_moiety=en-XP evidence=experimental (Bergman et al., 2005, Schwartz et al., 1995) protein binding site FBsf0000160579 4:80,105..80,117 bound_moiety=en-XP evidence=experimental (Schwartz et al., 1995, Bergman et al., 2005) regulatory region FBsf0000435096 4:76,479..83,352 evidence=Reporter construct (in vivo) (Schwartz et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000435193 4:79,474..80,720 evidence=Reporter construct (in vivo) (Schwartz et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000435680 4:76,480..77,667 evidence=Reporter construct (in vivo) (Schwartz et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000435872 4:79,474..81,706 evidence=Reporter construct (in vivo) (Schwartz et al., 1995, Halfon, 2012.6.19) regulatory region FBsf0000436467 4:79,474..80,871 evidence=Reporter construct (in vivo) (Schwartz et al., 1995, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ectoderm   (Orenic et al., 1990) presumptive embryonic/larval central nervous system   (Eaton and Kornberg, 1990) embryonic/larval foregut   (Orenic et al., 1990) embryonic stage 5   organism | ubiquitous   (Orenic et al., 1990) larval stage   imaginal disc | anterior   (Eaton and Kornberg, 1990) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   mesectoderm   (Eaton and Kornberg, 1990) organism | segment polarity expression pattern   (Eaton and Kornberg, 1990) embryonic/larval hindgut   (Orenic et al., 1990) mesoderm   (Orenic et al., 1990) embryonic stage 4 -- 6   central brain anlage in statu nascendi   (Fisher et al., 2012) dorsal ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi organism | ubiquitous   (Fisher et al., 2012) 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 5     (Schwartz et al., 1995) Comment:expressed in three broad stripes gastrula stage     (Orenic et al., 1990) embryonic stage 7   segment   (Schweizer and Basler, 1998) 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 dorsal ectoderm   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) extended germ band stage   ectoderm | striped   (Orenic et al., 1990) 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 dorsal ectoderm   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) Comment:reported as dorsal epidermis anlage organism | segmentally repeated   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) embryonic stage 10 -- 11   ventral midline   (Schwartz et al., 1995) embryonic stage 11 -- 12   dorsal epidermis primordium   (Fisher et al., 2012) dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium organism | segmentally repeated   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic dorsal epidermis   (Fisher et al., 2012) embryonic head epidermis   (Fisher et al., 2012) embryonic optic lobe   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) organism | segmentally repeated   (Fisher et al., 2012) third instar larval stage   wing disc | anterior compartment   (Chanas et al., 2004)
Additional Descriptive Data
	Expression of ci in the wing disc does not overlaps that of en. (Chanas et al., 2004) The ci transcript is expressed in the anterior compartment of each segment during embryogenesis. (Schweizer and Basler, 1998) In wghs.PN embryos, after heat shock, ci transcripts become restricted to those cells that are outside the expanded en domain and coincide with the ptc stripe. This is a similar expression pattern to that found in nkd mutant embryos. (Noordermeer et al., 1992) ci is expressed ubiquitously in early embryos. Expression later resolves into 15 stripes encompassing the anterior compartment of each segment. ci is also expressed in the anterior compartments of imaginal discs. In engrailed mutants, ci expression is derepressed in the posterior compartments, suggesting that ci expression is normally repressed by en in these cells. (Eaton and Kornberg, 1990) ci is uniformly expressed throughout the cellular blastoderm and at gastrulation. At germband extension, expression resolves into 15 broad stripes that encompass the anterior 3/4 of each segment. ci transcripts are also found in the hindgut and foregut. Expression peaks at 5-8hrs of embryonic development. (Orenic et al., 1990)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 8   organism | ubiquitous   (Chanas et al., 2004) embryonic stage 11   organism | segmentally repeated   (Chanas et al., 2004) larval stage   wing disc | anterior compartment   (Bajpai et al., 2004) third instar larval stage   male genital disc | restricted   (Freeland and Kuhn, 1996) female genital disc | restricted   (Freeland and Kuhn, 1996) morphogenetic furrow   (Fu and Baker, 2003) wing disc | anterior compartment   (Strutt et al., 2004) wing disc | anterior compartment & anterior/posterior compartment boundary   • cytoplasm (Aza-Blanc et al., 1997) Comment:expression is anterior to the compartment boundary wandering third instar larval stage   wing disc | anterior compartment   (Bornemann et al., 2004) wing disc | anterior/posterior compartment boundary   (Bornemann et al., 2004) mass spectroscopy Stage Tissue/Position (including subcellular localization) Reference day 5 of adulthood & male -- day 7 of adulthood & male   spermatozoon   (Wasbrough et al., 2010)
Additional Descriptive Data
	The full length ci protein is detected primarily near the anterior/posterior compartment boundary in the anterior compartment, with lower levels detected elsewhere as determined by an antibody that is specific for the full length protein. Cellular fractionation indicates that full length ci protein is cytoplasmic. (Aza-Blanc et al., 1997) The segmentally repeated expression of ci protein does not overlap the expression of en protein. (Chanas et al., 2004) ci protein is localized to the anterior compartment of the wing disc. (Bajpai et al., 2004) Immunoreactivity to ci protein detected throughout the anterior compartment of the wing disc, and is most pronounced along the anterior/posterior compartment boundary (Bornemann et al., 2004)
Marker for
	anterior compartment &&of dorsal mesothoracic disc dorsal mesothoracic disc | anterior compartment
Subcellular Localization (GO Cellular Component)
CV term Evidence References
cytoplasm inferred from direct assay (Wang and Holmgren, 2000, Croker et al., 2006, Forbes et al., 1996, Wang et al., 2000) Hedgehog signaling complex inferred from physical interaction with cos AND inferred from physical interaction with fu (Stegman et al., 2000) membrane inferred from direct assay (Stegman et al., 2004) nucleus inferred from direct assay (Wang and Holmgren, 2000, Croker et al., 2006, Wang et al., 2000, Usha and Shashidhara, 2010) protein complex inferred from physical interaction with Su(fu) (Monnier et al., 1998)
Expression Deduced from Reporters
Reporter: P{1.2prx-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) organism | segmentally repeated   (Schwartz et al., 1995) Reporter: P{1.3dis+1.2prx-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc   (Schwartz et al., 1995) Reporter: P{1.4dis+1.2prx-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc | anterior compartment   (Schwartz et al., 1995) Reporter: P{1.6dis-ci57g+HS} Stage Tissue/Position (including subcellular localization) Reference extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc   (Schwartz et al., 1995) Reporter: P{2.2dis+1.2prx-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc | anterior compartment   (Schwartz et al., 1995) Reporter: P{2.2dis-ci+HS} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc | anterior compartment   (Schwartz et al., 1995) Reporter: P{3.7dis+1.2prx-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) larval stage   imaginal disc | anterior compartment   (Schwartz et al., 1995) Reporter: P{7.1-ci} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ventral midline   (Schwartz et al., 1995) embryonic stage 5     (Schwartz et al., 1995) Comment:expressed in two broad stripes extended germ band stage   organism | segmentally repeated   (Schwartz et al., 1995) embryonic stage 10 -- 11   ventral midline   (Schwartz et al., 1995) larval stage   imaginal disc | anterior compartment   (Schwartz et al., 1995) Reporter: P{lacW}ciDplac Stage Tissue/Position (including subcellular localization) Reference embryonic stage   organism | segment polarity expression pattern   (Eaton and Kornberg, 1990) larval stage   wing disc | anterior compartment   (Blair, 1992) imaginal disc | posterior   (Eaton and Kornberg, 1990) pupal stage   wing | anterior compartment   (Blair, 1992)
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: larval trachea. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, larval central nervous system, adult crop, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, adult spermathecae, larval/adult 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) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea  (685.825) Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea  685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    455.175 Larval Midgut    23.1 Larval Hindgut    150.3 Larval Malpighian Tubules    241.7 Larval Fat Body    301.2 Larval Salivary Gland    92.7 Larval Trachea    685.825 Larval Carcass    351.85 Adult Head    147.3 Adult Eye    83.175 Adult Brain    82.5 Adult Thoracic-Abdominal Ganglion    80.8 Adult Crop    137.7 Adult Midgut    11.6 Adult Hindgut    168.4 Adult Malpighian Tubules    329.7 Adult Fat Body    191.5 Adult Salivary Gland    96.3 Adult Heart    107.7 Adult VirginFemale Spermatheca    264.8 Adult InseminatedFemale Spermatheca    251.2 Adult Ovary    46 Adult Testis    23.1 Adult Male Accessory Gland    29.5 Adult Carcass    132.3 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    147.3   NA  Eye    83.175   NA  Brain    82.5   455.175  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    80.8   NA  Crop    137.7   23.1  Midgut    11.6   150.3  Hindgut    168.4   241.7  Malpighian Tubules    329.7   301.2  Fat Body    191.5   92.7  Salivary Gland    96.3   NA  Heart    107.7   685.825  Trachea    NA   NA  VirginFemale Spermatheca    264.8   NA  InseminatedFemale Spermatheca    251.2   NA  Ovary    46   NA  Testis    23.1   NA  Male Accessory Gland    29.5   351.85  Carcass    132.3 FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (53) central nervous system, larvae L3  (28) central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering  (39) carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 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    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (53) central nervous system, larvae L3  28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering  (39) carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 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    53 central nervous system, larvae L3    28 central nervous system, pupae P8    10 head, virgin 1-day female    12 head, virgin 4-day female    