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Gene Dmel\tra

General Information
Symbol	Dmel\tra	Species	D. melanogaster
Name	transformer	Annotation symbol	CG16724
Feature type	protein_coding_gene	FlyBase ID	FBgn0003741
Gene Model Status	Current	Stock availability	11 publicly available
Also Known As	Dmtra
Genomic Location
Chromosome (arm)	3L	Recombination map	3-45
Cytogenetic map	73A10-73A10	Sequence location	3L:16,583,159..16,584,150 [-]
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 transformer is referred to in FlyBase by the symbol Dmel\tra (CG16724, FBgn0003741). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding; pre-mRNA binding. There is experimental evidence that it is involved in the biological process: female sex determination; mRNA splicing, via spliceosome. 60 alleles are reported. The phenotypes of these alleles are annotated with: organ system; organ system subdivision; cytoplasmic part; larval abdominal segment; adult segment; imaginal precursor; portion of tissue; multicellular structure; spermatozoon; fusome; organelle; female genitalia. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: Fruit fly transformer. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-12 hour embryonic stages, during early pupal stages. Summary of FlyAtlas Anatomical Expression Data: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at high levels in the following post-embryonic organs or tissues: adult ovary. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, adult midgut, adult hindgut, larval Malpighian tubules, adult heart, larval fat body, adult salivary gland, larval trachea, adult testis. Gene sequence location is 3L:16583159..16584150.
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	tra: transformer (M. McKeown and J.M. Belote) XX flies homozygous for tra transformed into sterile males with fully developed sex combs, male-colored abdomen, male abdominal tergites and plates, external and internal male genitalia. Mate readily with females. Testes rudimentary, without sperm, and with ovarian nurse-cell-like cells [Brown and King, 1961]. Testes reduced in size, but of normal color and shape. Transformed female slightly larger than normal male, developmental rate about that of female. X/X/Y; tra/tra also sterile. tra not required in male since X/Y, tra/tra flies are normal males. X/X/X and X/X/Y, tra/tra/tra like diploid, i.e. male in phenotype, but with larger wing cells as expected of triploids. Normal testis anlagen transplanted into tra female becomes attached to duct apparatus and produces sperm. Not needed for female germ cell development since X/X, tra/tra pole cells transplanted into a wild-type female embryo give rise to progeny of both sexes [Marsh and Wieschaus, 1978]. Cell autonomous in mitotic clones [Baker and Ridge, 1980, Genetics 94: 383-423].
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03	Controlled Vocabulary Terms male courtship behavior, veined wing generated song production
FB2013_02	Controlled Vocabulary Terms pre-mRNA binding protein binding
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 73A10-73A10   Limits computationally determined from genome sequence between P{lacW}l(3)j10E8j10E8&P{PZ}l(3)1053210532 and P{PZ}Baldspot02281
Experimentally Determined Cytological Location
Cytogenetic map Notes References 73A8-73A9   (determined by in situ hybridisation)   (Ranz et al., 1997) 73A7-73A10   (determined by in situ hybridisation)   (McKeown et al., 1987)
Experimentally Determined Recombination Data
Location	3-45 (Duncan and Kaufman, 1975, Sturtevant, 1944)
Left of (cM)	in (Sturtevant, 1944) cp
Right of (cM)	st (Ashburner et al., 1981) th (Sturtevant, 1944)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\tra for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.45
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) tra-RA FBtr0075364  NM_079390   687   197 tra-RB FBtr0100244  NM_001014588   862   36
Additional Transcript Data & Comments
Reported size (kB)	1.2, 1.0 (northern blot) (McKeown et al., 1987)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein tra-PA   FBpp0075123   24.1   197   12.42     NP_524114   AAF49441 tra-PB   FBpp0099630   4.4   36   8.79     NP_001014588   AAX53589
Additional Polypeptide Data & Comments
Reported size (kDa)	197 (aa); 22 (kD predicted) (Boggs et al., 1987) 197 (aa) (Belote et al., 1989)
Comments	tra and tra2 proteins as well as a set of SR proteins isolated from HeLa cells were shown to be necessary for the formation of a complex which commits the dsx pre-mRNA to the female-specific splicing pathway. The factors bind to a regulatory element located downstream of the 3' female-specific splice site. (Tian and Maniatis, 1993) tra protein binds the 13 nucleotide cis regulatory elements of dsx pre-mRNA, strongly suggesting a role in the female-specific splicing of dsx pre-mRNA. (Inoue et al., 1992)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Fruit fly transformer (IPR010519)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014296 AAF49441   AE014296 AAX53589   AY183382 AAO38890   AY183383 AAO38891   AY183384 AAO38892   AY183385 AAO38893   AY183386 AAO38894   AY183387 AAO38895   AY183388 AAO38896   AY183389 AAO38897   AY183390 AAO38898   BT028774   EC237417   EC250103   EL869899   EL869900   L19464 AAA75340   L19465 AAA75341   L19466 AAA75342   L19467 AAA28958   L19468 AAA28959   L19469 AAA28960   L19470 AAA28961   L19618 AAA28962   L19619 AAA28963   L19620 AAA28964   M17478 AAB59226
UniProtKB/Swiss-Prot	P11596
UniProtKB/TrEMBL	Q59E32
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
northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage -- adult stage     (Boggs et al., 1987) larval stage -- adult stage | female   organism   (McKeown et al., 1987) pupal stage -- adult stage     (McKeown et al., 1987)
