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Gene Dmel\lt

General Information
Symbol	Dmel\lt	Species	D. melanogaster
Name	light	Annotation symbol	CG18028
Feature type	protein_coding_gene	FlyBase ID	FBgn0002566
Gene Model Status	Current	Stock availability	54 publicly available
Genomic Location
Chromosome (arm)	2L	Recombination map	2-55.0
Cytogenetic map		Sequence location	2L:22,811,944..22,834,955 [+]
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 light is referred to in FlyBase by the symbol Dmel\lt (CG18028, FBgn0002566). It is a protein_coding_gene from Drosophila melanogaster. An electronic pipeline based on InterPro domains suggests that it has the molecular function: zinc ion binding. There is experimental evidence that it is involved in the biological process: Notch receptor processing; dsRNA transport; endocytosis; determination of adult lifespan; ommochrome biosynthetic process. 50 alleles are reported. The phenotypes of these alleles are annotated with: eye; Malpighian tubule; wing; ocellus pigment granule; pigment cell. It has 5 annotated transcripts and 5 annotated polypeptides. Protein features are: Clathrin, heavy chain/VPS, 7-fold repeat; Tetratricopeptide-like helical; Vacuolar protein sorting-associated protein 41; WD40 repeat; WD40-repeat-containing domain; WD40/YVTN repeat-like-containing domain; Zinc finger, RING-type. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, during late larval stages, at stages throughout the pupal period. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male reproductive system, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1631509_a_at completely aligns to an exonic region common to each of the 3 FlyBase-annotated transcript isoforms of lt. Gene sequence location is 2L:22811944..22834955.
User Contributed Data
	Beta version, feedback welcome
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	lt: light Eye color yellowish pink-lighter at high temperature, darker at low. Ocelli colorless; Drosopterins drastically reduced; no maternal effect on eye pigmentation (Nickla, 1972, Can. J. Genet. Cytol. 14: 105-11). When combined with st, eye color only slightly lighter than with lt alone; with bw it is clear yellow, pinkish in old flies (Schultz and Dobzhansky, 1934, Genetics 19: 344-64; Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Eye color autonomous in mutant optic discs transplanted into wild-type hosts (Beadle and Ephrussi, 1936, Genetics 21: 230). Larval Malphighian tubes colorless in lt offspring of lt mothers; some color in tubes if mother is lt/+. The quantity of yellow pigment, composed primarily of riboflavin, in Malpighian tubes exhibits parallel maternal effects in larvae, pupae, and adults (Nickla, 1972, Can. J. Genet. Cytol. 14: 391-96); the amount of such pigment increases with maternal age for both lt/+ and lt/lt parental females (Nickla, 1973, Can. J. Genet. Cytol. 15: 437-42). lt stw homozygotes completely inviable (Purdom); however, lt stw3 homozygotes have good viability. car lt double mutants are also invariably lethal; the time of death varying from the third larval instar to late pupa, depending on the number of normal alleles of either gene carried by the mother (Nickla, 1977, Nature 268: 638-339). Lethal focus of the lethal interaction as measured in car/+; lt/lt, car/0; lt/lt gynandromorphs is in ventral nervous tissue (Nickla, Lilly, and Brown, 1980, Experientia 36: 402-03); larval brain histologically abnormal (McCarthy and Nickla, 1980, Experientia 36: 1361-62). ltv: light variegated
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location
Experimentally Determined Cytological Location
Cytogenetic map Notes References 40E-40F   (determined by in situ hybridisation)   (Koryakov et al., 1996) 40F-40F   (determined by in situ hybridisation)   (Devlin et al., 1990)   Relative order with respect to l(2)40Fc and l(2)40Fd is unknown.   (Hilliker, 1976)
Experimentally Determined Recombination Data
Location	2-55.0 (Meyer et al., 1950)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\lt 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 5.46 Low-frequency RNA-Seq exon junction(s) not annotated.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) lt-RA FBtr0111125  NM_001042951   2804   841 lt-RB FBtr0111124  NM_001042950   2799   804 lt-RC FBtr0111123  NM_001042952   2760   528 lt-RD FBtr0333518  NM_001273765   2784   804 lt-RE FBtr0333519  NM_001273766   4404   841