11 head, virgin 20-day female    5 head, mated 1-day female    8 head, mated 4-day female    7 head, mated 20-day female    6 head, mated 1-day male    11 head, mated 4-day male    11 head, mated 20-day male    11 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    11 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    2 digestive system, 4-day adult    3 digestive system, 20-day adult    1 fat body, larvae L3 wandering    10 fat body, white prepupae    14 fat body, pupae P8    7 carcass, larvae L3 wandering    39 carcass, 1-day adult    9 carcass, 4-day adult    7 carcass, 20-day adult    5 ovary, virgin 4-day female    2 ovary, mated 4-day female    3 testis, mated 4-day male    1 accessory gland, mated 4-day male    3 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 high expression to a trough of low expression. Peak expression observed within 00-12 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    2 embryo 02-04hr    36 embryo 04-06hr    106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr  (36) embryo 04-06hr  (106) embryo 06-08hr  (63) embryo 08-10hr  (53) embryo 10-12hr  (32) embryo 12-14hr  (42) embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9  (27) white prepupae new  (28) white prepupae 12hr  (33) white prepupae 24hr  (49) pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    36 embryo 04-06hr  106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 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    2 embryo 02-04hr    36 embryo 04-06hr    106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    36 embryo 04-06hr    106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr  (36) embryo 04-06hr  (106) embryo 06-08hr  (63) embryo 08-10hr  (53) embryo 10-12hr  32 embryo 12-14hr  (42) embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9  27 white prepupae new  28 white prepupae 12hr  (33) white prepupae 24hr  (49) pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    2 embryo 02-04hr    36 embryo 04-06hr  106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 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    2 embryo 02-04hr    36 embryo 04-06hr    106 embryo 06-08hr    63 embryo 08-10hr    53 embryo 10-12hr    32 embryo 12-14hr    42 embryo 14-16hr    10 embryo 16-18hr    15 embryo 18-20hr    10 embryo 20-22hr    6 embryo 22-24hr    11 larva L1    7 larva L2    5 larva L3 12hr old    6 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    16 larva L3 puffstage 7-9    27 white prepupae new    28 white prepupae 12hr    33 white prepupae 24hr    49 pupae 2d postWPP    16 pupae 3d postWPP    8 pupae 4d postWPP    3 adult male 01day    5 adult male 05day    3 adult male 30day    2 adult female 01day    3 adult female 05day    2 adult female 30day    2 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+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8    205 wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    16 embryonic 1182-4H  (46) embryonic GM2    9 embryonic Kc167  26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2  (84) wing disc ML-DmD8  (205) wing disc ML-DmD9  (34) wing disc ML-DmD16-c3  (89) wing disc ML-DmD21  (48) wing disc ML-DmD32  (43) haltere disc ML-DmD17-c3  (72) eye-antennal disc ML-DmD11  (32) antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1  (49) CNS ML-DmBG1-c1  (34) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS  (68) ovary OSC  (68) ovary OSS  (48) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8  (205) wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 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+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8    205 wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8    205 wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    16 embryonic 1182-4H  (46) embryonic GM2    9 embryonic Kc167  26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2  (84) wing disc ML-DmD8  (205) wing disc ML-DmD9  (34) wing disc ML-DmD16-c3  (89) wing disc ML-DmD21  (48) wing disc ML-DmD32  (43) haltere disc ML-DmD17-c3  (72) eye-antennal disc ML-DmD11  32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1  (49) CNS ML-DmBG1-c1  (34) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS  (68) ovary OSC  (68) ovary OSS  (48) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8  (205) wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 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+    0 Schneider line 2 Sg4    16 embryonic 1182-4H    46 embryonic GM2    9 embryonic Kc167    26 embryonic S1    0 embryonic S3    10 leg disc CME L1    17 wing disc CME-W2    84 wing disc ML-DmD8    205 wing disc ML-DmD9    34 wing disc ML-DmD16-c3    89 wing disc ML-DmD21    48 wing disc ML-DmD32    43 haltere disc ML-DmD17-c3    72 eye-antennal disc ML-DmD11    32 antennal disc ML-DmD20-c5    21 mixed discs ML-DmD4-c1    49 CNS ML-DmBG1-c1    34 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    1 ovary fGS/OSS    68 ovary OSC    68 ovary OSS    48 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3  (28) Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3  28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 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    2 cold shock, 4-day adult    1 heat shock, 4-day adult    6 Cadmium 50 mM 6 hrs, larvae L3    10 Cadmium 50 mM 12 hrs, larvae L3    28 Cadmium 50 mM 48 hrs, 4-day adult    8 Cadmium 100 mM 48 hrs, 4-day adult    4 Copper 0.5 mM 12 hrs, larvae L3    3 Copper 15 mM 48 hrs, 4-day adult    11 Zinc 5 mM 12 hrs, larvae L3    4 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    2 Ethanol 5% 3 hrs, larvae L3    15 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    19 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    5 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    6 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    13 Rotenone 8 μg 12 hrs, larvae L3    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_11 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • PC00395 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004859 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2125-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for ci 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, with Scer\GAL430A ciScer\UAS.cAa lethal, with Scer\GAL4en-e16E ci76.Scer\UAS lethal, with Scer\GAL4prd.RG1 cim1-3.Scer\UAS.T:Ivir\HA1 lethal, with Scer\GAL4ptc-559.1 ci76.Scer\UAS lethal | embryonic stage ciD lethal | embryonic stage, with Scer\GAL4en-e16E ciScer\UAS.cAa lethal | embryonic stage | partially, with Scer\GAL4e22c ci3m.Scer\UAS.T:Ivir\HA1 ci3m.Scer\UAS ci5m.Scer\UAS.T:Hsap\TBP ci5m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS lethal | embryonic stage | partially, with Scer\GAL4en-e16E ci3m.Scer\UAS ci5m.Scer\UAS.T:Hsap\TBP ci5m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS lethal | embryonic stage | partially, with Scer\GAL4ptc-559.1 ci3m.Scer\UAS.T:Ivir\HA1 ci3m.Scer\UAS ci5m.Scer\UAS.T:Hsap\TBP ci5m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS lethal | embryonic stage | recessive ci94 ci183 ci217 ci228 ciCe-2 ciCe-3 ciCe-r1 ciD ciDplac lethal | partially, with Scer\GAL471B ci3m.Scer\UAS.T:Ivir\HA1 ci3m.Scer\UAS ci5m.Scer\UAS.T:Hsap\TBP ci5m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS ciScer\UAS.cPa ciWT.Scer\UAS.T:Hsap\TBP lethal | partially, with Scer\GAL4prd.RG1 cim1-4.Scer\UAS.T:Ivir\HA1 lethal | pupal stage (with ci94) cin lethal | pupal stage (with ciD) cin lethal | pupal stage (with cin) ci94 ciD lethal | recessive ciCe-2 ciCe-r1 ciCe-r2 ciD+rev3A-32A ciD+rev9A-101A ciD ciD-l ciDRP ciDrv viable cin viable, with Scer\GAL471B ci7m.Scer\UAS.T:Hsap\TBP ci7m.Scer\UAS.T:Ivir\HA1 ci7m.Scer\UAS viable, with Scer\GAL4e22c ci7m.Scer\UAS.T:Hsap\TBP ci7m.Scer\UAS.T:Ivir\HA1 ci7m.Scer\UAS ciWT.P.Scer\UAS.T:Ivir\HA1 ciWT.Scer\UAS.T:Hsap\TBP viable, with Scer\GAL4en-e16E ci7m.Scer\UAS.T:Hsap\TBP ci7m.Scer\UAS.T:Ivir\HA1 ci7m.Scer\UAS viable, with Scer\GAL4prd.RG1 cim1-3*103.Scer\UAS.T:Ivir\HA1 cim1-3*459.Scer\UAS.T:Ivir\HA1 ciwt.Scer\UAS.T:Ivir\HA1 viable, with Scer\GAL4ptc-559.1 ci7m.Scer\UAS.T:Hsap\TBP ci7m.Scer\UAS.T:Ivir\HA1 ci7m.Scer\UAS ciWT.Scer\UAS.T:Hsap\TBP viable | partially, with Scer\GAL471B ciWT.P.Scer\UAS.T:Ivir\HA1 viable | partially, with Scer\GAL4e22c ciScer\UAS.cPa viable | partially, with Scer\GAL4en-e16E ci3m.Scer\UAS.T:Ivir\HA1 ciScer\UAS.cPa ciWT.P.Scer\UAS.T:Ivir\HA1 ciWT.Scer\UAS.T:Hsap\TBP viable | partially, with Scer\GAL4ptc-559.1 ciScer\UAS.cPa ciWT.P.Scer\UAS.T:Ivir\HA1 Sterility Allele sterile, with Scer\GAL4ci.PC, ci94 ciScer\UAS.cHb sterile, with Scer\GAL4ci.PC, ciScer\UAS.cHb ci94 Other Phenotypes Allele mitotic cell cycle defective | cell autonomous | somatic clone ci94 mitotic cell cycle defective | somatic clone ci94 mitotic cell cycle defective | somatic clone, with Scer\GAL4Act5C.PP ci5m.Scer\UAS neuroanatomy defective, with Scer\GAL4neur-GAL4-A101 ciN:Zn.Scer\UAS visible ciD ciW ciαTub84B.T:Hsap\MYC,T:Ivir\HA1 ciαTub84B.T:Ivir\HA1 visible, with Scer\GAL4bs-1348 ciScer\UAS.cAa visible, with Scer\GAL4c591 ci76.Scer\UAS ciScer\UAS.cHb ciZn:C.Scer\UAS visible, with Scer\GAL4C-765 ci75.Scer\UAS ciPKA1.Scer\UAS.T:Ivir\HA1 visible, with Scer\GAL4cad-em459 ciScer\UAS.cAa visible, with Scer\GAL4dpp.blk1 ci76.Scer\UAS visible, with Scer\GAL4GMR.PF ciΔN1.Scer\UAS.T:Ivir\HA1 ciΔNC1.Scer\UAS.T:Ivir\HA1 visible, with Scer\GAL4nub-AC-62 ci75.Scer\UAS visible, with Scer\GAL4ptc-559.1 ciScer\UAS.T:Ivir\HA1 ciU.Scer\UAS.T:Ivir\HA1 visible | adult stage, with Scer\GAL4en-e16E ciJF01271 ciJF01272 visible | cold sensitive ci+3 ci+5 visible | dominant ciCe-2 ciCe-3 ciCe-4 ciD ciW visible | dominant | cold sensitive ciW visible | homeotic, with Scer\GAL4ey.PB ciwt.Scer\UAS visible | recessive ci1 ci36 ci57 ciD cin visible | recessive | somatic clone ci94 visible | somatic clone ci94 visible | somatic clone, with Scer\GAL4tub.PU ci75.Scer\UAS.cKa wild-type ci+2 ci+C ci+t16 Phenotype manifest in Allele 1st posterior cell, with Scer\GAL4dpp.blk1 ci76.Scer\UAS adult hindgut, with Scer\GAL4cad-em459 ciScer\UAS.cAa alula ciD anal plate, with Scer\GAL4cad-em459 ciScer\UAS.T:Ivir\HA1 ciScer\UAS.cAa antenna cin antenna | ectopic, with Scer\GAL4ey.PB ciwt.Scer\UAS anterior crossvein, with Scer\GAL4ptc-559.1 ciScer\UAS.T:Ivir\HA1 Bolwig organ ciCe-2 Bolwig organ, with Scer\GAL4da.G32 ciN:Zn.Scer\UAS denticle cidsRNA.cRa denticle, with Scer\GAL469B ciScer\UAS.cAa denticle | ectopic ci94 denticle belt ci94 ciCe-2 denticle belt, with Scer\GAL4ci.PC ciN:Zn.Scer\UAS.T:Ivir\HA1 denticle belt, with Scer\GAL4ci.PC, ci94 ciScer\UAS.T:SV40\nls2 denticle belt, with Scer\GAL4ci.PC, ciScer\UAS.T:SV40\nls2 ci94 denticle belt, with Scer\GAL4en-e16E ciN:Zn.Scer\UAS ciZn:C.Scer\UAS denticle belt, with Scer\GAL4prd.RG1 cim1-4.Scer\UAS.T:Ivir\HA1 denticle belt, with Scer\GAL4ptc-559.1 ciN:Zn.Scer\UAS