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: Two or more Affy2 ProbeSets identify exons of this gene. This is a summary of the tissue expression peaks exhibited in at least one of these ProbeSets. Expression at high levels in the following post-embryonic organs or tissues: adult ovary. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, adult midgut, adult hindgut, larval Malpighian tubules, adult heart, larval fat body, adult salivary gland, larval trachea, adult testis. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8  (32) carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 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    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8  32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 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    14 central nervous system, larvae L3    24 central nervous system, pupae P8    21 head, virgin 1-day female    6 head, virgin 4-day female    7 head, virgin 20-day female    9 head, mated 1-day female    11 head, mated 4-day female    11 head, mated 20-day female    8 head, mated 1-day male    11 head, mated 4-day male    16 head, mated 20-day male    19 salivary gland, larvae L3 wandering    2 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    6 digestive system, 4-day adult    8 digestive system, 20-day adult    7 fat body, larvae L3 wandering    4 fat body, white prepupae    7 fat body, pupae P8    32 carcass, larvae L3 wandering    14 carcass, 1-day adult    5 carcass, 4-day adult    6 carcass, 20-day adult    6 ovary, virgin 4-day female    11 ovary, mated 4-day female    11 testis, mated 4-day male    2 accessory gland, mated 4-day male    4 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 low expression. Peak expression observed within 00-12 hour embryonic stages, during early pupal 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    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    14 embryo 02-04hr    25 embryo 04-06hr  (35) embryo 06-08hr  (47) embryo 08-10hr  (34) embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr  26 white prepupae 24hr  (27) pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 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    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    14 embryo 02-04hr    25 embryo 04-06hr  (35) embryo 06-08hr  (47) embryo 08-10hr  (34) embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr  26 white prepupae 24hr  27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 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    14 embryo 02-04hr    25 embryo 04-06hr    35 embryo 06-08hr    47 embryo 08-10hr    34 embryo 10-12hr    18 embryo 12-14hr    15 embryo 14-16hr    8 embryo 16-18hr    7 embryo 18-20hr    5 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    4 larva L2    3 larva L3 12hr old    3 larva L3 puffstage 1-2    8 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    14 white prepupae new    14 white prepupae 12hr    26 white prepupae 24hr    27 pupae 2d postWPP    21 pupae 3d postWPP    9 pupae 4d postWPP    7 adult male 01day    7 adult male 05day    9 adult male 30day    9 adult female 01day    10 adult female 05day    12 adult female 30day    12 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+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (29) Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167  (32) embryonic S1  (27) embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9  (29) wing disc ML-DmD16-c3  26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  (35) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS  (87) ovary OSC    23 ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 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+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 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+  29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167  32 embryonic S1  27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9  29 wing disc ML-DmD16-c3  26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  (35) CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS  (87) ovary OSC    23 ovary OSS    23 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 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+    29 Schneider line 2 Sg4    11 embryonic 1182-4H    24 embryonic GM2    13 embryonic Kc167    32 embryonic S1    27 embryonic S3    15 leg disc CME L1    22 wing disc CME-W2    11 wing disc ML-DmD8    15 wing disc ML-DmD9    29 wing disc ML-DmD16-c3    26 wing disc ML-DmD21    21 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    15 eye-antennal disc ML-DmD11    11 antennal disc ML-DmD20-c5    10 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    35 CNS ML-DmBG2-c2    21 tumorous blood cells mbn2    8 ovary fGS/OSS    87 ovary OSC    23 ovary OSS    23 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    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 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    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 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    10 cold shock, 4-day adult    5 heat shock, 4-day adult    19 Cadmium 50 mM 6 hrs, larvae L3    3 Cadmium 50 mM 12 hrs, larvae L3    7 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    13 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    5 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    8 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    4 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    4 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    10 Caffeine 25 mg/ml 48 hrs, 4-day adult    7 Paraquat 5 mM 48 hrs, 4-day adult    13 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    4 Rotenone 8 μg 12 hrs, larvae L3    3 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_05