Additional Transcript Data & Comments
Reported size (kB)	3.6, 3.2 (northern blot) (Devlin et al., 1990) 3.3, 3.0 (northern blot) (Warner et al., 1998)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein lt-PA   FBpp0110417   96.9   841   6.88     NP_001036416   EAA46034 lt-PB   FBpp0110416   92.6   804   7.00     NP_001036415   EAA46035 lt-PC   FBpp0110415   61.5   528   5.96     NP_001036417   EAL24548 lt-PD   FBpp0305698   92.6   804   7.00     NP_001260694   AGB93229 lt-PE   FBpp0305699   96.9   841   6.88     NP_001260695   AGB93230
Additional Polypeptide Data & Comments
Reported size (kDa)	841 (aa) (Warner et al., 1998)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • WD40/YVTN repeat-like-containing domain (IPR015943) WD40-repeat-containing domain (IPR017986) Clathrin, heavy chain/VPS, 7-fold repeat (IPR000547) WD40 repeat (IPR001680) Zinc finger, RING-type (IPR001841) Vacuolar protein sorting-associated protein 41 (IPR016902) Tetratricopeptide-like helical (IPR011990)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA202040   AABU01002768 EAA46034   AABU01002768 EAA46035   AF034571   AE014134 AGB93229   AE014134 AGB93230   AI944437   AI944824   AY118388 AAM48417   BF505979   BI163992   BI168587   BI172742   BI231199   BI238393   BI239022   BI239487   BI240252   BI240671   BI240989   BI364022   BI365583   BI366163   BI578193   BI579466   BT023508   BT024228   CA805139   CA806767   CK658066   CO154007   CO265903   CO266633   CO281879   CO284889   CO298887   CO315826   CO317086   CO323850   CO324425   CO325075   CO332706   CO342979   CO345169   CO345224   AE014134 EAA46034   AE014134 EAA46035   AE014134 EAL24548   EC060702   EC074701   EC074783   EC077797   EC083589   EC086370   EC089302   EC198937   EC210109   EC210399   EC211078   EC216643   EC217945   EC222740   EC250049   EC250163   EC253718   EC255216   EC257301   ES691745   GH941491   GH942029   GH943402   GH943985   GH946124   GH946871   GH947094   GH947124   GH947239   GH947651   GH950605   GH950769   GH950864   GH954852   GH955166   GH956497   GH956770   GH957390   GH957914   GH958495   GH958690   GH959384   GH960201   GH961742   GH962343   GH963866   GH966813   GH967833   GH969511   GH969724   GH969833   GH969880   GH971658   GH972279   GH974461   GH974594   GH974833   GH975007   GH975382   GH976171   GH976420   GH977798   GH977822   GH977843   GH977889   GH978084   GH979115   GH979252   GH979365   GH980878   GH981127   GH981256   GH981363   GH981445   GH982745   GH983606   GH984842
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q7PL76 Q7PL77 Q8MT46 O76248
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism | ubiquitous   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism | ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   organism | ubiquitous   (Fisher et al., 2012) embryonic stage 9 -- 10   organism | ubiquitous   (Fisher et al., 2012) yolk nucleus   (Fisher et al., 2012) embryonic stage 11 -- 12   organism | faint & ubiquitous   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) yolk nucleus   (Fisher et al., 2012) embryonic stage 13 -- 16   organism | faint & ubiquitous   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) yolk nucleus   (Fisher et al., 2012) third instar larval stage   embryonic/larval brain   (Weiler and Wakimoto, 1998) embryonic/larval circulatory system   (Weiler and Wakimoto, 1998) embryonic/larval digestive system   (Weiler and Wakimoto, 1998) embryonic/larval fat body   (Weiler and Wakimoto, 1998) Malpighian tubule   (Weiler and Wakimoto, 1998) imaginal disc   (Weiler and Wakimoto, 1998) gonad   (Weiler and Wakimoto, 1998) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage   organism | ubiquitous   (Warner et al., 1998)   (Warner et al., 1998) embryonic stage -- adult stage     (Devlin et al., 1990) larval stage   Malpighian tubule   (Devlin et al., 1990) imaginal disc   (Devlin et al., 1990) embryonic/larval brain   (Devlin et al., 1990) embryonic/larval salivary gland   (Devlin et al., 1990) embryonic/larval fat body   (Devlin et al., 1990) embryonic/larval digestive system   (Devlin et al., 