ciN:Zn.Scer\UAS.T:Ivir\HA1 denticle belt, with Scer\GAL4ptc-559.1, ci76.Scer\UAS ci94 denticle belt, with Scer\GAL4ptc-559.1, ci94 ci76.Scer\UAS denticle belt (with ci94), with Scer\GAL4ci.PC ciScer\UAS.T:SV40\nls2 denticle belt (with ciScer\UAS.T:SV40\nls2), with Scer\GAL4ci.PC ci94 denticle belt | supernumerary ci94 denticle belt | supernumerary, with Scer\GAL4ci.PC, ci94 ciΔZ2.Scer\UAS.T:Hsap\MYC denticle belt | supernumerary, with Scer\GAL4ci.PC, ciΔZ2.Scer\UAS.T:Hsap\MYC ci94 denticle belt | supernumerary (with ci94), with Scer\GAL4ci.PC ciΔZ2.Scer\UAS.T:Hsap\MYC denticle belt | supernumerary (with ciΔZ2.Scer\UAS.T:Hsap\MYC), with Scer\GAL4ci.PC ci94 denticle row 1 ci183 ci217 ci228 ci94 ciCe-r2 denticle row 2 ciCe-2 denticle row 2 | ectopic ci94 denticle row 3 ciCe-2 denticle row 3 | ectopic ci94 denticle row 4 ci94 ciCe-2 denticle row 4 | ectopic ci94 denticle row 5 ciCe-2 denticle row 6 ciCe-2 dorsal branch primordium, with Scer\GAL4btl.PS ciZn:C.Scer\UAS egg chamber | somatic clone, with Scer\GAL4Act5C.PP ciCe-2.Scer\UAS.T:Ivir\HA1 embryo | segment polarity expression pattern ciCe-2 embryonic/first instar larval cuticle ci94 ciCe-1 ciCe-2 ciD embryonic/first instar larval cuticle, with Scer\GAL469B ciScer\UAS.cAa embryonic/first instar larval cuticle, with Scer\GAL4ptc-559.1, ci76.Scer\UAS ci94 embryonic/first instar larval cuticle, with Scer\GAL4ptc-559.1, ci94 ci76.Scer\UAS embryonic/first instar larval cuticle | ventral ci183 ci217 ci228 ci94 ciCe-r2 embryonic/larval dorsal branch, with Scer\GAL4btl.PS ciAct.Scer\UAS ciInh.Scer\UAS embryonic/larval dorsal vessel ciDR50 embryonic epidermis ci94 ciCe-2 ciCe-3 ciDRP cidsRNA.cRa embryonic epidermis, with Scer\GAL469B ciScer\UAS.cAa embryonic epidermis, with Scer\GAL4prd.RG1 cim1-4.Scer\UAS.T:Ivir\HA1 eye, with Scer\GAL4ey.PB ciwt.Scer\UAS eye, with Scer\GAL4GMR.PF ciΔN1.Scer\UAS.T:Ivir\HA1 ciΔNC1.Scer\UAS.T:Ivir\HA1 eye disc | cell autonomous | somatic clone ci94 eye disc | somatic clone ci94 filzkorper, with Scer\GAL4ems.HRE ciN:Zn.Scer\UAS follicle stem cell | somatic clone ci94 follicle stem cell | somatic clone, with Scer\GAL4Act5C.PP ci5m.Scer\UAS germarium | somatic clone, with Scer\GAL4Act5C.PP ciCe-2.Scer\UAS.T:Ivir\HA1 glial cell & eye disc | somatic clone, with Scer\GAL4Act5C.PP ciZn:C.Scer\UAS head capsule | dorsal, with Scer\GAL4c591 ci76.Scer\UAS interfollicle cell | somatic clone, with Scer\GAL4Act5C.PP ciCe-2.Scer\UAS.T:Ivir\HA1 interfollicle cell | somatic clone | supernumerary, with Scer\GAL4Act5C.PP ci5m.Scer\UAS interommatidial bristle, with Scer\GAL4lz-gal4 ci5m.Scer\UAS keyhole structure ciD lamina, with Scer\GAL4αTub84B.PP ci76.Scer\UAS lamina & neuron | precursor, with Scer\GAL4αTub84B.PP ci76.Scer\UAS larval abdominal segment, with Scer\GAL469B ciScer\UAS.cAa larval thoracic segment, with Scer\GAL469B ciScer\UAS.cAa leg, with Scer\GAL4en-e16E ci76.Scer\UAS leg (with ciD) ciW leg (with ciW) ciD mesothoracic tarsal bristle longitudinal row 1 ciD morphogenetic furrow | somatic clone, with Scer\GAL4Act5C.PP ciScer\UAS.cDa morphogenetic furrow | ventral, with Scer\GAL4fng-B ciCe-2.Scer\UAS.T:Ivir\HA1 ocellar bristle ciCe-2 ciCe-3 ocellus ciCe-2 ciCe-3 ocellus, with Scer\GAL4c591 ci76.Scer\UAS ciScer\UAS.cHb ciZn:C.Scer\UAS ocellus | somatic clone ci94 ommatidial precursor cluster ciW ommatidial precursor cluster, with Scer\GAL4lz-gal4 ci5m.Scer\UAS ommatidium | somatic clone, with Scer\GAL4tub.PU ci75.Scer\UAS.cKa postvertical bristle ciCe-2 ciCe-3 prothoracic ventral denticle belt ci94 pseudotracheal sensillum, with Scer\GAL4pb.PJ ciScer\UAS.cAa retina, with Scer\GAL4lz-gal4 ci5m.Scer\UAS scutellar bristle ciCe-2 ciCe-3 sensory mother cell, with Scer\GAL4MD-638 ciScer\UAS.T:Ivir\HA1 sensory mother cell | ectopic, with Scer\GAL4MD-638 ciScer\UAS.T:Ivir\HA1 S phase | ectopic, with Scer\GAL4bbg-C96 ciScer\UAS.cDa S phase | ectopic | somatic clone, with Scer\GAL4Act5C.PP ciScer\UAS.cDa stigmatophore, with Scer\GAL4salm-459.2 ciN:Zn.Scer\UAS thorax, with Scer\GAL4en-e16E ci76.Scer\UAS tracheal tip cell | embryonic stage, with Scer\GAL4btl.PS ciN:Zn.Scer\UAS ciZn:C.Scer\UAS trichome of the posterior wing margin ciD ventral multidendritic neuron vdaB, with Scer\GAL4neur-GAL4-A101 ciN:Zn.Scer\UAS ventral thoracic disc (with ci94) cin ventral thoracic disc (with cin) ci94 wing ciαTub84B.T:Hsap\MYC,T:Ivir\HA1 ciCe-4 ciD ciW cin wing, with Scer\GAL4en-e16E ci76.Scer\UAS wing, with Scer\GAL4ptc-559.1 ci76.Scer\UAS ciScer\UAS.T:Ivir\HA1 wing | anterior | somatic clone ci94 wing | anterior compartment ciW wing | distal, with Scer\GAL4ptc-559.1 ciU.Scer\UAS.T:Ivir\HA1 wing | ectopic | somatic clone ci94 wing | posterior compartment ci57 wing | proximal, with Scer\GAL430A ciScer\UAS.cAa wing blade, with Scer\GAL4C-765 ciPKA1.Scer\UAS.T:Ivir\HA1 ci75.Scer\UAS wing blade, with Scer\GAL4nub-AC-62 ci75.Scer\UAS wing disc, with Scer\GAL471B ciWT.P.Scer\UAS.T:Ivir\HA1 wing disc, with Scer\GAL4bbg-C96 ciScer\UAS.cDa wing disc, with Scer\GAL4Bx-MS1096 ci-3P.Scer\UAS.W.T:Ivir\HA1 wing disc (with ci94) cin wing disc (with cin) ci94 wing disc | anterior | somatic clone ci94 ciCe-2 wing disc | anterior | somatic clone, with Scer\GAL4Act5C.PP ciCe-2.Scer\UAS.T:Ivir\HA1 wing disc | anterior compartment ciU wing disc | anterior compartment, with Scer\GAL471B ci3m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS.T:Ivir\HA1 wing disc | anterior compartment, with Scer\GAL4MD-638 ciScer\UAS.T:Ivir\HA1 wing disc | anterior compartment | somatic clone, with Scer\GAL4Act5C.PP ciScer\UAS.cDa wing disc | anterior compartment | somatic clone, with Scer\GAL4hh-Gal4 ciScer\UAS.cDa wing disc | posterior compartment, with Scer\GAL471B ci3m.Scer\UAS.T:Ivir\HA1 ci5m.Scer\UAS.T:Ivir\HA1 ciWT.P.Scer\UAS.T:Ivir\HA1 wing disc | posterior compartment, with Scer\GAL4MD-638 ciScer\UAS.T:Ivir\HA1 wing disc | somatic clone, with Scer\GAL4Act5C.PP ciScer\UAS.cDa wing margin | posterior ciD wing margin bristle ciD wing margin bristle, with Scer\GAL4ptc-559.1 ciU.Scer\UAS.T:Ivir\HA1 wing vein ciαTub84B.T:Ivir\HA1 ci1 ci36 ci57 ciCe-2 ciCe-3 ciD ciD-G ciW wing vein, with Scer\GAL4bs-1348 ciScer\UAS.cAa wing vein, with Scer\GAL4en-e16E ciJF01271 ciJF01272 ciZn:AD.Scer\UAS.T:Hsap\MYC,T:Scer\GAL4 wing vein, with Scer\GAL4ptc-559.1 ciU.Scer\UAS.T:Ivir\HA1 wing vein | cold sensitive ci+5 wing vein | ectopic ciD wing vein L2 | somatic clone ci94 wing vein L3 ciCe-2 wing vein L3, with Scer\GAL4ptc-559.1 ciZn.Scer\UAS.T:Hsap\MYC wing vein L3 | somatic clone ci94 wing vein L4 ciαTub84B.T:Hsap\MYC,T:Ivir\HA1 ci+2 ci1 ciCe-2 ciD ciW wing vein L4, with Scer\GAL4ptc-559.1 ciZn.Scer\UAS.T:Hsap\MYC wing vein L4 & sensillum campaniformium | ectopic | somatic clone ci94 wing vein L4 & wing sensillum | ectopic | somatic clone ci94 wing vein L4 | cold sensitive ci+3 wing vein L4 | somatic clone ci94 wing vein L5 ci1
Classical Alleles ( 37 )
For All Classical Alleles Show
Allele of ci Class Mutagen Stocks Known lesion ciD loss of function allele, amorphic allele - genetic evidence, gain of function allele X ray 91 Yes ci1 spontaneous 17 Yes ci57 X ray 3 Yes ciCe-2 spontaneous 3 Yes ciDplac P-element activity 2 Yes ciE1 2 Yes ciW gain of function allele spontaneous 2 Yes ci36 spontaneous 1 Yes ciKG05811 P-element activity 1 -- ci+2 hypomorphic allele - genetic evidence 0 -- ci+3 0 -- ci+5 spontaneous 0 -- ci+ 0 -- ci+C hypomorphic allele - genetic evidence 0 -- ci1482 spontaneous 0 Yes ci183 Delta2-3 0 Yes ci2-M1021.R P-element activity 0 Yes ci217 Delta2-3 0 Yes ci228 Delta2-3 0 Yes ci52g X ray 0 -- ci94 loss of function allele Delta2-3 0 Yes ciBelleville natural population 0 -- ciCe-1 spontaneous 0 Yes ciCe-3 X ray 0 -- ciCe-4 0 -- ciCe-r1 X ray 0 -- ciCe-r2 X ray 0 -- ciD+rev3A-32A 0 Yes ciD+rev9A-101A 0 Yes ciD-G recombination 0 -- ciD-l 0 -- ciDR50 loss of function allele gamma ray 0 -- ciDRP PM hybrid dysgenesis 0 -- ciDrv 0 -- ciE2 0 Yes cin spontaneous 0 Yes ciunspecified 0 --
Alleles Carried on Transgenic Constructs ( 161 )
For All Alleles Carried on Transgenic Constructs Show
Allele of ci Class Mutagen Stocks Known lesion ciGD1403 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ciJF01271 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ciJF01272 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ciJF01715 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ciJF01744 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ciKK100760 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cim1-4.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes ciwt.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 1 Yes ci+t16 in vitro construct - genomic fragment 0 Yes ci-3P.Scer\UAS.W.T:Ivir\HA1 in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes ci103.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci167.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci272.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci279.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci289.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci316.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci324.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci376.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci3m.Scer\UAS.T:Hsap\TBP in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci3m.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci3m.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ci44.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci442.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci459.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci5m.Scer\UAS.T:Hsap\TBP in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci5m.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci5m.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ci616.NZn.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ci66.Act5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci75.MtnA in vitro construct - regulatory fusion 0 Yes ci75.Scer\UAS.cKa in vitro construct - regulatory fusion 0 Yes ci75.Scer\UAS 0 -- ci76.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ci76.Scer\UAS in vitro construct - regulatory fusion 0 Yes ci76ΔCDN.Scer\UAS.T:Ivir\HA1 0 Yes ci7m.Scer\UAS.T:Hsap\TBP in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci7m.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - amino acid replacement 0 Yes ci7m.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ci92.Scer\UAS in vitro construct - regulatory fusion 0 Yes ciAct.Scer\UAS in vitro construct - regulatory fusion 0 Yes ciAct5C.PA in vitro construct - regulatory fusion 0 -- ciAct5C.PC in vitro construct - regulatory fusion 0 Yes ciAct5C.PH FLPase 0 Yes ciAct5C.PN in vitro construct - regulatory fusion 0 Yes ciAct5C.PO in vitro construct - regulatory fusion 0 Yes ciAct5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes ciAct5C.T:Scer\GAL4 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciAct5C.