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003741 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG16724-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable trae01760 viable, with Scer\GAL4hs.PB traScer\UAS.cFa viable, with Scer\GAL4pnr-MD237 traGD764 Sterility Allele female sterile tra1 fertile trae01760 fertile | reduced, with Scer\GAL455B traScer\UAS.cFa male fertile tra1 male sterile traScer\UAS.cFa male sterile | partially, with Scer\GAL455B traScer\UAS.cFa sterile traF.Hsp83 Other Phenotypes Allele behavior defective, with Scer\GAL47B traScer\UAS.cFa behavior defective, with Scer\GAL430B traScer\UAS.cFa behavior defective, with Scer\GAL453B traScer\UAS.cFa behavior defective, with Scer\GAL4Tdc2.PC traScer\UAS.cFa behavior defective | male, with Scer\GAL4npf.1 traScer\UAS.cFa courtship behavior defective traScer\UAS.cFa courtship behavior defective, with Scer\GAL453B traScer\UAS.cFa courtship behavior defective, with Scer\GAL4c309 traScer\UAS.cFa courtship behavior defective, with Scer\GAL4Gp150-52A traScer\UAS.cFa courtship behavior defective, with Scer\GAL4hs.PB traScer\UAS.cFa courtship behavior defective, with Scer\GAL4MJ286 traScer\UAS.cFa courtship behavior defective, with Scer\GAL4pros.PMG traScer\UAS.cFa courtship behavior defective, with Scer\GAL4retn-89.GAL4 traScer\UAS.cFa courtship behavior defective, with Scer\GAL4Tdc2.PC traScer\UAS.cFa courtship behavior defective, with Scer\GAL4to.PD traScer\UAS.cFa courtship behavior defective | male traF.Hsp83 traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4c123a traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4c739 traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4dsf.1.8 traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4elav.PLu traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4npf.1 traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4pros-V1 traScer\UAS.cFa courtship behavior defective | male, with Scer\GAL4Tab2-201Y traScer\UAS.cFa courtship behavior defective | male | recessive tra4 tra5 courtship behavior defective | male limited, with Scer\GAL4Tab2-201Y traScer\UAS.cFa locomotor behavior defective, with Scer\GAL4Tdc2.PC traScer\UAS.cFa locomotor behavior defective | male, with Scer\GAL430Y traScer\UAS.cFa locomotor behavior defective | male, with Scer\GAL4103Y traScer\UAS.cFa locomotor behavior defective | male, with Scer\GAL4121Y traScer\UAS.cFa locomotor behavior defective | male, with Scer\GAL4elav-C155 traScer\UAS.cFa locomotor behavior defective | male, with Scer\GAL4pros-V1 traScer\UAS.cFa mating behavior defective | male limited, with Scer\GAL4hec.PL traScer\UAS.cFa mating defective, with Scer\GAL4pros-V1 traScer\UAS.cFa mating defective | male, with Scer\GAL455B traScer\UAS.cFa neuroanatomy defective tra1 trahs.PB neuroanatomy defective | male, with Scer\GAL469B traScer\UAS.cFa sex-determination defective trahs.PB sex-determination defective | adult stage | male, with Scer\GAL4ptc-559.1 traScer\UAS.cFa sex-determination defective | dominant trahs.PB sex-determination defective | female traunspecified sex-determination defective | female, with Scer\GAL4dsx.KI traGD764 sex-determination defective | female | recessive tra1 sex-determination defective | male traF.Hsp83 trahs.PB traHsp83.PS sex-determination defective | recessive tra1 tra4 song defective, with Scer\GAL4003 traScer\UAS.cFa song defective, with Scer\GAL4010 traScer\UAS.cFa song defective, with Scer\GAL411Y traScer\UAS.cFa song defective, with Scer\GAL4102Y traScer\UAS.cFa song defective, with Scer\GAL4123 traScer\UAS.cFa song defective, with Scer\GAL4169Y traScer\UAS.cFa song defective, with Scer\GAL4203Y traScer\UAS.cFa song defective, with Scer\GAL4333 traScer\UAS.cFa song defective, with Scer\GAL4369 traScer\UAS.cFa song defective, with Scer\GAL4383 traScer\UAS.cFa song defective, with Scer\GAL4385 traScer\UAS.cFa song defective, with Scer\GAL4463 traScer\UAS.cFa song defective, with Scer\GAL4470 traScer\UAS.cFa song defective, with Scer\GAL4483 traScer\UAS.cFa song defective, with Scer\GAL4496 traScer\UAS.cFa song defective, with Scer\GAL4499 traScer\UAS.cFa song defective, with Scer\GAL4C60 traScer\UAS.cFa song defective, with Scer\GAL4C115 traScer\UAS.cFa song defective, with Scer\GAL4C318a traScer\UAS.cFa song defective, with Scer\GAL4C404 traScer\UAS.cFa song defective, with Scer\GAL4C502a traScer\UAS.cFa song defective, with Scer\GAL4C552 traScer\UAS.cFa song defective, with Scer\GAL4C560 traScer\UAS.cFa song defective, with Scer\GAL4C689 traScer\UAS.cFa song defective | dominant traScer\UAS.cFa visible | male limited, with Scer\GAL4c739 tramw(-).Scer\UAS.cFa traScer\UAS.cFa wild-type tra+t3.8 traM4 traM5 traM6 traM7 traM11 traM12 traRB Phenotype manifest in Allele abdomen | male, with Scer\GAL4c35 traScer\UAS.cFa abdomen | male, with Scer\GAL4c739 traScer\UAS.cFa adult brain & neuron | medial | female tra1 adult brain | female (with Df(3L)st-j7) tra1 adult external abdomen, with Scer\GAL4c739 traScer\UAS.cFa tramw(-).Scer\UAS.cFa adult nervous system | male, with Scer\GAL455B traScer\UAS.cFa antennal lobe glomerulus DA1 | male, with Scer\GAL469B traScer\UAS.cFa female genital disc | ectopic | male, with Scer\GAL4ptc-559.1 traScer\UAS.cFa female genitalia traunspecified female genitalia | male, with Scer\GAL4elav-C155 traScer\UAS.cFa female repressed primordium, with Scer\GAL4ptc-559.1 traScer\UAS.cFa fusome tra1 tra4 germline cell tra1 tra4 germline cell | embryonic stage, with Scer\GAL4twi.PB traScer\UAS.cFa gonad tra1 tra4 traF.Hsp83 traunspecified gonadal sheath proper primordium | female tra1 gonadal sheath proper primordium | male, with Scer\GAL4αTub84B.PL traScer\UAS.cFa hub cell, with Scer\GAL4how-24B, Scer\GAL4twi.PG traScer\UAS.cFa hub cell, with Scer\GAL4αTub84B.PL traScer\UAS.cFa hub cell (with Df(3L)st-j7) tra1 male genital disc, with Scer\GAL4ptc-559.1 traScer\UAS.cFa male genitalia trahs.PB male genitalia, with Scer\GAL4c35 traScer\UAS.cFa male genitalia, with Scer\GAL4c739 traScer\UAS.cFa male reproductive system trahs.PB nurse cell ring canal tra1 tra4 ovary trahs.PB prothoracic leg taste bristle, with Scer\GAL4pros-V1 traScer\UAS.cFa seminal receptacle | ectopic, with Scer\GAL4c309 traScer\UAS.cFa serotonergic neuron tra1 sex comb traF.Hsp83 sex comb, with Scer\GAL4c309 traScer\UAS.cFa spectrosome tra1 tra4 spermathecum, with Scer\GAL4c309 traScer\UAS.cFa spermatocyte fusome trahs.PB spermatocyte ring canal trahs.PB spermatozoon, with Scer\GAL4c309 traScer\UAS.cFa testis, with Scer\GAL4c309 traScer\UAS.cFa
Classical Alleles ( 21 )