1990) adult stage | female   ovary   (Devlin et al., 1990) unfertilized egg stage   unfertilized egg | ubiquitous   (Warner et al., 1998) unfertilized egg   (Warner et al., 1998)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male reproductive system, 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    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    336.5 Larval Midgut    204.1 Larval Hindgut    279.9 Larval Malpighian Tubules    253.4 Larval Fat Body    302.1 Larval Salivary Gland    404.8 Larval Trachea    366.1 Larval Carcass    322.4 Adult Head    283.1 Adult Eye    211.575 Adult Brain    396.5 Adult Thoracic-Abdominal Ganglion    429.4 Adult Crop    406.9 Adult Midgut    249.8 Adult Hindgut    343.3 Adult Malpighian Tubules    178.9 Adult Fat Body    200.4 Adult Salivary Gland    493.7 Adult Heart    211.925 Adult VirginFemale Spermatheca    226.9 Adult InseminatedFemale Spermatheca    245.9 Adult Ovary    309.9 Adult Testis    121.9 Adult Male Accessory Gland    370.6 Adult Carcass    301.7 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    283.1   NA  Eye    211.575   NA  Brain    396.5   336.5  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    429.4   NA  Crop    406.9   204.1  Midgut    249.8   279.9  Hindgut    343.3   253.4  Malpighian Tubules    178.9   302.1  Fat Body    200.4   404.8  Salivary Gland    493.7   NA  Heart    211.925   366.1  Trachea    NA   NA  VirginFemale Spermatheca    226.9   NA  InseminatedFemale Spermatheca    245.9   NA  Ovary    309.9   NA  Testis    121.9   NA  Male Accessory Gland    370.6   322.4  Carcass    301.7 FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 accessory gland, mated 4-day male    3 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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    8 central nervous system, larvae L3    9 central nervous system, pupae P8    12 head, virgin 1-day female    7 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    5 head, mated 4-day female    5 head, mated 20-day female    5 head, mated 1-day male    8 head, mated 4-day male    9 head, mated 20-day male    10 salivary gland, larvae L3 wandering    4 salivary gland, white prepupae    7 digestive system, larvae L3 wandering    6 digestive system, 1-day adult    4 digestive system, 4-day adult    4 digestive system, 20-day adult    4 fat body, larvae L3 wandering    2 fat body, white prepupae    5 fat body, pupae P8    6 carcass, larvae L3 wandering    6 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    15 ovary, mated 4-day female    9 testis, mated 4-day male    3 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 moderately high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, during late larval stages, at stages throughout the pupal period. [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    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 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    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 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    11 embryo 02-04hr    15 embryo 04-06hr    17 embryo 06-08hr    13 embryo 08-10hr    19 embryo 10-12hr    13 embryo 12-14hr    24 embryo 14-16hr    7 embryo 16-18hr    13 embryo 18-20hr    7 embryo 20-22hr    11 embryo 22-24hr    17 larva L1    6 larva L2    7 larva L3 12hr old    6 larva L3 puffstage 1-2    7 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    16 white prepupae new    13 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    13 pupae 3d postWPP    10 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    7 adult male 30day    6 adult female 01day    5 adult female 05day    10 adult female 30day    9 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+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (36) Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2  (51) embryonic Kc167    22 embryonic S1  26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11  (27) antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2  (32) ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 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+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (36) Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2  (51) embryonic Kc167    