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciC.Scer\UAS.T:Avic\GFP-S65T in vitro construct - coding region fusion 0 Yes ciC.Scer\UAS.T:Ivir\HA1,T:SV40\nls2 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciC.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciC1.Act5C.T:Ecol\lacZ in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciCe-2.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciCim1.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciCim2.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciCim3.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciCm.Scer\UAS.T:Ivir\HA1 in vitro construct - site directed mutagenesis 0 Yes ciCORD.NLS.Scer\UAS.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cicyt.Scer\UAS.T:Avic\GFP-S65T in vitro construct - coding region fusion 0 Yes cicyt.T:Avic\GFP-S65T in vitro construct - coding region fusion 0 Yes ciDAG.Scer\UAS.T:Ivir\HA1 in vitro construct - site directed mutagenesis 0 Yes ciDSG.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciDSGX2.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes cidsRNA.cLa in vitro construct - RNAi 0 Yes cidsRNA.cRa in vitro construct - RNAi 0 Yes ciGA1.Scer\UAS.T:Ivir\HA1,T:Scer\GAL4 in vitro construct - deletion in vitro construct - coding region fusion 0 Yes ciGA2.Scer\UAS.T:Ivir\HA1,T:Scer\GAL4 in vitro construct - deletion in vitro construct - coding region fusion 0 Yes ciInh.Scer\UAS in vitro construct - regulatory fusion 0 Yes cim1,2.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim1,3,4.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim1,3.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim1,4.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim1-3*103.Act5C.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1-3*103.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1-3*459.Act5C.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1-3*459.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1-3.Act5C.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1-3.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes cim1.Act5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes cim1.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim2,3.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim2,4.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim2.Act5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes cim2.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim3,4.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim3.Act5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes cim3.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes cim4.Act5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes cim4.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes ciMtnA.PvO in vitro construct - regulatory fusion 0 Yes cimutNLS.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciN.Scer\UAS.T:Ivir\HA1,T:SV40\nls2 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciN:Zn.Scer\UAS.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes ciN:Zn.Scer\UAS in vitro construct - deletion 0 Yes ciNCm.Scer\UAS.T:Ivir\HA1 in vitro construct - site directed mutagenesis 0 Yes ciNIG.2125R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes ciNLS.Act5C.T:Ecol\lacZ in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciNm.Scer\UAS.T:Ivir\HA1 in vitro construct - site directed mutagenesis 0 Yes cinull.Act5C.T:Ivir\HA1 in vitro construct - coding region fusion 0 Yes cinull.Act5C in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes ciNZnΔNLS.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciP1X3.Scer\UAS.W.T:Ivir\HA1 in vitro construct 0 Yes ciPKA.αTub84B.T:Ivir\HA1 in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciPKA1.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion 0 Yes ciPKA4.Scer\UAS in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes ciS849A.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciSA16.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA34.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA34C.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA34G.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA36.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA56.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciSA855.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes ciScer\FRT.Act5C in vitro construct - regulatory fusion 0 Yes ciScer\UAS.cAa in vitro construct - regulatory fusion 0 Yes ciScer\UAS.cDa in vitro construct - regulatory fusion 0 Yes ciScer\UAS.cHa in vitro construct - regulatory fusion 0 Yes ciScer\UAS.cHb in vitro construct - regulatory fusion 0 Yes ciScer\UAS.cPa in vitro construct - regulatory fusion 0 Yes ciScer\UAS.P1,3A in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciScer\UAS.PC.T:Ivir\HA1 in vitro construct - regulatory fusion 0 Yes ciScer\UAS.SL.T:Zzzz\FLAG,T:Ivir\HA1,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciScer\UAS.SLD.T:Zzzz\FLAG,T:Ivir\HA1,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciScer\UAS.SLG.T:Zzzz\FLAG,T:Ivir\HA1,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes ciScer\UAS.T:Avic\GFP-S65T,T:Hsap\MYC in vitro construct - coding region fusion 0 Yes ciScer\UAS.T:Hsap\MYC,T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciScer\UAS.T:Hsim\VP16 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciScer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciScer\UAS.T:SV40\nls2 0 Yes ciScer\UAS.T:Zzzz\His6 in vitro construct - regulatory fusion 0 Yes ciScer\UAS.W.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 -- ciScer\UAS.WT.T:Zzzz\FLAG,T:Ivir\HA1,T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciU-3P.Scer\UAS.W.T:Ivir\HA1 in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes ciU.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciU.αTub84B.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciU in vitro construct - deletion 0 Yes ciWT.P.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciWT.Scer\UAS.T:Hsap\TBP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciwt.Scer\UAS in vitro construct - regulatory fusion 0 Yes ciZF.Scer\UAS.T:Hsim\VP16 in vitro construct - coding region fusion 0 Yes ciZn.Scer\UAS.T:Hsap\MYC in vitro construct - deletion in vitro construct - coding region fusion 0 Yes ciZn:AD.Scer\UAS.T:Hsap\MYC,T:Scer\GAL4 in vitro construct - coding region fusion 0 Yes ciZn:C.Scer\UAS in vitro construct - deletion 0 Yes ciαTub84B.T:Hsap\MYC,T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciαTub84B.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciΔ.Act5C in vitro construct - deletion in vitro construct - regulatory fusion 0 Yes ciΔ3'.Scer\UAS in vitro construct - deletion 0 Yes ciΔ5'.Scer\UAS in vitro construct - deletion 0 Yes ciΔ603-835.Act5C.T:Scer\GAL4 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔC1-A.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes ciΔCDN.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔCORD.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔN.PKA4.Scer\UAS in vitro construct - deletion 0 Yes ciΔN1.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciΔN2.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciΔNC1.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciΔNC2.Scer\UAS.T:Ivir\HA1 in vitro construct - deletion 0 Yes ciΔNR.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔNΔC.Scer\UAS.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔZ2.Scer\UAS.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - deletion 0 Yes ciΔZn.Scer\UAS.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Duplicated in	Dp(1;4)193   Dp(4;2)ci24 (Stern and Kodani, 1955) Dp(4;2)ci+15 (Stern and Kodani, 1955) Ts(1Lt;4Lt)wmJ
Not disrupted in	Df(4)ED6382 (Ryder and Roote, 2004.11.10) Df(4)ED6384 (Ryder and Roote, 2004.11.10) Df(4)G (Hochman et al., 1964, Hochman, 1971) Df(4)Δ9M (Kronhamn and Rasmuson-Lestander, 1999) T(1;2;4)wvD2   T(1;4)scH (Sousa-Neves, 1999.11.10, Sousa-Neves, 2000) T(3;4)e   Ts(2Lt;4Rt)ci+21 (Stern and Kodani, 1955)
Disrupted in	Df(4)ci24 (Stern and Kodani, 1955) Df(4)M101-1 (Hochman, 1971, Hochman, 1974, Hochman, 1976) Df(4)M101-4 (Stern and Kodani, 1955, Hochman et al., 1964) Df(4)M101-62f (Cavallo et al., 1998, Kronhamn and Rasmuson-Lestander, 1999, Locke and Tartof, 1994, Slusarski et al., 1995, Harbecke and Lengyel, 1995, Johnson et al., 1995, Dominguez et al., 1996) Df(4)M101-63a (Kronhamn and Rasmuson-Lestander, 1999, Hochman, 1971, Hochman, 1974, Hochman, 1976, Locke and Tartof, 1994) Df(4)Δ3M (Kronhamn and Rasmuson-Lestander, 1999) In(4)ciD (Schweizer and Basler, 1998, Hochman, 1974, Hochman, 1976, Brunner et al., 1997)
Not duplicated in	Dp(2;4)eyD (Hochman et al., 1964)
Transgenic Constructs & Insertions
Transgenic Constructs
UAS construct	Name Expression Data P{GD1403} NA P{GFP-Ci} NA P{KK100760} NA P{TRiP.JF01271} NA P{TRiP.JF01272} NA P{TRiP.JF01715} NA P{TRiP.JF01744} NA P{UAS-ci::VP16} NA P{UAS-ci.3m.HA} NA P{UAS-ci.3m.TBP} NA P{UAS-ci.3m} NA P{UAS-ci.5m.HA} NA P{UAS-ci.5m.TBP} NA P{UAS-ci.5m} NA P{UAS-ci.7m.HA} NA P{UAS-ci.7m.TBP} NA P{UAS-ci.7m} NA P{UAS-ci.75.K} NA P{UAS-ci.75} NA P{UAS-ci.76} NA P{UAS-ci.616.NZn.HA} NA P{UAS-ci.A} NA P{UAS-ci.Act} NA P{UAS-ci.C.HA} NA P{UAS-ci.Ce-2.HA} NA P{UAS-ci.Cim1} NA P{UAS-ci.Cim2} NA P{UAS-ci.Cim3} NA P{UAS-ci.Cm} NA P{UAS-ci.D} NA P{UAS-ci.HA.-3P} NA P{UAS-ci.HA.76} NA P{UAS-ci.HA.76ΔCDN} NA P{UAS-ci.HA.DAG} NA P{UAS-ci.HA.DSG} NA P{UAS-ci.HA.DSGX2} NA P{UAS-ci.HA.m1-4} NA P{UAS-ci.HA.NLS-C} NA P{UAS-ci.HA.NLS-N} NA P{UAS-ci.HA.P} NA P{UAS-ci.HA.SA16} NA P{UAS-ci.HA.SA34} NA P{UAS-ci.HA.SA34C} NA P{UAS-ci.HA.SA34G} NA P{UAS-ci.HA.SA36} NA P{UAS-ci.HA.SA56} NA P{UAS-ci.HA.SA855} NA P{UAS-ci.HA.U-3P} NA P{UAS-ci.HA.W} NA P{UAS-ci.HA.wt} NA P{UAS-ci.HA.ΔCDN} NA P{UAS-ci.HA.ΔCORD} NA P{UAS-ci.HA.ΔNΔC} NA P{UAS-ci.HA} NA P{UAS-ci.Inh} NA P{UAS-ci.mutNLS} NA P{UAS-ci.NCm} NA P{UAS-ci.Nm} NA P{UAS-ci.NZnΔNLS.HA} NA P{UAS-CI.P1,3A} NA P{UAS-ci.P1X3.HA} NA P{UAS-ci.P} NA P{UAS-ci.PKA1} NA P{UAS-ci.PKA4} NA P{UAS-ci.S849A} NA P{UAS-ci.SL} NA P{UAS-ci.SLD} NA P{UAS-ci.SLG} NA P{UAS-ci.TBP} NA P{UAS-ci.U.HA} NA P{UAS-ci.WT} NA P{UAS-ci.wt} NA P{UAS-ci.Δ3'} NA P{UAS-ci.Δ5'} NA P{UAS-ci.ΔC1-A.HA} NA P{UAS-ci.ΔNR.myc} NA P{UAS-ci.ΔZ2.myc} NA P{UAS-ci.ΔZn.GFP} NA P{UAS-ci-cDNA} NA P{UAS-ciGA1} NA P{UAS-ciGA2} NA P{UAS-ci-genomic} NA P{UAS-ciN/Zn} NA P{UAS-ciN[HA]/Zn} NA P{UAS-ci-SV40NLS} NA P{UAS-ciZn/C} NA P{UAS-ciZn/GAL4AD} NA P{UAS-ciZn} NA P{UAS-ciΔN1} NA P{UAS-ciΔN2} NA P{UAS-ciΔNC1} NA P{UAS-ciΔNC2} NA P{UAS-GFP-ci-cyt} NA P{UAS-HA.ci.m1-3} NA P{UAS-HA.ci.m1-3*103} NA P{UAS-HA.ci.m1-3*459} NA P{UAS-HAci.PC} NA P{UAS-MYC.ci.HA} NA P{UASZFciVP16} NA P{UAS-ΔN.PKA4.ci} NA
GAL4 construct	Name Expression Data P{ci-GAL4.C} No P{ci-GAL4.U} No P{UAS-ciGA1} No P{UAS-ciGA2} No P{UAS-ciZn/GAL4AD} No