For All Classical Alleles Show
Allele of tra Class Mutagen Stocks Known lesion tra1 amorphic allele - genetic evidence spontaneous 4 Yes trae01760 piggyBac transposase 2 -- tra+RB10-18 wild-type allele PM hybrid dysgenesis 0 Yes tra2 spontaneous 0 Yes tra3 spontaneous ethyl methanesulfonate 0 Yes tra4 loss of function allele ethyl methanesulfonate 0 Yes tra5 loss of function allele ethyl methanesulfonate 0 Yes tra6 PM hybrid dysgenesis IR-hybrid dysgenesis 0 Yes trae01761 0 -- traenu loss of function allele ethyl nitrosourea 0 Yes traF283 natural population 0 -- traF296 natural population 0 -- traST03 natural population 0 -- traST05 natural population 0 -- traST06 natural population 0 -- traST08 natural population 0 -- traST09 natural population 0 -- traST12 natural population 0 -- traST15 natural population 0 -- traST16 natural population 0 -- traunspecified loss of function allele 0 --
Alleles Carried on Transgenic Constructs ( 39 )
For All Alleles Carried on Transgenic Constructs Show
Allele of tra Class Mutagen Stocks Known lesion traGD764 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes traScer\UAS.cFa in vitro construct - regulatory fusion 2 Yes traJF03132 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes tra+t3.8 in vitro construct - genomic fragment 0 Yes traAct5C.PR in vitro construct - genomic fragment in vitro construct - minigene in vitro construct - regulatory fusion 0 Yes traBH in vitro construct - genomic fragment 0 Yes traBL in vitro construct - genomic fragment 0 Yes traF.Hsp70 in vitro construct - regulatory fusion 0 -- traF.Hsp83 in vitro construct - regulatory fusion 0 Yes traF.U2af50 in vitro construct - regulatory fusion 0 Yes trahs.PB in vitro construct - regulatory fusion 0 Yes trahs.PBa in vitro construct - regulatory fusion 0 Yes trahs.PH in vitro construct - regulatory fusion 0 Yes traHsp83.PS in vitro construct - regulatory fusion 0 Yes traLTR.P in vitro construct - regulatory fusion 0 Yes traM.LTR in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes traM10 in vitro construct - site directed mutagenesis 0 Yes traM11 in vitro construct - site directed mutagenesis 0 Yes traM12 in vitro construct - site directed mutagenesis 0 Yes traM3 in vitro construct - site directed mutagenesis 0 Yes traM4 in vitro construct - site directed mutagenesis 0 Yes traM5 in vitro construct - site directed mutagenesis 0 Yes traM6 in vitro construct - site directed mutagenesis 0 Yes traM7 in vitro construct - site directed mutagenesis 0 Yes traM8 in vitro construct - site directed mutagenesis 0 Yes traM9 in vitro construct - site directed mutagenesis 0 Yes tramut in vitro construct - site directed mutagenesis 0 Yes tramw(-).Scer\UAS.cFa ethyl methanesulfonate 0 Yes tramw(-).Scer\UAS.cFb ethyl methanesulfonate 0 Yes traNIG.16724R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes traRB.cBa in vitro construct 0 Yes traRB in vitro construct - genomic fragment 0 Yes tratBa in vitro construct - genomic fragment 0 Yes traΔF.LTR in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes traΔM1 in vitro construct 0 Yes traΔM2 in vitro construct 0 Yes traΔM3 in vitro construct 0 Yes traΔM4 in vitro construct - deletion 0 Yes traΔN.LTR in vitro construct - regulatory fusion in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)DTS5-3 (Velissariou and Ashburner, 1981) Df(3L)DTS5-4 (Velissariou and Ashburner, 1981) Df(3L)st (Ryner et al., 1996) Df(3L)st2 (Ashburner et al., 1981) Df(3L)st4 (Bedian, 1998.10.2, Velissariou and Ashburner, 1981, Ashburner et al., 1981) Df(3L)st7 (Bedian, 1998.10.2, Velissariou and Ashburner, 1981) Df(3L)st62 (Bedian, 1998.10.2) Df(3L)st100.62 (McKeown et al., 1987, Belote et al., 1990) Df(3L)st103 (Velissariou and Ashburner, 1981, Nothiger et al., 1989) Df(3L)st-b11 (Bedian, 1998.10.2) Df(3L)st-E23 (Nothiger et al., 1989) Df(3L)st-E34 (Butler et al., 1986, Belote et al., 1990) Df(3L)st-E36 (Butler et al., 1986, Belote et al., 1990) Df(3L)st-E48 (Butler et al., 1986) Df(3L)st-E52 (Belote et al., 1985, Butler et al., 1986, Belote et al., 1990) Df(3L)st-E73 (Nothiger et al., 1989) Df(3L)st-g24 (Belote et al., 1985, McKeown et al., 1987, Belote et al., 1990) Df(3L)st-j7 (Le Bras and Van Doren, 2006, Hager and Cline, 1997, Bedian, 1998.10.2, McKeown et al., 1987, Belote et al., 1990) Df(3L)st-j11 (Bedian, 1998.10.2) Df(3L)st-LM3 (Marsh and Mock, 1985) Df(3L)st-LM19 (Marsh and Mock, 1985) Df(3L)tra (McKeown et al., 1987, Belote et al., 1990) Df(3R)st4 (Oliver et al., 1993)
Not disrupted in	Df(3L)st3 (Ashburner et al., 1981) Df(3L)st6 (Bedian, 1998.10.2) Df(3L)st7P (Belote et al., 1985, McKeown et al., 1987, Belote et al., 1990) Df(3L)st-a20 (McKeown et al., 1987, Belote et al., 1990) Df(3L)st-e4 (McKeown et al., 1987, Belote et al., 1990) Df(3L)st-E5 (Belote et al., 1985, Butler et al., 1986) Df(3L)st-f13 (Bedian, 1998.10.2, McKeown et al., 1987, Belote et al., 1990) Df(3L)th1 (Velissariou and Ashburner, 1981) Df(3L)th2 (Bedian, 1998.10.2, Velissariou and Ashburner, 1981) Df(3L)th45 (Velissariou and Ashburner, 1981) Df(3L)th102 (Velissariou and Ashburner, 1981) Df(3L)th112 (Velissariou and Ashburner, 1981) Df(3L)th113 (Velissariou and Ashburner, 1981) Df(3L)th117 (Velissariou and Ashburner, 1981) Df(3L)thSS102 (Bedian, 1998.10.2) Df(3L)VB-33 (Bedian, 1998.10.2) In(3L)std11 (McKeown et al., 1987, Belote et al., 1990)
Duplicated in	Ts(YSt;3Lt)ST1 (Lindsley and Zimm, 1992, Brizuela et al., 1994)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{Adh-tra} No P{tra-CAT.123} No heat-shock construct P{Hsp70-tra.F} NA P{Hsp83-tra.F} NA P{hsp83-tra} NA P{hsp-tra-female} NA P{hs-tra.B} NA UAS construct P{GD764} NA P{NIG.16724R} NA P{TRiP.JF03132} NA P{UAS-tra.F} NA P{UAS-tra.w(-).1} NA characterization construct P{5'RB18} NA P{hs-TK-tra} NA P{M10} NA P{M11} NA P{M12} NA P{mut} NA P{RB18} NA P{TK-Adh-cons-tra} NA P{TK-Adh-T8C} NA P{TK-tra} NA P{tra::tra2C.T:FLAG} NA P{tra.BH} NA P{tra.BL} NA P{tra.RB} NA P{tra} NA P{tra+3.8} NA P{tratBa} NA P{traM3} NA P{traM4} NA P{traM5} NA P{traM6} NA P{traM7} NA P{traM8} NA P{traM9} NA P{traRS} NA P{U2af50-traF} NA P{ΔM1} NA P{ΔM2} NA P{ΔM3} NA P{ΔM4} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{5'RB18}RB10-18 NA PBac{RB}trae01760 NA PBac{RB}trae01761 NA