22 embryonic S1  26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11  27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2  32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 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+    36 Schneider line 2 Sg4    11 embryonic 1182-4H    9 embryonic GM2    51 embryonic Kc167    22 embryonic S1    26 embryonic S3    22 leg disc CME L1    8 wing disc CME-W2    23 wing disc ML-DmD8    15 wing disc ML-DmD9    8 wing disc ML-DmD16-c3    10 wing disc ML-DmD21    10 wing disc ML-DmD32    9 haltere disc ML-DmD17-c3    19 eye-antennal disc ML-DmD11    27 antennal disc ML-DmD20-c5    17 mixed discs ML-DmD4-c1    8 CNS ML-DmBG1-c1    13 CNS ML-DmBG2-c2    20 tumorous blood cells mbn2    32 ovary fGS/OSS    9 ovary OSC    11 ovary OSS    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    12 Cadmium 50 mM 48 hrs, 4-day adult    6 Cadmium 100 mM 48 hrs, 4-day adult    8 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    9 Zinc 5 mM 12 hrs, larvae L3    2 Zinc 4.5 mM 48 hrs, 4-day adult    7 Ethanol 2.5% 3 hrs, larvae L3    5 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    10 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    9 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    9 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_05 mE1_20_mRNA_expression_cluster_09
External Data & Images
Linkouts	BDGP expression data • RE35406 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002566 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18028-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal lt5 lt11 lt12 lt13 lthdS2 ltX84 lethal | dominant lt11 lethal | partially | recessive lt20 lethal | pupal stage | recessive lt12 lt13 lethal | recessive lt21 lthd3f lthd3m lthd4v ltIR1 ltIR2 viable lt1 lt56c Sterility Allele sterile | recessive lt4 Other Phenotypes Allele enhancer of variegation, with Su(var)2055/Su(var)205205 ltunspecified eye color defective lt1 lthdS1 lthdS1A lthdS1Y ltpk ltunspecified eye color defective | recessive lt1 lt11 short lived | male lt1 suppressor of variegation (with In(2L)ltX2), with E(var)3-93 lt1 suppressor of variegation | dominant (with In(2L)ltX2), with E(var)3-91 lt1 suppressor of variegation | dominant (with In(2L)ltX2), with E(var)3-92 lt1 visible lt6 lt7 lt8 lt9 lt10 visible | recessive ltunspecified wild-type lttDa lttDb lttDc lttDd Phenotype manifest in Allele eye ltunspecified Malpighian tubule lt1 lt3 ocellus pigment granule lt1 pigment cell lt1 lt11 lthdS1 lthdS1A lthdS1Y ltpk ltunspecified wing ltpk
Classical Alleles ( 41 )
For All Classical Alleles Show
Allele of lt Class Mutagen Stocks Known lesion lt1 hypomorphic allele - genetic evidence spontaneous 21 Yes ltv 20 -- lt16 ethyl methanesulfonate 8 -- lt3 spontaneous 5 -- lt11 amorphic allele - genetic evidence, hypomorphic allele - genetic evidence ethyl methanesulfonate 1 -- lt10 ethyl methanesulfonate 0 -- lt12 ethyl methanesulfonate 0 -- lt13 ethyl methanesulfonate 0 -- lt14 P-element activity 0 Yes lt15 P-element activity 0 Yes lt17 X ray 0 -- lt18 X ray 0 -- lt19 spontaneous 0 -- lt20 P-element activity PM hybrid dysgenesis 0 Yes lt21 P-element activity PM hybrid dysgenesis 0 Yes lt2 spontaneous 0 -- lt4 U.V. 0 -- lt56c spontaneous 0 -- lt5 U.V. 0 -- lt6 ethyl methanesulfonate 0 -- lt7 ethyl methanesulfonate 0 -- lt8 ethyl methanesulfonate 0 -- lt9 ethyl methanesulfonate 0 -- lthd3f PM hybrid dysgenesis 0 -- lthd3m PM hybrid dysgenesis 0 -- lthd4v PM hybrid dysgenesis 0 -- lthd5 PM hybrid dysgenesis 0 -- lthd7v PM hybrid dysgenesis 0 -- lthdS1 PM hybrid dysgenesis 0 Yes lthdS1A+R1 P-element activity 0 Yes lthdS1A+R2 P-element activity 0 Yes lthdS1A PM hybrid dysgenesis 0 Yes lthdS1B PM hybrid dysgenesis 0 -- lthdS1Y P-element activity 0 Yes lthdS2 PM hybrid dysgenesis 0 -- ltIR1 IR-hybrid dysgenesis 0 -- ltIR2 IR-hybrid dysgenesis 0 -- ltpk spontaneous 0 -- ltunspecified 0 -- ltX84 hypomorphic allele - genetic evidence X ray 0 Yes ltX99 hypomorphic allele - genetic evidence X ray 0 --