reporter construct	Name Expression Data P{1.2prx-ci} No P{1.3dis+1.2prx-ci} No P{1.4dis+1.2prx-ci} No P{1.6dis-ci57g+HS} No P{2.2dis+1.2prx-ci} No P{2.2dis-ci+HS} No P{3.7dis+1.2prx-ci} No P{4bs-lacZ} No P{7.1-ci} No P{ci-grh-lacZ} No
characterization construct	Name Expression Data P{Act5C(FRT.polyA)ci.H} NA P{Act5C(-FRT)ci.H} NA P{ci+t16} NA P{ciU} NA P{NIG.2125R} NA P{UAS-ci::pan.ciD.S28N} NA P{UAS-ci::pan.ciD.ΔN} NA P{UAS-ci::pan.ciD} NA P{UAS-ci::pan.ciDΔ} NA P{UAS-ci.ΔEn} NA P{UAS-ciZn/EnRD} NA P{αTub84B-ci.HA} NA P{αTub84B-MYC.ci.HA} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions ?{}ci36 NA ?{}cin NA ?{}ciW NA gypsy{}ci1 NA gypsy{}ciE1 NA gypsy{}ciE2 NA I{}ciCe-1 NA P{}ciDRP NA P{hsp26-pt-T}ci2-M1021.R NA P{SUPor-P}ciKG05811 NA PBac{Dmw}M17-4 NA insertion of enhancer trap P{lacW}ciDplac No
Gene Ontology: Function, Process & Cellular Component ( 32 unique terms )
Terms Based on Experimental Evidence ( 26 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with A2bp1 (Usha and Shashidhara, 2010) inferred from physical interaction with hyx (Mosimann et al., 2009) inferred from physical interaction with nej (Chen et al., 2000) inferred from physical interaction with slmb (Jia et al., 2005) contributes_to RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription inferred from genetic interaction with nej (Chen et al., 2000) RNA polymerase II regulatory region sequence-specific DNA binding inferred from direct assay (Von Ohlen et al., 1997) transcription regulatory region DNA binding inferred from direct assay (Usha and Shashidhara, 2010)
Biological Process
CV term Evidence References
cuticle pattern formation inferred from mutant phenotype (Croker et al., 2006) dendrite morphogenesis inferred from mutant phenotype (Parrish et al., 2006) epidermis development inferred from mutant phenotype (Parrish et al., 2006) eye morphogenesis inferred from mutant phenotype (Kent et al., 2006) genital disc anterior/posterior pattern formation inferred from expression pattern (Freeland and Kuhn, 1996) heart formation inferred from mutant phenotype (Park et al., 1996) labial disc development inferred from mutant phenotype (Joulia et al., 2005) neuron development inferred from mutant phenotype (Parrish et al., 2006) oogenesis inferred from expression pattern (Forbes et al., 1996) positive regulation of epithelial cell differentiation inferred from mutant phenotype (Takashima et al., 2008) positive regulation of S phase of mitotic cell cycle inferred from mutant phenotype (Firth and Baker, 2005) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Von Ohlen et al., 1997) inferred from genetic interaction with nej (Chen et al., 2000) inferred from mutant phenotype (Chen et al., 2000) regulation of mitotic cell cycle inferred from mutant phenotype (Zhang and Kalderon, 2001) segment polarity determination inferred from mutant phenotype (assigned by UniProtKB) (Orenic et al., 1990) smoothened signaling pathway inferred from expression pattern (Forbes et al., 1996) inferred from mutant phenotype (Methot and Basler, 2001, Yao et al., 2006, Chen et al., 2000) spiracle morphogenesis, open tracheal system inferred from mutant phenotype (Merabet et al., 2005) wing disc anterior/posterior pattern formation inferred from mutant phenotype (Shen and Dahmann, 2005)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Wang and Holmgren, 2000, Croker et al., 2006, Forbes et al., 1996, Wang et al., 2000) Hedgehog signaling complex inferred from physical interaction with cos AND inferred from physical interaction with fu (Stegman et al., 2000) membrane inferred from direct assay (Stegman et al., 2004) nucleus inferred from direct assay (Wang and Holmgren, 2000, Croker et al., 2006, Wang et al., 2000, Usha and Shashidhara, 2010) protein complex inferred from physical interaction with Su(fu) (Monnier et al., 1998)
Terms Based on Predictions or Assertions ( 9 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity non-traceable author statement (Swiss-Prot Project Members, 1990.11.1) traceable author statement (Lee and Orr-Weaver, 2003) zinc ion binding inferred from electronic annotation with InterPro:IPR007087, InterPro:IPR015880 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
blastoderm segmentation traceable author statement (Galis et al., 2002) negative regulation of transcription from RNA polymerase II promoter traceable author statement (Marsh and Theisen, 1999) ovarian follicle cell development traceable author statement (Dobens and Raftery, 2000) positive regulation of transcription from RNA polymerase II promoter traceable author statement (Farese and Herz, 1998, Marsh and Theisen, 1999) regulation of transcription, DNA-dependent traceable author statement (Lee and Orr-Weaver, 2003) smoothened signaling pathway non-traceable author statement (Curtiss et al., 2002) traceable author statement (Lee and Orr-Weaver, 2003, Ogden et al., 2004)
Cellular Component
CV term Evidence References
nucleus non-traceable author statement (Swiss-Prot Project Members, 1990.11.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
ci - A2bp1 pull down, western blot, anti tag coimmunoprecipitation, anti bait coimmunoprecipitation, anti tag western blot (Usha and Shashidhara, 2010) ci - CkIα anti tag coimmunoprecipitation, anti tag western blot (Shi et al., 2011) ci - Su(fu) fluorescent resonance energy transfer, anti tag coimmunoprecipitation, anti tag western blot (Shi et al., 2011) ci - cos anti tag coimmunoprecipitation, anti tag western blot (Shi et al., 2011) ci - sgg anti tag coimmunoprecipitation, anti tag western blot (Shi et al., 2011)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions ci allele Gene References ci1 en (Locke and Hanna, 1996) ci36 en (Locke and Hanna, 1996) ci57 en (Locke and Hanna, 1996) ci94 arm (Angelats et al., 2002) hh (Gallet et al., 2000) Pka-C1 (Kiger and O'Shea, 2001) ptc (Methot and Basler, 2001) smo (Fu and Baker, 2003) tsh (Gallet et al., 2000, Angelats et al., 2002) wg (Methot and Basler, 2001) ciCe-1 ptc (Johnson et al., 1995) ciCe-2.Scer\UAS.T:Ivir\HA1 ey (Kango-Singh et al., 2003) hh (Kango-Singh et al., 2003) ciCe-2 fu (Alves et al., 1998) hh (Suzuki and Saigo, 2000) ciCe-4 fu (Alves et al., 1998) ciD arm (Cavallo et al., 1998) kn (Vervoort et al., 1999) nej (Akimaru et al., 1997, Florence and McGinnis, 1998) ptc (Sanchez-Herrero et al., 1996) cim1-4.Scer\UAS.T:Ivir\HA1 hh (Chen et al., 1999) ciN:Zn.Scer\UAS hh (Suzuki and Saigo, 2000) ciScer\UAS.cAa arm (Angelats et al., 2002) Su(hh)II (Haines and van Den Heuvel, 2000) Su(hh)III (Haines and van Den Heuvel, 2000) Su(hh)IV (Haines and van Den Heuvel, 2000) tsh (Angelats et al., 2002) wg (Angelats et al., 2002) ciScer\UAS.cDa bi (Shen and Dahmann, 2005) dap (Duman-Scheel et al., 2002) ciScer\UAS.cHa cg (Campbell and Tomlinson, 2000) ciScer\UAS.T:Ivir\HA1 cg (Svendsen et al., 2000) ey (Kango-Singh et al., 2003) fu (Alves et al., 1998) ciunspecified ato (White and Jarman, 2000) Egfr (Diaz-Benjumea and Garcia-Bellido, 1990) en (Locke and Hanna, 1995) ciW cg (House, 1953, Campbell and Tomlinson, 2000, Svendsen et al., 2000) en (Locke and Hanna, 1996) ph-p (Randsholt et al., 2000) Psc (Randsholt et al., 2000) unspecified Dfd (Florence and McGinnis, 1998) en (House, 1953, House, 1953, House, 1961, Mukherjee, 1965, Datta and Mukherjee, 1971, Dahmann and Basler, 2000) hh (Pankratz and Hoch, 1995) inv (Dahmann and Basler, 2000) N (House and McClanahan Lutes, 1975) pb (Joulia et al., 2005) Pka-C1 (Johnson et al., 1995) rho (Sturtevant and Bier, 1995) su(Hw) (Lindsley and Grell, 1968) wg (Pankratz and Hoch, 1995)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 68605 DroID - A comprehensive database of gene and protein interactions. • FBgn0004859 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 43767 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P19538
Orthologs
OrthoDB Orthologs (39) - 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 EOG60K8J4 Dipteran inclusive ortholog search EOG6W6P3X Insect inclusive ortholog search EOG6WH7FR Arthropod inclusive ortholog search EOG6J9KDT Metazoa inclusive ortholog search EOG6W9WWS
Orthologs in Drosophila Species (EOG60K8J4)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\ci     Drosophila simulans   Dsim\ci Y   Drosophila sechellia   Dsec\GM23237 Y   Drosophila erecta   Dere\GG16466 Y   Drosophila yakuba   Dyak\ci Y   Drosophila ananassae   Dana\GF19046 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA27838 Y   Drosophila persimilis   Dper\GL18388 Y   Drosophila willistoni   Dwil\GK13666 Y   Drosophila virilis   Dvir\GJ14655 Y
Orthologs in non-Drosophila Dipterans (EOG6W6P3X)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Anopheles gambiae Malaria mosquito  Agam\AGAP004637   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ000614
Orthologs in non-Dipteran Insects (EOG6WH7FR)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB54885   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG009158   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH27147   Atta cephalotes Leafcutter ant  Acep\ACEP11155   Atta cephalotes Leafcutter ant  Acep\ACEP11153   Camponotus floridanus Florida carpenter ant  Cflo\CFLO26628   Linepithema humile Argentine ant  Lhum\LH17564   Pogonomyrmex barbatus Red harvester ant  Pbar\PB16979   Solenopsis invicta Red fire ant  Sinv\SINV10056   Solenopsis invicta Red fire ant  Sinv\SINV10052   Acyrthosiphon pisum Pea aphid  Apim\ACYPI45156   Bombyx mori Silkmoth  Bmor\BGIBMGA004545   Pediculus humanus Human body louse  Phum\PHUM413310   Tribolium castaneum Red flour beetle  Tcas\ci
Orthologs in non-Insect Arthropods (EOG6J9KDT)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\matK   Ixodes scapularis Deer tick  Isca\ISCW005490
Orthologs in non-Arthropod Metazoa (EOG6W9WWS)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\Y47D3A.6   Danio rerio Zebrafish  Drer\gli3   Xenopus tropicalis Western clawed frog  Xtro\gli3   Gallus gallus Domestic chicken  Ggal\ENSGALG00000014639   Gallus gallus Domestic chicken  Ggal\GLI3   Mus musculus House mouse  Mmus\Gli1   Mus musculus House mouse  Mmus\Gli3   Rattus norvegicus Norway rat  Rnor\Gli1   Rattus norvegicus Norway rat  Rnor\Gli3   Homo sapiens Human  Hsap\GLI3   Homo sapiens Human  Hsap\GLI1
Human Orthologs (2)
Gene OMIM HGNC Hsap\GLI3     Hsap\GLI1
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\ci Drosophila sechellia Dsec\GM23237 Drosophila erecta Dere\GG16466 Drosophila yakuba Dyak\ci Drosophila ananassae Dana\GF19046 Drosophila pseudoobscura pseudoobscura Dpse\GA27838 Drosophila persimilis Dper\GL18388 Drosophila willistoni Dwil\GK13666 Drosophila virilis Dvir\GJ14655 Drosophila mojavensis Dmoj\GI14119 Drosophila grimshawi Dgri\GH23992
Stocks & Reagents
Stocks Listed in FlyBase ( 127 )
Bloomington	646 ciW 643 ci36 644 ci57 642 ci1 svn 4229 ci1 eyR
Kyoto	101771 ci1 106024 ciW 101773 ci57 106023 ci57 103321 Df(4)G / ciD 107646 ci1 eyR
VDRC	v105620 P{KK100760}VIE-260B
	More stocks available...