Gene Ontology: Function, Process & Cellular Component ( 16 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function
CV term Evidence References
pre-mRNA binding inferred from direct assay (Inoue et al., 1992) protein binding inferred from physical interaction with tra2 (Amrein et al., 1994)
Biological Process
CV term Evidence References
female sex determination inferred from mutant phenotype (Butler et al., 1986) male courtship behavior, veined wing generated song production inferred from mutant phenotype (Moran and Kyriacou, 2009) mRNA splicing, via spliceosome inferred from direct assay (Inoue et al., 1992)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 12 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
female sex differentiation inferred from electronic annotation with InterPro:IPR010519 (FlyBase Curators et al., 2004-) female somatic sex determination traceable author statement (Williamson and Lehmann, 1996) mRNA splicing, via spliceosome non-traceable author statement (Swiss-Prot Project Members, 1990.1.1) traceable author statement (Saccone et al., 2002) negative regulation of translation non-traceable author statement (Zarkower, 2001) RNA splicing traceable author statement (Billeter et al., 2002) sex determination traceable author statement (Saccone et al., 2002, Beye, 2004) sex determination, primary response to X:A ratio non-traceable author statement (Swiss-Prot Project Members, 1990.1.1) sex differentiation traceable author statement (Billeter et al., 2002) somatic sex determination non-traceable author statement (Schutt and Nothiger, 2000, Baker et al., 2001) spliceosomal complex assembly non-traceable author statement (Schutt and Nothiger, 2000)
Cellular Component
CV term Evidence References
nucleus inferred from electronic annotation with InterPro:IPR010519 (FlyBase Curators et al., 2004-) spliceosomal complex non-traceable author statement (Swiss-Prot Project Members, 1990.1.1)
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 tra allele Gene References tra1 fru (Ryner et al., 1996) otu (Hinson and Nagoshi, 1999) Sxl (Cline et al., 1999) tra4 otu (Hinson and Nagoshi, 1999) traF.Hsp83 Sxl (Waterbury et al., 2000) traHsp83.PS Doa (Du et al., 1998) traunspecified Doa (Du et al., 1998) dsx (Nothiger et al., 1987) unspecified otu (Waterbury et al., 2000)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 65151 DroID - A comprehensive database of gene and protein interactions. • FBgn0003741 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39849
Orthologs
OrthoDB Orthologs (4) - 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 EOG6JHD2M Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6JHD2M)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\tra     Drosophila simulans   Dsim\tra Y   Drosophila erecta   Dere\tra Y   Drosophila yakuba   Dyak\GE22208 Y
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (4) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\tra Drosophila sechellia Dsec\tra Drosophila erecta Dere\tra Drosophila yakuba Dyak\GE22208
Stocks & Reagents
Stocks Listed in FlyBase ( 11 )
Bloomington	675 wa; tra1/TM2 4590 w1118; P{UAS-tra.F}20J7 17984 w1118; PBac{RB}trae01760 28512 y1 v1; P{TRiP.JF03132}attP2
Harvard	- PBac{RB}trae01760
Kyoto	107812 w*; P{UAS-tra.F}20J7 106034 wa; tra1/TM2 102014 tra1 ; Tp(2;3)Me, Me1 Sbsbd-l 101894 Dp(1;Y)BS / wa ; st1 tra1 / TM2, Ubx130 es
VDRC	v2560 w1118; P{GD764}v2560 v2561 w1118; P{GD764}v2561/TM3
Genomic Clones ( 2 )
	BACR08H06 BACR11G05 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 5 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	IP02034
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	117731 166674 IP02033 IP02035
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0003741 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39849
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	In gynanders (XX/XO mosaics) feminised by traF.U2af50, traF protein in XO somatic cells of the gonad is sufficient (even in the absence of detectable SxlF protein) to elicit all nonautonomous feminising signals required by XX germ cells, as well as all other somatic-cell functions required for normal oogenesis, so that functional eggs are produced. However, some of these feminised gynanders fail to lay their eggs, indicating that there are diplo-X cells outside the gonad for which traF.U2af50-feminised haplo-X cells cannot substitute. (Evans and Cline, 2007) The Hrp59 protein binds preferentially to a subset of mRNAs, including tra mRNA. (Kiesler et al., 2005) tra is necessary in order to prevent the continued presence of male-specific somatic gonadal precursors in the female somatic gonad. (DeFalco et al., 2003) Ectopic somatic expression of the female product of tra is sufficient to feminise XY germ cells. This feminisation depends upon the tra2 gene, but does not seem to require a functional dsx gene. However, feminisation of XY germ cells by the female product of tra can be blocked by the male form of dsx protein. (Waterbury et al., 2000) The crystal structure has been determined at 2.6A resolution of the complex formed between two tandemly arranged RNA-binding domains of the Sxl protein and a 12 nucleotide, single stranded RNA derived from the tra polypyrimidine tract. The two RNA-binding domains have their β-sheet platforms facing each other to form a V-shaped cleft. The RNA is bound in this cleft, where the tra UGUUUUUUU sequence is specifically recognized by the Sxl protein. (Handa et al., 1999) tra is not required for the development of the internal organisation of the male terminal segment. (Acharyya and Chatterjee, 1998) The female nervous system is substantially responsible for controlling the process of sperm transport from the bursa copulatrix to the storage organs. (Arthur et al., 1998) Mutants carrying a heat inducible female form of tra exhibit indiscriminate sexual behaviour. Studies suggest a disturbed nervous system, and not