Alleles Carried on Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Allele of lt Class Mutagen Stocks Known lesion ltHMS00190 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes lt+tCH321-64G01 in vitro construct - genomic fragment 0 Yes lttCH321-05E14 in vitro construct - genomic fragment 0 Yes lttCH321-16H04 in vitro construct - genomic fragment 0 Yes lttDa in vitro construct - genomic fragment 0 Yes lttDb in vitro construct - genomic fragment 0 Yes lttDc in vitro construct - genomic fragment 0 Yes lttDd in vitro construct - genomic fragment 0 Yes lttDe in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Duplicated in	C(2R)RM-VK2   Dp(2;Y)Sd (Temin, 1991)
Not disrupted in	Df(2L)061b (Siegel, 1981) Df(2L)D (Hilliker and Holm, 1975, Hilliker, 1976, Ganetzky, 1977, Cicchetti and Loverre, 1989) Df(2L)D' (Hilliker and Holm, 1975, Hilliker, 1976, Ganetzky, 1977, Cicchetti and Loverre, 1989) Df(2L)E55 (Wright et al., 1976) Df(2L)E71 (Wright et al., 1976, Ganetzky, 1977) Df(2L)F (Hilliker and Holm, 1975, Hilliker, 1976, Ganetzky, 1977) Df(2L)H   Df(2L)L138D-81 (Siegel, 1981) Df(2L)L138D-C2 (Siegel, 1981) Df(2L)L138D-C15 (Siegel, 1981) Df(2L)L138D-FB15 (Siegel, 1981) Df(2L)L138D-X1 (Siegel, 1981) Df(2L)L138D-X14 (Siegel, 1981) Df(2L)L138D-XR (Siegel, 1981) Df(2L)pr-A8 (Ganetzky, 1977) Df(2L)pr-A14 (Ganetzky, 1977) Df(2L)pr-A16 (Ganetzky, 1977) Df(2L)pr-A20 (Ganetzky, 1977) Df(2L)pr-B12 (Ganetzky, 1977) Df(2L)Sd37 (Ganetzky, 1977) Df(2L)TW1 (Wright et al., 1976) Df(2L)TW2 (Wright et al., 1976) Df(2L)TW3 (Wright et al., 1976) Df(2L)TW9 (Wright et al., 1976) Df(2L)TW12 (Wright et al., 1976, Siegel, 1981) Df(2L)TW50 (Wright et al., 1976) Df(2L)TW65 (Wright et al., 1976, Ganetzky, 1977, Siegel, 1981, Cicchetti and Loverre, 1989) Df(2L)TW84 (Wright et al., 1976, Siegel, 1981) Df(2L)TW119 (Wright et al., 1976) Df(2L)TW130 (Wright et al., 1976) Df(2L)TW137 (Wright et al., 1976) Df(2L)TW150 (Wright et al., 1976) Df(2L)TW158 (Wright et al., 1976, Ganetzky, 1977) Df(2L)TW161 (Wright et al., 1976, Ganetzky, 1977, Siegel, 1981, Cicchetti and Loverre, 1989) Df(2R)B (Hilliker and Holm, 1975) Df(2R)M41A4 (Hilliker and Holm, 1975, Cicchetti and Loverre, 1989) Df(2R)M41A8 (Hilliker and Holm, 1975, Cicchetti and Loverre, 1989) Df(2R)M41A10 (Hilliker and Holm, 1975, Cicchetti and Loverre, 1989) Df(2R)rl-D (Hilliker and Holm, 1975, Cicchetti and Loverre, 1989) Dp(2;Y)H1 (Hodgetts, 1980) Dp(2;Y)H2 (Hodgetts, 1980) In(2R)bwVDe2LCyR (Cicchetti and Loverre, 1989)
Not duplicated in	C(2R)RM-P4   Dp(2;Y)H
Disrupted in	Ab(2R)IR36 (Dimitri et al., 1997) Df(2L)C (Hilliker and Holm, 1975, Hilliker, 1976, Ganetzky, 1977, Cicchetti and Loverre, 1989) Df(2L)C' (Hilliker, 1976, Ganetzky, 1977, Cicchetti and Loverre, 1989, Dimitri, 1991, Russell and Kaiser, 1994) Df(2L)E(SD)1 (Ganetzky, 1977, Temin, 1991) Df(2L)E(SD)3 (Ganetzky, 1977, Temin, 1991) Df(2L)E(SD)36 (Ganetzky, 1977, Temin, 1991) Df(2L)lt1 (Temin, 1991, Dimitri, 1991, Russell and Kaiser, 1994) Df(2L)lt5 (Temin, 1991, Dimitri, 1991, Russell and Kaiser, 1994) Df(2L)lt8 (Temin, 1991, Dimitri, 1991, Russell and Kaiser, 1994) Df(2L)lt8a (Sharp et al., 1985) Df(2L)lt10 (Weiler and Wakimoto, 1998, Wakimoto and Hearn, 1990) Df(2L)lt23 (Temin, 1991) Df(2L)lt28 (Wakimoto and Hearn, 1990) Df(2L)lt45 (Sharp et al., 1985, Wakimoto, 2008.11.19) Df(2L)lt47 (Sharp et al., 1985) Df(2L)lt59 (Temin, 1991) Df(2L)lt61 (Sharp et al., 1985) Df(2L)lt64 (Wakimoto and Hearn, 1990) Df(2L)lt73 (Temin, 1991) Df(2L)lt105 (Wakimoto and Hearn, 1990, Russell and Kaiser, 1994) Df(2L)lt109 (Wakimoto, 2008.11.19) Df(2L)lt120 (Wakimoto and Hearn, 1990) Df(2L)lt121 (Wakimoto, 2008.11.19) Df(2L)lt329 (Wakimoto and Hearn, 1990) Df(2L)lthd6 (Devlin et al., 1990) Df(2L)ltx5 (Palopoli and Wu, 1996) Dp(2;Y)H3 (Hodgetts, 1980) T(2;3)ClassII (Howe et al., 1995) T(2;3)EHH (Hilliker and Holm, 1975)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{TRiP.HMS00190} NA characterization construct PBac{CH321-05E14} NA PBac{CH321-16H04} NA PBac{CH321-64G01} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{}lt15 NA P{}lt20 NA P{}lt21 NA P{}lthdS1 NA P{}lthdS1A NA P{}lthdS1Y NA
Gene Ontology: Function, Process & Cellular Component ( 11 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
determination of adult lifespan inferred from mutant phenotype (Simonsen et al., 2007) dsRNA transport inferred from mutant phenotype (Saleh et al., 2006) endocytosis inferred from mutant phenotype (Wilkin et al., 2008) Notch receptor processing inferred from mutant phenotype (Wilkin et al., 2008) ommochrome biosynthetic process inferred from mutant phenotype (Tearle, 1991)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term Evidence References
