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Gene Dmel\Hr39

General Information
Symbol	Dmel\Hr39	Species	D. melanogaster
Name	Hormone receptor-like in 39	Annotation symbol	CG8676
Feature type	protein_coding_gene	FlyBase ID	FBgn0261239
Gene Model Status	Current	Stock availability	30 publicly available
Also Known As	DHR39, βFTZ-F1, ftz-F1β, ftz-F1, NR5B1
Genomic Location
Chromosome (arm)	2L	Recombination map	2-
Cytogenetic map	39C-60	Sequence location	2L:21,237,250..21,259,675 [+]
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 Hormone receptor-like in 39 is referred to in FlyBase by the symbol Dmel\Hr39 (CG8676, FBgn0261239). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II core promoter proximal region sequence-specific DNA binding; ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity. There is experimental evidence that it is involved in the biological process: female meiosis chromosome segregation; activation of cysteine-type endopeptidase activity involved in apoptotic process; spermathecum morphogenesis; regulation of gene silencing; ecdysone-mediated induction of salivary gland cell autophagic cell death. 43 alleles are reported. The phenotypes of these alleles are annotated with: spermathecum; eye; trichogen cell; ovary; macrochaeta; female accessory gland; wing. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: Nuclear hormone receptor, ligand-binding; Nuclear hormone receptor, ligand-binding, core; Steroid hormone receptor; Zinc finger, NHR/GATA-type; Zinc finger, nuclear hormone receptor-type. 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 06-18 hour embryonic stages, during late larval 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 moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, adult crop, larval midgut, larval hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult testis, larval carcass. Gene sequence location is 2L:21237250..21259675.
User Contributed Data
	Beta version, feedback welcome
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03	Alleles Hr39[hs.PA] Hr39[C318a] Transgenic Constructs P{hs-Hr39.A} Controlled Vocabulary Terms male courtship behavior, veined wing generated song production
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 39C-60   Limits computationally determined from genome sequence between P{lacW}l(2)k07215k07215&P{lacW}snRNA:U4:39Bk09410 and P{lacW}l(2)k14505k14505&P{lacW}l(2)k05106k05106; Left limit from (method unavailable) (FBrf0106405) Right limit from (method unavailable) (FBrf0106405)
Experimentally Determined Cytological Location
Cytogenetic map Notes References 39C-39C     (Ayer, 1993) 39C1-39C2     (BDGP Project Members, 1994-1999) 39B-39C   (determined by in situ hybridisation)   (Ayer et al., 1993) 39C-39C   (determined by in situ hybridisation)   (Ohno and Petkovich, 1993)
Experimentally Determined Recombination Data
Location	2- (Horn et al., 2003, )
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Hr39 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 Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated Annotated transcripts do not represent all supported alternative splices within 5' UTR. Low-frequency RNA-Seq exon junction(s) not annotated.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Hr39-RA FBtr0081480  NM_057584   3291   808 Hr39-RB FBtr0081479  NM_134296   4844   808 Hr39-RC FBtr0081478  NM_057585   2722   701 Hr39-RD FBtr0081481  NM_165364   4828   808
Additional Transcript Data & Comments
Reported size (kB)	5.1, 3.5 (northern blot) (Ohno and Petkovich, 1993) 5.0, 3.5 (northern blot); 2.734 (longest cDNA) (Ayer et al., 1993)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Hr39-PA   FBpp0081009   87.3   808   7.50     NP_476932   AAN11107 Hr39-PB   FBpp0081008   87.3   808   7.50     NP_599123   AAF53984 Hr39-PC   FBpp0081007   74.8   701   7.49     NP_476933   AAN11109 Hr39-PD   FBpp0081010   87.3   808   7.50     NP_724322   AAN11108
Additional Polypeptide Data & Comments
Reported size (kDa)	808, 701 (aa) (Ayer et al., 1993)