self-stimulation, is the most probable cause for this behaviour. Sexual behaviour is irreversibly programmed during a critical period as a result of the activity or inactivity or a single control gene. (Arthur et al., 1998) tra and tra2 regulate sex-specific splicing of fru, inducing female-specific splicing of fru by activating the female-specific fru 5' splice site. (Heinrichs et al., 1998) Sex determining genes tra, ix and dsx have no role in regulating the template organisation of the X chromosome(s) for dosage compensation. (Acharyya and Chatterjee, 1997) The Sxl RBD1+2/tra PPT interaction is analysed by chemical shift perturbation mapping of the protein backbone. Data suggests the two domains respond quite differently to the presence of tra PPT RNA. (Lee et al., 1997) The roX1 gene shows a male-specific expression pattern in adult flies. roX1 expression is dependent on Sxl, but is independent of tra activity, and is positively regulated by genes of the dosage compensation system such as mle. (Meller et al., 1997) The simultaneous influence of different male and female pheromones on male courtship behaviour is measured using tra mosaic flies. (Ferveur and Sureau, 1996) fl(2)d function is necessary for the female-specific splicing of tra pre-mRNA, but not for the female-specific splicing of dsx pre-mRNA. (Granadino et al., 1996) Both HeLa and Kc cell nuclear extracts have been used for UV cross-linking experiments to determine which proteins bind to dsxRE as part of the native tra- and tra2-dependent dsx enhancer complex (dsxEC). Rbp1 and SRp30 have been identified that bind the 13-nucleotide repeats and purine rich element (PRE), respectively, of the dsx repeat element (dsxRE). (Lynch and Maniatis, 1996) Anatomical and behavioural studies of fru mutants are consistent with the function of fru being downstream of tra and tra2. (Ryner et al., 1996) Both of the RNA-binding domains (RBDs) of Sxl are required for efficient and specific binding of Sxl protein to the tra cis-acting element. (Sakashita and Sakamoto, 1996) Using the Scer\GAL4-Scer\UAS system to express tra males have been produced with regionally feminized brains. Flies feminized in a portion of the antennal lobes or in a subset of the mushroom bodies court both males and females. (Ferveur et al., 1995) Female specific form of the tra gene, expressed using the GAL4 system, has been used to give a pattern of feminization. Feminization of certain brain structures in the male is associated with different types of sexual behaviour. These intersexual flies produce a large variety of pheromonal bouquets which combine male and female pheromones in different amounts. There is a significant correlation between the production of different pheromones and the induction of different male behaviours. (Ferveur et al., 1995) Amino acid sequences required to direct the tra protein to nuclear speckles have been identified. The tra nuclear localisation can be uncoupled from localisation to the speckle domains. An amino sequence in tra is capable of directing a heterologous protein to nuclear speckles of mammalian cells, regions of the nucleus previously shown to contain high concentrations of spliceosomal small nuclear RNAs and splicing factors. tra2 and tra colocalise in the speckle domains. (Hedley et al., 1995) Genetic and molecular analyses suggest that vir is required for female-specific splicing of Sxl and of tra pre-mRNA. (Hilfiker et al., 1995) Female-specific expression of genes in the germline is dependent on a somatic signalling pathway which requires the sex-non-specific tra2 but not the sex-specific tra and dsx. (Horabin et al., 1995) l(3)73Ah shares 3' untranslated sequence with tra. (Irminger-Finger and Nothiger, 1995) Regulated alternative splicing of dsx pre-mRNA requires the dsxRE splicing enhancer, dsx repeat element. The activity of dsxRE requires tra and tra2 and one or more general splicing factors. A purine rich enhancer (PRE) sequence within the RE has been identified, this element functionally synergises with the dsxRE and is required for specific binding of tra2 to the dsxRE. Results demonstrate that positive control of dsx pre-mRNA splicing requires tra- and tra2- dependent assembly of a multiprotein complex on at least two distinct enhancer elements. (Lynch and Maniatis, 1995) The expression of tra under the control of Scer\GAL4 in sub domains of the male mushroom bodies causes feminisation of the cells in which tra is expressed and a subsequent insertion-specific non-discriminatory courtship behaviour where males court other males as vigorously as females. This supports the notion that at least some sub-domains of the mushroom bodies develop in a sex-specific manner. (O'Dell and Kaiser, 1995) tra is expressed in genetically defined subregions of the male brain, in particular within different domains of the mushroom bodies. Expression in a Scer\GAL4 line that marks a component of the antennal lobe causes males to exhibit nondiscriminatory sexual behaviour (court males and females). Expression in other mushroom body domains has no such effect. (O'Dell et al., 1995) her- intersexuality cannot be rescued by constitutive tra expression. (Pultz and Baker, 1995) The Sxl splice site consensus is a highly specific sequence, explaining why it can regulate splicing of tra pre-mRNA and autoregulate splicing of its own mRNA. (Singh et al., 1995) The choice of female identity in the germ line is dependent upon a somatic signalling pathway that requires the sex-non-specific tra2 gene but not the sex specific genes tra and dsx. (Waterbury et al., 1995) The sex-specific requirement of sov in gonadal development is controlled by the somatic sex regulatory genes tra, tra2 and dsx. (Wayne et al., 1995) The tra2 product interacts with itself, and with the tra and SF2 products in vitro and in the yeast two-hybrid system. (Amrein et al., 1994) The tra gene is regulated by Sxl-dependent 3' splice site blockage. 