zinc ion binding inferred from electronic annotation with InterPro:IPR001841 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
eye pigment biosynthetic process non-traceable author statement (Warner, 1997.11.13) intracellular protein transport inferred from electronic annotation with InterPro:IPR000547 (FlyBase Curators et al., 2004-) intracellular transport traceable author statement (Narayanan and Ramaswami, 2001) lysosomal transport traceable author statement (Luzio et al., 2000) vacuole organization non-traceable author statement (Warner, 1997.11.13)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions lt allele Gene References lt1 car (Nickla et al., 1980, Warner et al., 1998) dor (Warner et al., 1998) g (Warner et al., 1998) lt11 car (Warner et al., 1998) dor (Warner et al., 1998) g (Warner et al., 1998) ltunspecified w (Lloyd et al., 2002) unspecified Su(var)3-7 (Delattre et al., 2000)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 78255 DroID - A comprehensive database of gene and protein interactions. • FBgn0002566 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 3355130 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • O76248
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 EOG6B8JZF Dipteran inclusive ortholog search EOG62BXHM Insect inclusive ortholog search EOG6T4BQD Arthropod inclusive ortholog search EOG64F4R3 Metazoa inclusive ortholog search EOG680WPH
Orthologs in Drosophila Species (EOG6B8JZF)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\lt     Drosophila sechellia   Dsec\GM26693     Drosophila erecta   Dere\GG21404     Drosophila yakuba   Dyak\GE14043     Drosophila ananassae   Dana\GF22734     Drosophila pseudoobscura pseudoobscura   Dpse\GA29085     Drosophila persimilis   Dper\GL21142     Drosophila willistoni   Dwil\GK24377     Drosophila virilis   Dvir\GJ13125     Drosophila mojavensis   Dmoj\GI11759     Drosophila grimshawi   Dgri\GH13627
Orthologs in non-Drosophila Dipterans (EOG62BXHM)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001157   Anopheles gambiae Malaria mosquito  Agam\AGAP009174   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ010406
Orthologs in non-Dipteran Insects (EOG6T4BQD)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\lt   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG004760   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH25407   Atta cephalotes Leafcutter ant  Acep\ACEP18304   Camponotus floridanus Florida carpenter ant  Cflo\CFLO15342   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL16936   Linepithema humile Argentine ant  Lhum\LH11640   Pogonomyrmex barbatus Red harvester ant  Pbar\PB17050   Solenopsis invicta Red fire ant  Sinv\SINV17117   Acyrthosiphon pisum Pea aphid  Apim\ACYPI008427   Bombyx mori Silkmoth  Bmor\BGIBMGA005526   Pediculus humanus Human body louse  Phum\PHUM253950   Tribolium castaneum Red flour beetle  Tcas\GLEAN_15204
Orthologs in non-Insect Arthropods (EOG64F4R3)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\Polr2m   Ixodes scapularis Deer tick  Isca\ISCW017822
Orthologs in non-Arthropod Metazoa (EOG680WPH)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\F32A6.3   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_026979gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_000548gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_026978gn   Danio rerio Zebrafish  Drer\si:ch211-146l10.2   Xenopus tropicalis Western clawed frog  Xtro\vps41   Gallus gallus Domestic chicken  Ggal\VPS41   Mus musculus House mouse  Mmus\Vps41   Rattus norvegicus Norway rat  Rnor\Vps41   Homo sapiens Human  Hsap\VPS41
Human Orthologs (1)
Gene OMIM HGNC Hsap\VPS41
AAA Orthologs (0) based on analysis using Dmel annotation version 4.3
No orthologs identified
Stocks & Reagents
Stocks Listed in FlyBase ( 54 )
Bloomington	1592 lt3/SM5 1051 lt1 rl1 26190 l(2)40Fc1/SM1, lt16 26191 l(2)40Fg1/SM1, lt16 26192 l(2)40Fd2/SM1, lt16 26194 l(2)40Fa2/SM1, lt16 1056 lt1 rl1 stw3 26187 Df(2L)lt45, Bc1/SM1, lt16
Kyoto	103333 lt1 ; T(Y;2)A 101540 lt1 bw1 106184 lt1 rl1 106187 lt1 rl1 stw3
	More stocks available...