Comments	Hr39 protein binds to a AGGTCA binding site in vitro but does not require the presence of any of 5 Drosophila nuclear receptor superfamily members tested. (Horner et al., 1995) The Hr39 protein was shown to bind the Adh adult enhancer (AAE) and repress distal Adh expression in a dosage dependent manner (in co-transfection experiments). Hr39 protein binds the same DNA sequences as ftz-f1 protein. (Ayer et al., 1993) The 701aa Hr39 protein has the same N-terminal sequences as the 808aa Hr39 protein but is missing the carboxy terminal sequences which contain the ligand-binding domain. In cotransfection experiments, this protein had no effect on Adh distal transcription presumably due to the lack of the carboxy terminal end of the protein. (Ayer et al., 1993) Bacterially expressed Hr39 protein was shown to specifically bind to a site that is also bound by ftz-f1 protein in the zebra stripe promoter element of ftz. (Ohno and Petkovich, 1993) One of a couple of protein products generated by alternative splicing. (FlyBase, 1992-, FlyBase, 1992-)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Nuclear hormone receptor, ligand-binding, core (IPR000536) Zinc finger, nuclear hormone receptor-type (IPR001628) Steroid hormone receptor (IPR001723) Nuclear hormone receptor, ligand-binding (IPR008946) Zinc finger, NHR/GATA-type (IPR013088)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA440081   AA440466   AE014134 AAF53984   AE014134 AAN11107   AE014134 AAN11108   AE014134 AAN11109   AC005811   AI403999   AI455960   AI512911   AI532418   AI534002   AI544109   AQ254867   AW943758   AY069676 AAL39821   AZ300953   BG639653   BH011498   BI172005   BI214125   BI231216   BI235958   CA805123   CL705916   CO152923   CO177974   CO179259   CO184922   CO185675   CO187353   CO187540   CO263825   CO268397   CO270329   CO280238   CO281957   CO284276   CO291826   CO296785   CO296936   CO297286   CO303580   CO309824   CO310153   CO312143   CO312657   CO313548   CO315064   CO316027   CO318684   CO323192   CO323659   CO328844   CO332738   CO344758   CO344935   CZ473443   CZ473444   CZ474356   CZ474997   CZ474998   CZ476747   CZ477497   CZ480447   CZ483419   CZ487399   CZ489438   EC057471   EC057593   EC058283   EC060286   EC060807   EC063543   EC069061   EC069062   EC076919   EC087482   EC089757   EC090658   EC201811   EC211418   EC213132   EC221881   EC223650   EC224908   EC225000   EC231787   EC237489   EC237686   EC238435   EC240463   EC240949   EC242982   EC245197   EC248462   EC248554   EC252182   EC256345   EC263607   GH748805   GH750551   GH750636   GH750746   GH750903   GH751204   GH751445   GH752081   GH752364   GH752611   GH752655   GH753090   GH753395   GH753406   GH753884   GH754453   GH754616   GH755352   GH755595   GH755651   GH756714   GH758649   GH759990   GH760027   GH760192   GH761265   GH770989   GH771141   GH771854   GH773477   GH773479   GH774956   GH775135   GH777286   GH777718   GH778422   GH779935   GH780398   GH780498   GH781029   GH781193   GH781362   GH782250   GH782370   GH782547   GH782993   GH784122   GH784314   GH787020   GH787458   GH788855   GH789309   GH789541   GH790159   GH790660   GH790780   GH791148   GH791307   GH791555   GH791654   GH791988   GH792109   GH792370   GH794215   GH794696   GH795105   GH796787   GH798458   GH800655   GH802608   GH802735   GH802768   GH803632   GH803675   GH804040   GH805026   GH805213   GH805808   GH806971   GH807089   GH807466   GH808882   GH809668   GH810068   GH810285   GH811066   GH811116   GH811742   GH812275   GH812871   GH813845   GH814192   GH814286   GH816268   GH817968   GH818664   GH819093   GH819383   GH821302   GH822323   GH822534   GH824314   GH824540   GH826490   GH830114   GH830568   GH830570   GH830755   GH831906   GH831993   GH832712   GH832968   GH834963   GH835029   GH835655   GH835936   GH836108   GH836191   GH836546   GH837294   GH837547   GH839642   GH843176   GH843924   GH844153   GH844356   GH845515   GH845693   GH846342   GH846716   GH846724   GH848285   GH848753   GH849589   GH850320   GH851667   GH853588   GH853864   GH854422   GH854494   GH855808   GH856713   GH857070   GH857665   GH858004   GH858081   GH858218   GH859040   GH859347   GH861970   GH864229   GH864372   GH864557   GH864603   GH864650   GH866049   GH866656   GH867099   GH867367   GH867510   GH867643   GH868237   GH868324   GH869928   GH870610   GH871678   GH871969   GH872298   GH874668   GH875096   GH875124   GH875344   GH875375   GH875773   GH876627   GH876710   GH877562   GH877564   GH878257   GH880295   GH880495   GH880772   GH880993   GH881159   GH882188   GH882368   GH883342   GH884059   GH884650   GH884826   GH884922   GH887468   GH887879   GH888040   GH889518   GH889717   GH889819   GH890659   GH891482   GH891555   