40 nucleotides immediately upstream of the regulated splice site are sufficient to direct sex-specific regulated splicing. (Sosnowski et al., 1994) tra and dsx control early inductive signals that determine the sex of XX germ cells. tra product present in somatic cells of XY animals, or in backgrounds lacking the sex-determining function of Sxl, is sufficient to support developing XX germ cells through oogenesis. (Steinmann-Zwicky, 1994) There is no cost to a female to receive sperm: lifespan, egg production, egg hatchability and remating rate of females intermittently exposed to males that could (tra mutants) or could not (tud mutants) transfer sperm are not significantly different. (Chapman et al., 1993) The genetic hierarchy regulating female germ-line sex determination includes tra, tra2, dsx, fu, otu, ovo, snf and Sxl. (Oliver et al., 1993) Female specific splicing of dsx is regulated by tra and tra2, which recruit general, serine/arginine-rich splicing factors to a regulatory element located downstream of a female-specific 3' splice site. (Tian and Maniatis, 1993) In vitro system that recapitulates the regulation by Sxl of tra sex-specific splicing developed. Sxl blocks splicing to the non-sex specific, default site in tra by specifically binding to its polypyrimidine tract, blocking the binding of the essential splicing factor U2AF: U2AF then acivates the lower-affinity female-specific site. (Valcarcel et al., 1993) Mutants exhibit defective courtship song. (Bernstein et al., 1992) UV crosslinking/transfection of Kc cells showed female-specific tra protein binds to 13 nucleotide motif present in 6 copies in the female-specific fourth exon of dsx pre-mRNA. (Inoue et al., 1992) The tra-homologous genes from D.simulans, D.erecta, D.hydei and D.virilis have been cloned, sequenced and compared to the D.melanogaster tra gene. This comparison reveals as unusually high degree of evolutionary divergence among the tra coding sequences. In addition there is a highly conserved region within the first intron that may define a cis-acting regulator of sex-specific alternative splicing. (O'Neil and Belote, 1992) tra function directs the development of sexually dimorphic skeletal muscles. (Taylor, 1992) An in vitro splicing system to study the mechanism involved in positive control of dsx female specific splicing by tra and tra2 is used in HeLa cell nuclear extracts. (Tian and Maniatis, 1992) Wild type functions of tra and tra2 are necessary in females for the expression of the female specific dsx function. In the absence of tra or tra2 function the alternative pattern of processing produces the dsx mRNA that encodes the male specific dsx protein. (Baker et al., 1991) Cotransfection analyses in which dsx, tra and tra2 cDNAs are expressed in Kc cells revealed that female specific splicing of dsx transcript is positively regulated by tra and tra2 gene products. (Hoshijima et al., 1991) The functions of the arginine/serine-rich RS domains of su(wa) and tra have been studied. (Li and Bingham, 1991) Cotransfection assays to examine regulatory interactions between specific cis-acting sequence elements of dsx pre-mRNA, and tra and tra2 gene products establish that tra and tra2 function to activate the use of the female specific exon. (Ryner and Baker, 1991) Co-transfection experiments in which Sxl cDNA and the tra gene are expressed in Kc cells demonstrate that the female Sxl-encoded protein binds specifically to the tra transcript at or near the non-sex-specific acceptor site. This implies that the female Sxl gene product is the trans-acting factor that regulates alternative splicing. (Inoue et al., 1990) The mechanism of sex determination in the germ line has been analysed. (Nothiger et al., 1989) The information for proper 3' splice site choice in tra is contained within the regulated intron. (Sosnowski et al., 1989) The nature and function of the 2 different tra RNAs is determined and the mechanisms of their sex-specific regulation is elucidated. (Boggs et al., 1987) The tra locus has been molecularly isolated and characterized. P element mediated transformation has demonstrated that a fragment of 2kb is sufficient to supply tra+ function. (McKeown et al., 1987) Mutant females are transformed into sterile males. (Duncan and Kaufman, 1975) XX flies homozygous for tra transformed into sterile males with fully developed sex combs, male-colored abdomen, male abdominal tergites and plates, external and internal male genitalia. Mate readily with females. Testes rudimentary, without sperm and with ovarian nurse-cell-like cells <up>Brown and King, 1961</up>. Testes reduced in size, but of normal color and shape. Transformed female slightly larger than normal male, developmental rate about that of female. X/X/Y; tra/tra also sterile. tra not required in male since X/Y, tra/tra flies are normal males. X/X/X and X/X/Y, tra/tra/tra like diploid, i.e. male in phenotype, but with larger wing cells as expected of triploids. Normal testis anlagen transplanted into tra female becomes attached to duct apparatus and produces sperm. Not needed for female germ cell development since X/X, tra/tra pole cells transplanted into a wild-type female embryo give rise to progeny of both sexes <up>Marsh and Wieschaus, 1978</up>. Cell autonomous in mitotic clones <up>Baker and Ridge, 1980</up>.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079390 NM_001014588 RefSeq (Proteins) • NP_524114 NP_001014588 DDBJ / EMBL / GenBank • AAA28958 AAA28959 AAA28960 AAA28961 AAA28962 AAA28963 AAA28964 AAA75340 AAA75341 AAA75342 AAB59226 AAF49441 AAF49441.1 AAO38890 AAO38891 AAO38892 AAO38893 AAO38894 AAO38895 AAO38896 AAO38897 AAO38898 AAX53589 AY183382 AY183383 AY183384 AY183385 AY183386 AY183387 AY183388 AY183389 AY183390 L19464 L19465 L19466 L19467 L19468 L19469 L19470 L19618 L19619 L19620 M17478 Entrez Gene - A searchable database of RefSeq genes. • 39849 UniProtKB/Swiss-Prot • P11596 UniProtKB/TrEMBL • Q59E32
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Fruit fly transformer (IPR010519)
Linkouts