Genomic Clones ( 2 )
	BACR07M22 BACR20C06 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 115 )
	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	LD14863 LD33620 RE35406
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	14423 15286 19171 33679 35300 50504 51407 64939 65990 67432 157980 159595 165742 172674 214215.3 214339.16 214417.13 277273 AT08322 bs01d07 bs05h03 CK01.35C.D8 EK144414 EK147102 EK159012 EK167359 EK174041 EK191655 EK193637 EK195529 EK262633 EK267101 EK304322 EN03302 EP15849 EP21516 EP21640 ESG014d.E21_G09 ESG0116c.B21_G12 LD03646 LP14603 RE03543 RE09385 RE15413 RE20430 RE34821 RE35975 RE36953 RE37573 RE37958 RE49049 RE50943 RE51638 RE72026 RE73503 RP004000527 RP004026481 RP004031806 RP004047450 RP004059818 RP004072176 RP004077903 RP004102188 RP004107451 RP004164785 RP004167960 RP004173094 RP004206435 RP004208018 RP004211739 RP004212417 RP004213016 RP004215746 RP004217685 RP004224786 RP004231794 RP004232268 RP004232911 RP004235671 RP004236214 RP004243907 RP004251071 RP004251104 RP004252673 RP004253515 RP004260109 RP004264202 RP004266612 RP004274600 RP004276279 RP004277337 RP004277629 RP004319850 RP004325615 RP004344825 RP004351879 RP004355838 RP004359953 RP004363116 RP004399848 RP004408862 RP004434173 RP004435239 RP004436940 RP004440954 RP004462251 RP004475587 RP004510412 RP004526277 RP004532102 RP004548089 RP004551316
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0002566 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 3355130
Antibody Information
	polyclonal (Swetha et al., 2011)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: lt CG18028 (Misra, 2000.4.8)
Additional comments	'Light mottled' lt alleles are a series of X-ray induced light-variegated chromosome rearrangements. Some have a mixture of light and wild-type ommatidia and are classified as pale; others have a mixture of wild-type and occasional darker ommatidia and are classified as dark.