GH891982   GH892121   GH892300   GH892860   GH893142   GH894299   GH895121   GH896311   GH896428   GH897166   GH897673   GH897809   GH898683   GH900608   GH901257   GH903505   GH904356   GH904724   GH904893   GH904925   GH905526   GH906571   GH906987   GH907104   GH907227   GH908469   GH908882   GH909070   GH911559   GH911993   GH912387   GH912731   GH913442   GH914038   GH915662   GH916568   GH916770   GH917008   GH918033   GH918733   GH919416   GH920486   GH922009   GH922518   GH923191   GH924026   GH924171   GH924331   GH924834   GH925592   GH926399   GH926599   GH926868   GH927147   GH927545   GH928424   GH928544   GH930027   GH931367   GH931368   GH931885   GH932032   GH932364   GH933959   GH935485   GH937358   GH937384   GH938078   GH938240   GH939142   GH939145   GH939693   GH940561   GH940938   L06423 AAA28543   L07549 AAA28462   L07550 AAA28463   L07551 AAA28464
UniProtKB/Swiss-Prot	Q05192
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage 13   stomodeum   (Ayer et al., 1993) embryonic stage 16   supraesophageal ganglion   (Ayer et al., 1993) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 11 -- 12   dorsal epidermis primordium   (Fisher et al., 2012) foregut primordium   (Fisher et al., 2012) hindgut proper primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic dorsal epidermis   (Fisher et al., 2012) embryonic epipharynx   (Fisher et al., 2012) embryonic foregut   (Fisher et al., 2012) embryonic hindgut   (Fisher et al., 2012) embryonic hypopharynx   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) embryonic stage 16   presumptive embryonic/larval central nervous system   (Ayer et al., 1993) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic/larval hindgut   (Ohno and Petkovich, 1993) presumptive embryonic/larval central nervous system   (Ohno and Petkovich, 1993) embryonic stage | early     (Ayer et al., 1993, Ohno and Petkovich, 1993) embryonic stage -- adult stage     (Ohno and Petkovich, 1993)
Additional Descriptive Data
	Hr39 3.5kb transcripts are most abundant in 0-3 hour embryos and are probably maternally inherited. (Ayer et al., 1993) 3.5kb Hr39 transcripts are maternally expressed. They are uniformly distributed in early embryos. (Ohno and Petkovich, 1993) 5kb Hr39 transcripts are present at all developmental stages. In embryos, transcripts are most abundant at 6-9 hr. Hr39 transcripts are detected in the stomodeum of stage 13 embryos. In stage 16 embryos, transcripts are most prominent in the central nervous system and in the brain lobes. (Ayer et al., 1993) Hr39 expression was studied in staged third instar larvae and prepupae collected at two hour intervals. Transcripts can first be detected in early third instar larvae and continue to be present at low levels until 106-108hr. After that, they accumulate to high levels, peaking in early prepupae. Hr39 transcripts drop in abundance in mid prepupae, rise again in 10hr prepupae, and continue to be present through the beginning of pupal development. In staged prepupal salivary glands, Hr39 transcripts are abundant at 0hr, decline in 2hr glands, and then are reintroduced, peaking 6-8hr after puparium formation. Hr39 transcripts are rapidly induced by ecdysone. (Horner et al., 1995) 5.1kb Hr39 transcripts are not present in early embryos but are detected at all other stages of development. An elevated transcript level is observed during puparium formation. Transcripts are uniformly distributed in early embryos. At later stages, high levels of expression are observed in the ventral cord, brain, and hindgut. (Ohno and Petkovich, 1993)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (Ohno et al., 1994)
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 moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, adult crop, larval midgut, larval hindgut, larval/adult Malpighian tubules, larval fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult testis, larval carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (44) central nervous system, larvae L3  (35) central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae  (65) digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering  (32) carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female  (27) testis, mated 4-day male    9 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    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 