	BioGRID - A database of protein and genetic interactions • 65151 DroID - A comprehensive database of gene and protein interactions. • FBgn0003741 DRSC - Results from RNAi screens. • FBgn0003741 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003741 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG16724-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0003741 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39849 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /sturtevant/transformer1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39849 modMine - Data generated by the modENCODE project. • FBgn0003741
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	CG16724 (Perkins et al., 2009) Dmtra (Pane et al., 2005, Graham et al., 2003) TRA (Liu et al., 2004, Hempel and Oliver, 2006, Kpebe and Rabinow, 2007, Lalli et al., 2003, Farkas et al., 2009, Boucher et al., 2001) tra (Evans and Cline, 2007, Chan and Kravitz, 2007, Siera and Cline, 2007, Jones et al., 2007, Li et al., 2007, Acebes et al., 2004, Barmina et al., 2005, Lee et al., 2006, Park et al., 2006, Kiesler et al., 2005, An et al., 2000, Kimura et al., 2008, Nurminsky, 2007, Reiter et al., 2007, Lee et al., 2002, Lazareva et al., 2007, Billeter et al., 2006, Casper and Van Doren, 2006, Smith and Oliver, 2008, Chertemps et al., 2007, Chertemps et al., 2006, Lalli et al., 2003, Haag and Doty, 2005, Yu and Dickson, 2006, Nilsson et al., 2000, Kim et al., 2000, Robida et al., 2007, Shen et al., 2009, Avery et al., 2011, Rubinstein et al., 2010, Goldman and Arbeitman, 2007, Hartmann et al., 2011, Chang et al., 2011, Wawersik et al., 2005, Penn and Schedl, 2007, Kitadate et al., 2007, DeFalco et al., 2008, Rideout et al., 2007, Chan and Kravitz, 2007, Siera and Cline, 2008, Svensson et al., 2003, Kido and Ito, 2002, Yamamoto et al., 2004, Dankert et al., 2009, Ruedi and Hughes, 2009, Lacaille et al., 2009, Le Bras and Van Doren, 2006, Singh et al., 2000, Banerjee et al., 2003, Savarit and Ferveur, 2002, Tarone et al., 2005, Rehwinkel et al., 2005, Casper and Van Doren, 2009, Mundiyanapurath et al., 2009, Billeter et al., 2006, Fan et al., 2010, Johnson et al., 2010, McIntyre et al., 2006, Cachero et al., 2010, Saccone et al., 2008, Ruiz and Sanchez, 2010, Fernandez et al., 2010, Graveley et al., 2011, Chatterjee et al., 2011, Siwicki et al., 2005, Gleason, 2005, Ng and Kopp, 2008, Metzstein and Krasnow, 2006, Rehwinkel et al., 2004, Dierick and Greenspan, 2007, Rideout et al., 2010, Amrein et al., 1994, Japanese National Institute of Genetics, 2012.5.21, Frizzell et al., 2012, Yang et al., 2012, Kpebe and Rabinow, 2008) Tra (Sciabica and Hertel, 2006, Hartmann et al., 2008, Saulière et al., 2010)
Name Synonym	transformer (Evans and Cline, 2007, Chan and Kravitz, 2007, Siera and Cline, 2007, Casper and Doren, 2007, Lee et al., 2006, An et al., 2000, Hall, 2002, Kitamoto, 2002, Lee et al., 2002, Billeter et al., 2006, Casper and Van Doren, 2006, Casper and Doren, 2008, Chertemps et al., 2007, Chertemps et al., 2006, Lalli et al., 2003, Nilsson et al., 2000, Kim et al., 2000, Robida et al., 2007, Shen et al., 2009, Avery et al., 2011, Rubinstein et al., 2010, Goldman and Arbeitman, 2007, Hartmann et al., 2011, Chang et al., 2011, Kitadate et al., 2007, DeFalco et al., 2008, Rideout et al., 2007, Chan and Kravitz, 2007, Siera and Cline, 2008, Mok et al., 2005, Ruedi and Hughes, 2009, Lacaille et al., 2009, Singh et al., 2000, Savarit and Ferveur, 2002, Tarone et al., 2005, Casper and Van Doren, 2009, Mundiyanapurath et al., 2009, Johnson et al., 2010, McIntyre et al., 2006, Billeter et al., 2006, Fernandez et al., 2010, Graveley et al., 2011, Siwicki et al., 2005, Gleason, 2005, Ng and Kopp, 2008, Frizzell et al., 2012) Transformer (Sciabica and Hertel, 2006, Billeter et al., 2006, Chatterjee et al., 2011)
Secondary FlyBase IDs
References ( 433 )
Generate a list of	All references relating to this gene ( 433 )
List References by type	Research paper  ( 254 ) Supplementary material  ( 6 ) Review  ( 90 ) Personal communication to FlyBase  ( 8 ) Abstract  ( 63 ) FlyBase analysis  ( 2 ) Conference report  ( 1 ) Stock list  ( 1 ) Letter  ( 3 ) Protein sequence record  ( 1 ) Book  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 12 )
	Hoxha et al., 2013, PLoS Genet. 9(1): e1003217 Sex-specific signaling in the blood-brain barrier is required for male courtship in Drosophila. [FBrf0220616] Devineni and Heberlein, 2012, Proc. Natl. Acad. Sci. U.S.A. 109(51): 21087--21092 Acute ethanol responses in Drosophila are sexually dimorphic. [FBrf0220438] Fabre et al., 2012, Curr. Biol. 22(22): 2180--2185 Substrate-Borne Vibratory Communication during Courtship in Drosophila melanogaster. [FBrf0220008] Frizzell et al., 2012, RNA 18(8): 1475--1486 Drosophila mutants show NMD pathway activity is reduced, but not eliminated, in the absence of Smg6. [FBrf0218868] Mullon et al., 2012, BMC Evol. Biol. 12: 5 Molecular evolution of Drosophila Sex-lethal and related sex determining genes. [FBrf0217612] Yang et al., 2012, Dev. Cell 22(5): 1041--1051 Phf7 controls male sex determination in the Drosophila germline. [FBrf0218344] Avery et al., 2011, RNA 17(4): 624--638 Drosophila Upf1 and Upf2 loss of function inhibits cell growth and causes animal death in a Upf3-independent manner. [FBrf0213282] Chang et al., 2011, BMC Genomics 12: 364 Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing. [FBrf0214625] Chatterjee et al., 2011, Development 138(6): 1099--1109 The female-specific Doublesex isoform regulates pleiotropic transcription factors to pattern genital development in Drosophila. [FBrf0213054] Graveley et al., 2011, Nature 471(7339): 473--479 The developmental transcriptome of Drosophila melanogaster. [FBrf0213330] Hartmann et al., 2011, RNA 17(3): 453--468 Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster. [FBrf0212988] Li et al., 2011, PLoS ONE 6(11): e28269 The hector G-Protein Coupled Receptor Is Required in a Subset of fruitless Neurons for Male Courtship Behavior. [FBrf0216834] Show all research papers ...
Recent reviews ( 1 )
	Salz, 2011, Curr. Opin. Genet. Dev. 21(4): 395--400 Sex determination in insects: a binary decision based on alternative splicing. [FBrf0214566] Show all reviews ...