Genomic Clones ( 2 )
	BACR05L22 BACR21B19 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 103 )
	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	GM02381 RE55588
Other clones	FI19601
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM01595 GM20146 GM28357 HL07390 RE54613
Other clones	507 1383 12452 15733 17071 29762 29920 31286 31445 33007 34064 34527 35669 40272 54996 59259 62387 67841 69980 70955 78076 79193 79852 81085 97734 98053 122608 123145 148756 153397 192513 CK01.15B.F4 CK01.15B.H1 CK01.50C.G6 CK01.61B.G12 CK01.61C.F10 CK01.62C.D5 CK01.80B.C9 CK01.167B.G5 EC24089 EC27964 EC252184 EC252701 EC255393 EC255913 EC257510 EC258274 EC259582 EK015454 EK040559 EK044201 EK048455 EK049160 EK050415 EK051563 EK057402 EK062111 EK063860 EK102221 EK113546 EK121226 EK122651 EK128948 EK137923 EK141625 EK146925 EK148418 EK153517 EK155804 EK167151 EK181736 EK183655 EK184906 EK188018 EK196445 EK198511 EK211532 EK214614 EK219918 EK255035 EK256821 EK269803 EK295633 EK304003 EP08530 EP11753 EP12356 EP12434 EP19356 EP19444 EP21749 FGC031C03 FGM207C04 GM19621 LD07764
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0004859 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 43767
Antibody Information
	monoclonal antibody (Bajpai et al., 2004, Chanas et al., 2004) polyclonal antibody (Bornemann et al., 2004, Strutt et al., 2004)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: ci CG2125 (Milshina, 1999.11)
Source for database merge of
Additional comments
Other Comments
	The stability of endogenous ci protein is regulated by the ubiquitin-proteasome system and not lysosome-mediated protein degradation. (Du et al., 2011) The 'N-terminal Regulatory' (NR) domain of the ci protein is necessary for cytoplasmic retention of ci. The domain containing the first two zinc-fingers is necessary for processing of the ci protein into its repressor form. (Croker et al., 2006) dsRNA has been made from templates generated with primers directed against this gene. RNAi of ci causes a loss of dorsal class I da neurons without affecting the ventral class I neuron vpda and an overall reduction of dorsal md neurons. ci RNAi causes embryonic lethality at high concentrations of dsRNA. RNAi also causes defects in muscle, defects in the epidermis, alterations in the number of MD neurons and defects in dendrite morphogenesis. (Parrish et al., 2006) ci enters the nucleus in response to hh signaling. (Sisson et al., 2006) Processing of ci-155 to the repressor ci-75 is mediated by direct binding to slmb. (Smelkinson and Kalderon, 2006) Cell culture experiments show that ci acts downstream of smo. (Yao et al., 2006) ChEST reveals this is a target of Mef2. (Junion et al., 2005) One of 42 Drosophila genes identified as being most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to human Mental Retardation disorders. (Inlow and Restifo, 2004) dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology. (Kiger et al., 2003) ci, tsh and arm may act as a complex. (Angelats et al., 2002) Different combinations of the proteins ci, tsh and arm appear to be employed for the specification of naked cuticle at distinct positions both along the anterior posterior axis and within individual trunk segments. (Angelats et al., 2002) The analysis of target gene expression and morphogenetic read-outs of hh in embryonic, larval and adult stages indicates that ci is absolutely required for all examined aspects of hh outputs. (Methot and Basler, 2001) nej function is necessary for ci-mediated transactivation of wg during embryogenesis. (Chen et al., 2000) cg is required for the correct regulation of ci in limb development. (Svendsen et al., 2000) ci mediated activation of vn expression by hh requires the C terminus region of the ci protein. (Amin et al., 1999) Proteolysis of ci requires phosphorylation by PKA. (Price and Kalderon, 1999) The hh signalling components smo and ci are required in cells posterior to hh to maintain ptc expression, whereas fu is not necessary in these cells. (Therond et al., 1999) ci null alleles are partially functionally complemented by Hsap\GLI, which rescues viability to late third instar, but produces larvae with grossly enlarged wing discs. ci null alleles are also partially functionally complemented by a combination of Hsap\GLI and Hsap\GLI3, rescuing to pupal or late third instar larvae and producing wild-type wing discs. (von Mering and Basler, 1999) PKA inhibits the activity of full-length ci protein in addition to its role in regulating ci proteolysis. (Wang et al., 1999) There are three levels of apparent ci activity in the wing disc, corresponding to three zones along the antero-posterior axis with different sets of gene expression and different levels of hh signaling. (Wang and Holmgren, 1999) Modulation of the hh signaling pathway by Rnor\KAPA occurs directly at the level of ci phosphorylation. (Chen et al., 1998) Using the yeast two-hybrid method and an in vitro binding assay it is demonstrated that Su(fu), ci and fu can interact directly to form a trimolecular complex, with Su(fu) binding to both its partners simultaneously. In the absence of hh signalling results propose that Su(fu) inhibits ci by binding to it and that, upon reception of the hh signal, fu is activated and counteracts Su(fu), leading to the activation of ci. (Monnier et al., 1998) CrebA ci double mutant phenotype confirms that CrebA is not involved in segment polarity. (Andrew et al., 1997) Characterisation of ci protein reveals it exists in at least two forms, one full-length and the other truncated, these forms differ in activity and subcellular location. The N-terminal domain has nuclear localisation and DNA binding activities that are impotent in the full-length protein. Processing of the full length protein is inhibited by hh, an observation that represents the first direct evidence that ci transduces the hh signal. (Aza-Blanc et al., 1997) Each primordia of the genital disc (female genital, male genital and anal primordia) is divided into anterior and posterior compartments. Genes known to be expressed in compartment-specific manner in discs are expressed in analogous patterns in each primordia. (Chen and Baker, 1997) Genetic combinations with mutants of nub cause additive phenotypes. (Cifuentes and Garcia-Bellido, 1997) ci forms a negative feedback loop with ptc and regulates expression of hh target genes. (Hepker et al., 1997) hh elicits signal transduction via a complex that includes the products of the fu, ci and cos genes. The complex binds with high affinity to microtubules in the absence of hh protein, but not when hh is present. The complex may facilitate signalling from hh by governing access of the ci product to the nucleus. (Robbins et al., 1997) The ci protein associates with the cos product in a large protein complex, suggesting that cos directly controls the activity of ci. (Sisson et al., 1997) The pattern of expression of ci in the larval and adult abdomen has been analysed. (Struhl et al., 1997) hh and ptc can regulate transcription from a wg enhancer element containing ci protein binding sites by modulating the activity of ci protein. (Von Ohlen and Hooper, 1997) ci encodes a sequence-specific DNA binding protein that functions as a transcriptional activator in the hh signal transduction pathway. (Von Ohlen et al., 1997) Elevated levels of ci are sufficient to activate hh target genes, even in the absence of hh activity. Results strongly support a role for ci as the transcriptional activator that mediates hh signaling. (Alexandre et al., 1996) Cells in anterior compartments lacking ci express hh and adopt a posterior fate without expressing en. Increased levels of ci can induce the expression of dpp independent of hh. Expression of ci in anterior cells controls limb development by restricting hh secretion to posterior cells and by conferring competence to respond to hh by mediating transduction of the hh signal. (Dominguez et al., 1996) ptc and ci are expressed in a pattern complementary to hh and en in adult ovaries. hh directly effects region 2 somatic cells of the germarium via a signalling pathway which includes ptc and ci, but not wg or dpp. (Forbes et al., 1996) The expression pattern of a number of genes in the larval genital discs, including ci, has been studied to determine the segment-parasegment organisation of the genital discs. (Freeland and Kuhn, 1996) ara-caup expression at patches on the wing, located one at each side of the DV compartment border, is mediated by the hh signal through its induction of high levels of ci protein in anterior cells near to the AP compartment border. High levels of ci activate dpp expression and together ci and dpp positively control ara-caup expression. (Gomez-Skarmeta and Modolell, 1996) Elevated en levels repress dpp, ptc and ci expression but do not disrupt eye morphogenesis. (Strutt and Mlodzik, 1996) en+ is a dose-dependent modifier of the ci locus. Lack of pairing at the ci locus can facilitate the en--dependent expression of the ci phenotypes. (Locke and Hanna, 1995) The distribution of the ci protein during development is examined and epistasis analysis is used to position ci in the wg and hh signalling pathways. fu and hh modulate the post-transcriptional regulation of ci protein. ci is epistatic to ptc in the maintenance of wg expression and the formation of naked cuticle. (Motzny and Holmgren, 1995) Ecol\lacZ reporter gene constructs demonstrate that separate ci regulatory elements regulate ci expression in embryos and imaginal discs. The en protein directly represses ci expression in wing posterior compartment cells. (Schwartz et al., 1995) Proper regulation of both the ci RNA and protein appears to be critical for normal development. (Slusarski et al., 1995) Direct wg autoregulation differs from wg signalling to adjacent cells in the importance of fu, smo and ci relative to sgg and arm. (Hooper, 1994) pan and ci loci display a complex complementation pattern: viable alleles of ci complement lethal alleles of ci and complement pan, of the lethal alleles of ci, ciD fails to complement pan and ciCe-r1, ciCe-2 fails to complement ciCe-r1. (Locke and Tartof, 1994) fu and ci are required for normal wg transcription, acting downstream of ptc to regulate wg transcription. Transcriptional control of ptc is mediated by fu and ci. (Forbes et al., 1993) Segment polarity mutations cause stripes of abnormal patterning