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    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 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    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (44) central nervous system, larvae L3  (35) central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae  (65) digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering  32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female  27 testis, mated 4-day male    9 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    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 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    44 central nervous system, larvae L3    35 central nervous system, pupae P8    15 head, virgin 1-day female    6 head, virgin 4-day female    8 head, virgin 20-day female    6 head, mated 1-day female    7 head, mated 4-day female    5 head, mated 20-day female    6 head, mated 1-day male    10 head, mated 4-day male    8 head, mated 20-day male    9 salivary gland, larvae L3 wandering    23 salivary gland, white prepupae    65 digestive system, larvae L3 wandering    19 digestive system, 1-day adult    6 digestive system, 4-day adult    7 digestive system, 20-day adult    6 fat body, larvae L3 wandering    4 fat body, white prepupae    15 fat body, pupae P8    11 carcass, larvae L3 wandering    32 carcass, 1-day adult    5 carcass, 4-day adult    4 carcass, 20-day adult    4 ovary, virgin 4-day female    24 ovary, mated 4-day female    27 testis, mated 4-day male    9 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 06-18 hour embryonic stages, during late larval 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    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr  26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 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    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr  26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 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    15 embryo 02-04hr    2 embryo 04-06hr    3 embryo 06-08hr    11 embryo 08-10hr    17 embryo 10-12hr    26 embryo 12-14hr    19 embryo 14-16hr    5 embryo 16-18hr    7 embryo 18-20hr    15 embryo 20-22hr    9 embryo 22-24hr    11 larva L1    6 larva L2    5 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    11 larva L3 puffstage 7-9    24 white prepupae new    22 white prepupae 12hr    21 white prepupae 24hr    22 pupae 2d postWPP    14 pupae 3d postWPP    11 pupae 4d postWPP    9 adult male 01day    4 adult male 05day    5 adult male 30day    4 adult female 01day    7 adult female 05day    10 adult female 30day    10 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+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC  (45) ovary OSS    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 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+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC  (45) ovary OSS    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 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+    16 Schneider line 2 Sg4    9 embryonic 1182-4H    13 embryonic GM2    15 embryonic Kc167    15 embryonic S1    13 embryonic S3    11 leg disc CME L1    6 wing disc CME-W2    12 wing disc ML-DmD8    17 wing disc ML-DmD9    21 wing disc ML-DmD16-c3    17 wing disc ML-DmD21    6 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    16 eye-antennal disc ML-DmD11    13 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    12 CNS ML-DmBG1-c1    9 CNS ML-DmBG2-c2    7 tumorous blood cells mbn2    11 ovary fGS/OSS    8 ovary OSC    45 ovary OSS    6 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    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult  (27) cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 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    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult  27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 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    27 cold shock, 4-day adult    18 heat shock, 4-day adult    11 Cadmium 50 mM 6 hrs, larvae L3    7 Cadmium 50 mM 12 hrs, larvae L3    13 Cadmium 50 mM 48 hrs, 4-day adult    13 Cadmium 100 mM 48 hrs, 4-day adult    22 Copper 0.5 mM 12 hrs, larvae L3    10 Copper 15 mM 48 hrs, 4-day adult    13 Zinc 5 mM 12 hrs, larvae L3    14 Zinc 4.5 mM 48 hrs, 4-day adult    10 Ethanol 2.5% 3 hrs, larvae L3    19 Ethanol 5% 3 hrs, larvae L3    5 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    6 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    22 Caffeine 25 mg/ml 48 hrs, 4-day adult    20 Paraquat 5 mM 48 hrs, 4-day adult    17 Paraquat 10 mM 48 hrs, 4-day adult    13 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    6 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (Graveley et al., 2011) mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • LD45021 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0261239