Other Comments
	dsRNA made from templates generated with primers directed against lt that is transfected into S2 treated with Listeria monocytogenes reveals lt to be involved in Listeria monocytogenes intracellular growth. (Cheng et al., 2005) Variegation of lt and cta is manifest at phenotypic and gene expression levels in the adult eye, and the larval salivary glands and Malpighian tubules. The relative severity of the effect correlates with the chromosomal rearrangement. Larval imaginal discs do not display variegation, but show uniform reduction of transcription, which correlates in magnitude with the degree of variegation. (Weiler and Wakimoto, 1998) Mapping and complementation data of Class IV derivatives of the T(2;3)ltX13, P{wF} chromosome suggest that the amount of heterochromatin in cis to the lt gene is correlated with its level of activity. Chromosomes that carry the smallest deletion of heterochromatin have weaker effects on the lt+ gene when compared to those with the largest deletions. (Howe et al., 1995) Lesions in lt reduce or eliminate pigmentation in the eyes and ocelli and block pigmentation of the fat body and tubules: lt is required for normal pigmentation of all four tissues. (Tearle, 1991)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_001042950 NM_001042951 NM_001042952 NM_001273765 NM_001273766 RefSeq (Proteins) • NP_001036415 NP_001036416 NP_001036417 NP_001260694 NP_001260695 DDBJ / EMBL / GenBank • AABU01002768 AAC26488 AAM48417 AF034571 AGB93229 AGB93230 AI944437 AI944824 AY118388 BI239022 EAA46034 EAA46035 EAL24548 Entrez Gene - A searchable database of RefSeq genes. • 3355130 UniProtKB/TrEMBL • O76248 Q7PL76 Q7PL77 Q8MT46
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • WD40/YVTN repeat-like-containing domain (IPR015943) WD40-repeat-containing domain (IPR017986) Clathrin, heavy chain/VPS, 7-fold repeat (IPR000547) WD40 repeat (IPR001680) Zinc finger, RING-type (IPR001841) Vacuolar protein sorting-associated protein 41 (IPR016902) Tetratricopeptide-like helical (IPR011990) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE35406
Linkouts
	BioGRID - A database of protein and genetic interactions • 78255 DroID - A comprehensive database of gene and protein interactions. • FBgn0002566 DRSC - Results from RNAi screens. • FBgn0002566 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002566 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18028-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0002566 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 3355130 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 3355130 modMine - Data generated by the modENCODE project. • FBgn0002566 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • O76248
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	CG18028 (Saleh et al., 2006, Ni et al., 2011.7.19, Ying et al., 2011) Dm-lt(het) (Yasuhara et al., 2005) l(2)40Fb (Dimitri et al., 1997, ) lt (Falcon-Perez et al., 2007, Weiler, 2007, de Wit et al., 2007, Swetha et al., 2011, Yasuhara and Wakimoto, 2008, Wakimoto, 2008.11.19, Wilkin et al., 2008, Lu et al., 2009, Chinchore et al., 2009, Venken et al., 2009, Paredes and Maggert, 2009, Venken et al., 2009, Cherry and Perrimon, 2004, de Wit et al., 2005, Lemos et al., 2010, Ashton-Beaucage et al., 2010, Lin et al., 2012) Lt (Ying et al., 2011)
Name Synonym	light (Falcon-Perez et al., 2007, Schaeffer et al., 2008, Warner, 1997.11.13, Yasuhara and Wakimoto, 2006, Rossi et al., 2007, Simonsen et al., 2007, Dimitri et al., 2003, Li et al., 2002, de Wit et al., 2007, Swetha et al., 2011, Yasuhara and Wakimoto, 2008, Wilkin et al., 2008, Dimitri et al., 2003, Lu et al., 2009, Saleh et al., 2006, Fanti et al., 2008, Chinchore et al., 2009, Yasuhara et al., 2003, Paredes and Maggert, 2009, Cherry and Perrimon, 2004, Huang et al., 2010, Lemos et al., 2010, Roignant and Treisman, 2010, Zhang et al., 2011, Klenov et al., 2011) pinkoid   pink-wing
Secondary FlyBase IDs
	FBan0018028 FBgn0032992
References ( 156 )
Generate a list of	All references relating to this gene ( 156 )
List References by type	Research paper  ( 92 ) Supplementary material  ( 5 ) Review  ( 32 ) Personal communication to FlyBase  ( 9 ) Abstract  ( 9 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Website  ( 1 ) Book  ( 2 ) Curated genome annotation  ( 1 ) Conference report  ( 2 ) Stock list  ( 1 )
Recent research papers ( 5 )
	Lin et al., 2012, PLoS ONE 7(6): e39758 HP1a Targets the Drosophila KDM4A Demethylase to a Subset of Heterochromatic Genes to Regulate H3K36me3 Levels. [FBrf0218736] Klenov et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(46): 18760--18765 Separation of stem cell maintenance and transposon silencing functions of Piwi protein. [FBrf0216776] Swetha et al., 2011, Traffic 12(8): 1037--1055 Lysosomal Membrane Protein Composition, Acidic pH and Sterol Content are Regulated via a Light-Dependent Pathway in Metazoan Cells. [FBrf0214232] Ying et al., 2011, PLoS ONE 6(9): e23863 Comprehensively Surveying Structure and Function of RING Domains from Drosophila melanogaster. [FBrf0215242] Zhang et al., 2011, Chromosoma 120(1): 97--108 Drosophila melanogaster heterochromatin protein HP1b plays important roles in transcriptional activation and development. [FBrf0212898] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...