within sectors of the leg disc, which may be mediated by regional perturbations in growth. (Held, 1993) The role of ci in the regulation of run mRNA expression in the early embryo has been investigated. (Klingler and Gergen, 1993) Assayed in an analysis of chromosome 4 using pulsed field gel electrophoresis. (Locke and McDermid, 1993) wg and en expression patterns are studied in all known segment polarity mutants to investigate the requirement of other segment polarity genes in mediating the maintenance of wg and en. (van den Heuvel et al., 1993) Ectopic uniform wg expression results in change in ci expression: ci expressed in those cells that are not expressing en (as in wild type), but since the en stripe is broader the ci stripe is thinner. (Noordermeer et al., 1992) Mutations in ci cause pleiotropic phenotypes in embryonic patterns and affect several longitudinal veins. (Diaz-Benjumea and Garcia-Bellido, 1990) Late ptc transcription patterns depend upon selective repression by ciD. (Hidalgo and Ingham, 1990) ve, vn, ci, cg, svs, ast, H, Vno and vvl belong to the vein phenotypic group (Puro, 1982, Droso. Info. Serv. 58:205--208) within the 'lack-of-vein' mutant class. Loss-of-function alleles at these loci remove stretches of veins in two or more longitudinal veins. Double mutations within members of this group remove all veins, have smaller, slightly lanceolate wings, no sensilla and extra chaetae. (Diaz-Benjumea et al., 1989) ci has a specific role in the control of cell fates during neurogenesis. (Patel et al., 1989) The expression of ci+ can be altered in direction of ci by certain chromosome rearrangements that have one break in vicinity of ci locus. Rearranged fourth chromosomes carrying a mutant allele of ci, R(ci), may also show altered expression of gene (Stern and Kodani, 1955). R(ci) and R(ci+) terminology not retained here; interaction with ci included in descriptions of aberrations involving chromosome 4.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079878 NM_001258472 NM_001258473 RefSeq (Proteins) • NP_524617 NP_001245401 NP_001245402 DDBJ / EMBL / GenBank • AAC47752 AAF59373 AAG15271 AAM17953 AAS87249 AC010915 AC011250 AF242878 AF433680 AFH06761 AFH06762 AY573706 BI352516 BZ286250 CAA38244 U21389 U21390 U66884 X54360 Entrez Gene - A searchable database of RefSeq genes. • 43767 UniProtKB/Swiss-Prot • P19538 UniProtKB/TrEMBL • H9XVL6 H9XVL7 Q6J8P4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, C2H2 (IPR007087) Zinc finger C2H2-type/integrase DNA-binding domain (IPR013087) Zinc finger, C2H2-like (IPR015880) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • PC00395
Linkouts
	BioGRID - A database of protein and genetic interactions • 68605 DroID - A comprehensive database of gene and protein interactions. • FBgn0004859 DRSC - Results from RNAi screens. • FBgn0004859 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004859 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2125-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004859 FlyReactome - A curated knowledgebase of Drosophila melanogaster pathways • 87341 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 43767 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /segment/cubitus.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 43767 modMine - Data generated by the modENCODE project. • FBgn0004859 REDfly - A database of transcriptional regulatory elements. • FBgn0004859 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P19538
Synonyms & Secondary IDs ( 34 )
Reported As
Symbol Synonym	Ce (Martinez Arias, 1993, Green, 1952, ) CG2125 (Ryder et al., 2004, Whitfield, 2000.9.11, Quinones-Coello, 2007, Keleman et al., 2009.8.5, Perkins et al., 2009, Ni et al., 2008, Azad et al., 2012) Ci (Casso et al., 2008, Aikin et al., 2012, Tien et al., 2008, Friggi-Grelin et al., 2008, Ma, 2005, Holmgren et al., 2005, Zhang et al., 2002, Noureddine et al., 2002, Song et al., 2000, Ziegenhorn et al., 2006, Sisson et al., 2006, Jia and Jiang, 2006, Osterlund and Kogerman, 2006, Goodman et al., 2006, Jones et al., 2006, Zhou et al., 2006, Sun and Deng, 2007, Farzan et al., 2007, Galletti et al., 2007, Bejarano et al., 2007, Smelkinson and Kalderon, 2006, Beach et al., 2006, Ference and Barolo, 2006, Panakova and Eaton, 2006, Horabin, 2005, Liu et al., 2006, Dussillol-Godar et al., 2006, Croker et al., 2006, Chotard et al., 2005, Nolo et al., 2006, Wei et al., 2005, Hogarth et al., 2005, McNeill, 2000, Chien-Hsiang et al., 2007, Fisher and Howie, 2006, Parrish et al., 2006, Bossing and Brand, 2006, Beenken and Mohammadi, 2006, Legent et al., 2012, Giuliani et al., 2007, Price et al., 2007, Ogden et al., 2006, Tountas and Fortini, 2007, Pfleger et al., 2007, Jia et al., 2005, Ayyub et al., 2005, Carroll et al., 2012, Mandal et al., 2005, Matakatsu and Blair, 2012, Chanana et al., 2007, Du et al., 2011, Wilson and Chuang, 2006, Ascano et al., 2002, Alexandre et al., 2008, Vrailas and Moses, 2006, Kugler and Nagel, 2007, Lim et al., 2005, Seong et al., 2010, Torroja et al., 2005, Zhao et al., 2007, Hime et al., 2004, Becam et al., 2011, Wang and Price, 2008, Callejo et al., 2011, Zhou and Kalderon, 2011, Zhuang et al., 2009, Zhang et al., 2009, Sánchez et al., 2008, Kechris et al., 2010, You et al., 2011, Su et al., 2011, Wang and Jiang, 2004, Callejo et al., 2006, Katanaev et al., 2008, Sun and Deng, 2007, Eugster et al., 2007, Smelkinson et al., 2007, Zhang et al., 2008, Fan and Bergmann, 2008, Gallet et al., 2008, Zhang et al., 2006, Ruel et al., 2007, Umemori et al., 2007, Walthall et al., 2007, Nagaraj and Banerjee, 2009, Mitchell et al., 2008, Ogden et al., 2008, Jia et al., 2009, Monnier et al., 2002, Dawber et al., 2005, Shen et al., 2008, Xie et al., 2005, Carrera et al., 2008, Kim et al., 2007, Shi et al., 2011, Renault et al., 2009, Ayers et al., 2009, Smith-Bolton et al., 2009, Khaliullina et al., 2009, Yan et al., 2009, Zhang et al., 2008, Baker et al., 2009, Wang et al., 2000, Sisson et al., 2006, Heriche et al., 2003, Schlichting and Dahmann, 2008, Djagaeva and Doronkin, 2009, Takashima et al., 2008, Usha and Shashidhara, 2010, Sen et al., 2010, Maurel-Zaffran et al., 2010, Zheng et al., 2010, Molnar et al., 2007, Parker et al., 2011, Cheng et al., 2010, Raisin et al., 2010, Tamori et al., 2010, Kagey et al., 2012, Yan et al., 2010, Brankatschk and Eaton, 2010, Neto-Silva et al., 2010, Farzan et al., 2009, Sánchez-Hernández et al., 2012, Terriente-Félix et al., 2011, Kim et al., 2010, Zhou and Kalderon, 2010, Wu et al., 2012, Jia et al., 2010, Kugler and Nagel, 2010, Tian et al., 2005, Chang et al., 2010, Jiang et al., 2011, Liu et al., 2011, Wojcinski et al., 2011, Yue et al., 2012, Avanesov et al., 2012, Christiansen et al., 2012, Wang et al., 2011, Poon et al., 2011, Camp et al., 2010, Cheng et al., 2012, Michaut et al., 2011, Hartman et al., 2010, Zhang et al., 2011, Singh and Mlodzik, 2012) ci (Mosimann et al., 2009, Ramos and Mohler, 2006, Ishii, 2005, Briscoe and Therond, 2005, Wehn and Campbell, 2006, Smelkinson and Kalderon, 2006, von Mering and Basler, 1999, Locke and Tartof, 1994, Orenic et al., 1987, Joshi et al., 2006, Freeland and Kuhn, 1996, Sanchez and Guerrero, 2001, Forbes et al., 1996, Kent et al., 2006, Yao et al., 2006, Wang and Struhl, 2004, Masly et al., 2006, Mandal et al., 2007, Firth and Baker, 2005, D'Costa et al., 2006, Nybakken et al., 2005, Quinones-Coello, 2007, Wendler et al., 2006, Varjosalo et al., 2006, van Steensel and Henikoff, 2000, Firth and Baker, 2005, Chaves et al., 2009, Malpel et al., 2007, Julius et al., 2009, Sato et al., 2010, Ni et al., 2008, Biehs et al., 2010, Gibert et al., 2011, Toku et al., 2011, Escudero et al., 2007, Corrigall et al., 2007, Tien et al., 2008, McDermott and Kliman, 2008, Ou et al., 2007, Weake et al., 2011, Farzan et al., 2008, Escudero and Freeman, 2007, Foronda et al., 2009, Bejarano and Milán, 2009, Noor and Kliman, 2003, Fang et al., 2009, Makhijani et al., 2007, Bejarano et al., 2007, Orme and Leevers, 2005, Prince et al., 2008, Zhang et al., 2005, Mulinari and Häcker, 2009, Ni et al., 2009, Landsberg et al., 2009, Zúñiga et al., 2009, Firth et al., 2010, Li et al., 2010, Blanco et al., 2009, González et al., 2008, Yavari et al., 2010, Pospisilik et al., 2010, Beltran et al., 2007, Subramanian and Gadgil, 2010, Pilgram et al., 2011, Suh et al., 2006, Smolik, 2010.11.15, Wasbrough et al., 2010, Watson et al., 2011, Chou et al., 2010, Jia et al., 2010, Chaves and Albert, 2008, Karim and Moore, 2011, Callejo et al., 2011, Marks and Kalderon, 2011, Azad et al., 2012, Hurtado et al., 2012, Fan et al., 2012, Sousa-Neves and Schinaman, 2012, Zhou et al., 2012) CI (Roy and Ingham, 2002, Leahy, 1999, Stoll et al., 2010, Claret et al., 2007, Pallavi and Shashidhara, 2005) ci155 (Jia et al., 2003) Ci155 (Ambrus et al., 2007, Zhang et al., 2011) Ci-155 (Zhou and Kalderon, 2010) Ci/GLI (Sanial and Plessis, 2007) Ci/Gli (Zhao et al., 2007) ciD (Cifuentes and Garcia-Bellido, 1997, DiNardo et al., 1994, van den Heuvel et al., 1993, Martinez Arias, 1993, Garcia-Bellido and de Celis, 1992, Berry et al., 1991) CiD (Perrimon, 1994) CID (von Dassow et al., 2000, Bassett et al., 1997, Lince-Faria et al., 2009, Monk et al., 2010, Strukov et al., 2011) CiD (Dearden and Akam, 2000, Klingensmith and Nusse, 1994) ciD (Vivas et al., 1999, Simmonds and Bell, 1995) ci-D (Harbecke and Lengyel, 1995, Wilkins and Gubb, 1991, Tearle and Nusslein-Volhard, 1987, ) Gli (Venema and Auld, 2005, Joulia et al., 2005, White et al., 2012) l(4)13 (Dambly-Chaudiere and Leyns, 1992, Hochman, 1976, Hochman, 1974, Hochman, 1971) l(4)17 (van Beest et al., 1998, Dambly-Chaudiere and Leyns, 1992, Orr, 1992, Hochman, 1976, Hochman, 1974, Hochman, 1971, ) l(4)102ABc   Siah (Alexandre et al., 2008)
Name Synonym	Cell   cubitis interruptus (Bejarano et al., 2007) Cubitis Interruptus (Yavari et al., 2010) Cubitus interruptus (Lee and Orr-Weaver, 2003, Goodman et al., 2006, Dahmann and Schlichting, 2007, Bejarano et al., 2007, Ference and Barolo, 2006, Panakova and Eaton, 2006, Horabin, 2005, Chien-Hsiang et al., 2007, Giuliani et al., 2007, Tountas and Fortini, 2007, Pfleger et al., 2007, Chanana et al., 2007, Du et al., 2011, Ascano et al., 2002, Vrailas and Moses, 2006, Torroja et al., 2005, Reig et al., 2007, Wang and Price, 2008, Kechris et al., 2010, Wang and Jiang, 2004, Katanaev et al., 2008, Zhang et al., 2008, Claret et al., 2007, Farzan et al., 2008, Walthall et al., 2007, Ogden et al., 2008, Monnier et al., 2002, Foronda et al., 2009, Shen et al., 2008, Carrera et al., 2008, Shi et al., 2011, Blanco et al., 2009, Mosimann et al., 2009, Baker et al., 2009, Sisson et al., 2006, Mulinari and Häcker, 2009, Schlichting and Dahmann, 2008, Djagaeva and Doronkin, 2009, Sen et al., 2010, Zheng et al., 2010, Tamori et al., 2010, Yan et al., 2010, Terriente-Félix et al., 2011, Chou et al., 2010, Kim et al., 2010, Zhou and Kalderon, 2010, Tian et al., 2005, Wang et al., 2011, Marks and Kalderon, 2011) cubitus interruptus (Schwartz, 1995.2.21, Schwartz, 1995.2.21, Fraser, 2006, Hogarth et al., 2005, Masly et al., 2006, Ogden et al., 2006, Wendler et al., 2006, van Steensel and Henikoff, 2000, Escudero et al., 2007, Takashima et al., 2008, Tien et al., 2008, Ou et al., 2007, Ni et al., 2009, Farzan et al., 2009, Chang et al., 2010, Callejo et al., 2011, Ni et al., 2008, Sousa-Neves and Schinaman, 2012) Cubitus Interruptus (Becam et al., 2011) cubitus-interruptus (Ishihara and Shibata, 2008) Cubitus-interruptus (Usha and Shashidhara, 2010) cubitus-interruptus-Dominant (Blair, 1995) cubitus-interruptus-dominant   Cubitus interuptus (Beach et al., 2006) Cubitus Interuptus (Dawber et al., 2005) cubitus interuptus (Fang et al., 2009)
Secondary FlyBase IDs
	FBgn0000314 FBgn0000315 FBgn0010154 FBgn0010155 FBgn0017411 FBgn0019831
References ( 884 )
Generate a list of	All references relating to this gene ( 884 )
List References by type	Research paper  ( 512 ) Supplementary material  ( 8 ) Review  ( 159 ) Erratum  ( 2 ) Personal communication to FlyBase  ( 12 ) Abstract  ( 171 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 2 ) Stock list  ( 1 ) Conference report  ( 3 ) Curated genome annotation  ( 3 ) Letter  ( 5 ) Protein sequence record  ( 1 ) Website  ( 1 ) Book  ( 2 )
Recent research papers ( 52 )
	Aguilar-Hidalgo et al., 2013, Development 140(1): 82--92 A Hh-driven gene network controls specification, pattern and size of the Drosophila simple eyes. [FBrf0220162] Amoyel et al., 2013, Development 140(1): 56--65 Hedgehog is required for CySC self-renewal but does not contribute to the GSC niche in the Drosophila testis. [FBrf0220178] Aikin et al., 2012, PLoS ONE 7(3): e33665 A Genome-Wide RNAi Screen Identifies Regulators of Cholesterol-Modified Hedgehog Secretion in Drosophila. [FBrf0217808] Avanesov et al., 2012, PLoS Genet. 8(2): e1002503 The Role of Glypicans in Wnt Inhibitory Factor-1 Activity and the Structural Basis of Wif1's Effects on Wnt and Hedgehog Signaling. [FBrf0217590] Azad et al., 2012, G3 (Bethesda) 2(10): 1169--1178 Identification of Genes Underlying Hypoxia Tolerance in Drosophila by a P-element Screen. [FBrf0219647] Carroll et al., 2012, Development 139(3): 612--621 The extracellular loops of Smoothened play a regulatory role in control of Hedgehog pathway activation. [FBrf0217120] Cheng et al., 2012, Development 139(1): 85--94 Drosophila G-protein-coupled receptor kinase 2 regulates cAMP-dependent Hedgehog signaling. [FBrf0216860] Christiansen et al., 2012, Mech. Dev. 129(5-8): 98--108 Ligand-independent activation of the Hedgehog pathway displays non-cell autonomous proliferation during eye development in Drosophila. [FBrf0219046] Fan et al., 2012, Dev. Biol. 366(2): 172--184 Hh-induced Smoothened conformational switch is mediated by differential phosphorylation at its C-terminal tail in a dose- and position-dependent manner. [FBrf0218374] Hurtado et al., 2012, Mol. Pharm. 9(2): 325--333 Specific Inhibition of the Transcription Factor Ci by a Cobalt(III) Schiff Base-DNA Conjugate. [FBrf0217371] Kagey et al., 2012, Mech. Dev. 129(9-12): 339--349 Regulation of Yorkie activity in Drosophila imaginal discs by the Hedgehog receptor gene patched. [FBrf0219794] Legent et al., 2012, Genetics 190(2): 601--616 A screen for x-linked mutations affecting Drosophila photoreceptor differentiation identifies casein kinase 1α as an essential negative regulator of wingless signaling. [FBrf0217484] Matakatsu and Blair, 2012, Development 139(8): 1498--1508 Separating planar cell polarity and Hippo pathway activities of the protocadherins Fat and Dachsous. [FBrf0217773] Ranieri et al., 2012, Dev. Cell 22(2): 279--294 Distinct phosphorylations on Kinesin costal-2 mediate differential hedgehog signaling strength. [FBrf0217531] Singh and Mlodzik, 2012, Dev. Cell 23(1): 82--96 Hibris, a Drosophila Nephrin Homolog, Is Required for Presenilin-Mediated Notch and APP-like Cleavages. [FBrf0218978] Sousa-Neves and Schinaman, 2012, Fly 6(1): 49--56 A novel genetic tool for clonal analysis of fourth chromosome mutations. [FBrf0218421] Sánchez-Hernández et al., 2012, Development 139(20): 3849--3858 The WIF domain of the human and Drosophila Wif-1 secreted factors confers specificity for Wnt or Hedgehog. [FBrf0219478] Vied et al., 2012, Dev. Cell 23(4): 836--848 Regulation of stem cells by intersecting gradients of long-range niche signals. [FBrf0219709] Watson and Crews, 2012, Development 139(18): 3316--3325 Formation and specification of a Drosophila dopaminergic precursor cell. [FBrf0219248] White et al., 2012, Mol. Syst. Biol. 8: 614 A model of spatially restricted transcription in opposing gradients of activators and repressors. [FBrf0219560] Wu et al., 2012, FEBS Lett. 586(22): 4052--4060 Drosophila miR-5 suppresses Hedgehog signaling by directly targeting Smoothened. [FBrf0219894] Yue et al., 2012, Dev. Cell 22(2): 255--267 The cell adhesion molecule echinoid functions as a tumor suppressor and upstream regulator of the hippo signaling pathway. [FBrf0217474] Zhou et al., 2012, PLoS Genet. 8(3): e1002593 Phenotypic plasticity of the Drosophila transcriptome. [FBrf0217974] Babcock et al., 2011, Curr. Biol. 21(18): 1525--1533 Hedgehog signaling regulates nociceptive sensitization. [FBrf0216292] Becam et al., 2011, Development 138(17): 3781--3789 Notch-mediated repression of bantam miRNA contributes to boundary formation in the Drosophila wing. [FBrf0214603] Callejo et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(31): 12591--12598 Feature Article: From the Cover: Dispatched mediates Hedgehog basolateral release to form the long-range morphogenetic gradient in the Drosophila wing disk epithelium. [FBrf0214615] Casso et al., 2011, Genetics 187(2): 485--499 A Novel Interaction Between hedgehog and Notch Promotes Proliferation at the Anterior-Posterior Organizer of the Drosophila Wing. [FBrf0212986] Du et al., 2011, PLoS ONE 6(9): e24168 In Vivo RNAi Screen Reveals Neddylation Genes as Novel Regulators of Hedgehog Signaling. [FBrf0215574] Gibert et al., 2011, PLoS Genet. 7(1): e1001280 Segregating Variation in the Polycomb Group Gene cramped Alters the Effect of Temperature on Multiple Traits. [FBrf0212864] Jiang et al., 2011, Oncogene 30(29): 3248--3260 Sds22/PP1 links epithelial integrity and tumor suppression via regulation of myosin II and JNK signaling. [FBrf0214488] Karim and Moore, 2011, J. Neurosci. 31(47): 17017--17027 Convergent local identity and topographic projection of sensory neurons. [FBrf0216770] Liu et al., 2011, Dev. Growth Differ. 53(6): 822--841 Negative modulation of bone morphogenetic protein signaling by Dullard during wing vein formation in Drosophila. [FBrf0214664] Marks and Kalderon, 2011, Development 138(12): 2533--2542 Regulation of mammalian Gli proteins by Costal 2 and PKA in Drosophila reveals Hedgehog pathway conservation. [FBrf0213757] Michaut et al., 2011, Dev. Growth Differ. 53(9): 982--993 Analyzing the function of a hox gene: An evolutionary approach. [FBrf0216990] Mondal et al., 2011, Cell 147(7): 1589--1600 Interaction between Differentiating Cell- and Niche-Derived Signals in Hematopoietic Progenitor Maintenance. [FBrf0217084] Parker et al., 2011, Sci. Signal. 4(176): ra38 The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity. [FBrf0213871] Pilgram et al., 2011, J. Neurosci. 31(2): 492--500 The RhoGAP crossveinless-c Interacts with Dystrophin and Is Required for Synaptic Homeostasis at the Drosophila Neuromuscular Junction. [FBrf0212767] Poon et al., 2011, Dev. Cell 21(5): 896--906 The Sterile 20-like Kinase Tao-1 Controls Tissue Growth by Regulating the Salvador-Warts-Hippo Pathway. [FBrf0216620] Quan et al., 2011, Nat. Biotechnol. 29(5): 449--452 Parallel on-chip gene synthesis and application to optimization of protein expression. [FBrf0213642] Shi et al., 2011, Development 138(19): 4219--4231 The Hedgehog-induced Smoothened conformational switch assembles a signaling complex that activates Fused by promoting its dimerization and phosphorylation. [FBrf0216910] Strukov et al., 2011, PLoS Biol. 9(1): e1000574 Evidence of Activity-Specific, Radial Organization of Mitotic Chromosomes in Drosophila. [FBrf0212852] Su et al., 2011, Sci. Signal. 4(180): ra43 Sequential phosphorylation of smoothened transduces graded hedgehog signaling. [FBrf0216577] Swarup and Verheyen, 2011, Proc. Natl. Acad. Sci. U.S.A. 108(24): 9887--9892 Drosophila homeodomain-interacting protein kinase inhibits the Skp1-Cul1-F-box E3 ligase complex to dually promote Wingless and Hedgehog signaling. [FBrf0214241] Terriente-Félix et al., 2011, Dev. Biol. 350(2): 382--392 A conserved function of the chromatin ATPase Kismet in the regulation of hedgehog expression. [FBrf0212899] Toku et al., 2011, Comput. Biol. Chem. 35(5): 282--292 Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster. [FBrf0216393] Wang et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(27): 11139--11144 Sexually dimorphic regulation of the Wingless morphogen controls sex-specific segment number in Drosophila. [FBrf0214239] 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] 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] Wojcinski et al., 2011, Dev. Biol. 358(1): 168--180 DSulfatase-1 fine-tunes Hedgehog patterning activity through a novel regulatory feedback loop. [FBrf0215253] You et al., 2011, Dev. Dyn. 240(3): 640--648 Sulfated is a negative feedback regulator of wingless in Drosophila. [FBrf0213052] Zhang et al., 2011, Cell Res. 21(10): 1436--1451 Transduction of the Hedgehog signal through the dimerization of Fused and the nuclear translocation of Cubitus interruptus. [FBrf0217260] Zhou and Kalderon, 2011, Dev. Cell 20(6): 802--814 Hedgehog activates fused through phosphorylation to elicit a full spectrum of pathway responses. [FBrf0214655] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...