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL4Act5C.PI Hr39LA1.4 lethal | recessive Hr3980 viable Hr3902 Hr3904 Hr39CB05039 Hr39EY04579 Hr39k13215 viable, with Scer\GAL4pnr-MD237 Hr39GD4462 Sterility Allele female sterile Hr3903508 Hr3907154 Hr39ly92 Hr39neo8 female sterile | recessive Hr3903508 Hr3907154 Hr39ly92 Hr39neo8 fertile Hr39EY04579 Other Phenotypes Allele meiotic cell cycle defective | dominant Hr39Scim song defective Hr39C318a visible, with Scer\GAL4en-e16E Hr39EP2490 visible, with Scer\GAL4ey.PH Hr39EP2490 visible, with Scer\GAL4pnr-MD237 Hr39GD4462 Phenotype manifest in Allele eye, with Scer\GAL4ey.PH Hr39EP2490 female accessory gland Hr3904443 Hr3903508 macrochaeta Hr39BG01818 ovary Hr39neo8 spermathecum Hr39k13215 Hr39neo8 Hr39ly92 Hr3903508 Hr3907154 spermathecum | supernumerary Hr3904443 spermathecum | supernumerary, with Scer\GAL4hs.PB Hr39Scer\UAS.cAa trichogen cell, with Scer\GAL4pnr-MD237 Hr39GD4462 wing, with Scer\GAL4en-e16E Hr39EP2490
Classical Alleles ( 35 )
For All Classical Alleles Show
Allele of Hr39 Class Mutagen Stocks Known lesion Hr39Scim Delta2-3 2 Yes Hr3902 1 Yes Hr3904 1 Yes Hr395-HA-1182 1 -- Hr39BG02396 P-element activity 1 -- Hr39c739 P-element activity 1 Yes Hr39CB-5494-3 1 -- Hr39CB-5735-3 1 -- Hr39d03582 P-element activity 1 -- Hr39d05159 P-element activity 1 -- Hr39d06230 P-element activity 1 -- Hr39d09440 P-element activity 1 -- Hr39d10907 P-element activity 1 -- Hr39e02672 piggyBac transposase 1 -- Hr39EY04579 P-element activity 1 -- Hr39f00937 piggyBac transposase 1 -- Hr39f06712 piggyBac transposase 1 -- Hr39MI06174 1 -- Hr39neo8 P-element activity 1 -- Hr39NP7329 1 -- Hr39UM-8017-3 1 -- Hr3903508 0 -- Hr3904443 hypermorphic allele - genetic evidence P-element activity 0 -- Hr3907154 0 -- Hr3980 piggyBac transposase 0 Yes Hr39BG01818 P-element activity 0 Yes Hr39C318a 0 -- Hr39CB05039 P-element activity 0 Yes Hr39DG30508 P-element activity 0 -- Hr39EP2490 P-element activity 0 -- Hr39EP2507 P-element activity 0 -- Hr39f04827 piggyBac transposase 0 -- Hr39k13215 P-element activity 0 Yes Hr39LA1.4 P-element activity 0 -- Hr39ly92 0 --
Alleles Carried on Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Hr39 Class Mutagen Stocks Known lesion Hr39GD4462 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Hr39hs.T:Scer\GAL4.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 2 Yes Hr39ABD.T:Avic\GFP-SF,T:Zzzz\FLAG,T:Zzzz\PSP.CS,T:Zzzz\TEV.CS,T:Zzzz\BLRP in vitro construct - coding region fusion 1 Yes Hr39C.T:Avic\GFP-SF,T:Zzzz\FLAG,T:Zzzz\PSP.CS,T:Zzzz\TEV.CS,T:Zzzz\BLRP in vitro construct - coding region fusion 1 Yes Hr39HMS00018 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr39JF02432 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr39hs.PA in vitro construct - regulatory fusion 0 Yes Hr39MtnA.PC in vitro construct - regulatory fusion 0 Yes Hr39NIG.8676R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes Hr39Scer\UAS.cAa in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)Exel6048 (Allen and Spradling, 2008, Ryder, 2004.4.26) Df(2L)TW1 (Horner and Thummel, 1997)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4462} NA P{NIG.8676R} NA P{TRiP.HMS00018} NA P{TRiP.JF02432} NA P{UAS-Hr39.A} NA GAL4 construct P{hs-GAL4-DHR39.LBD.HA} No heat-shock construct P{hs-GAL4-DHR39.LBD.HA} NA P{hs-Hr39.A} NA characterization construct PBac{Hr39-GFP.ABD.FPTB} NA PBac{Hr39-GFP.C.FPTB} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions Mi{MIC}Hr39MI06174 NA P{GT1}Hr39BG01818 NA P{GT1}Hr39BG02396 NA P{hsneo}Hr39neo8 NA P{PTT-GB}Hr39CB05039 NA P{RS3}Hr39CB-5494-3 NA P{RS3}Hr39CB-5735-3 NA P{RS3}Hr39UM-8017-3 NA P{RS5}Hr395-HA-1182 NA P{ry11}Hr39ly92 NA P{SUPor-P}Hr39Scim NA P{UASp-YFP.RabX6}Hr3904 NA P{UAST-YFP.Rab19}Hr3902 NA P{wHy}Hr39DG30508 NA PBac{RB}Hr39e02672 NA PBac{WH}Hr39f00937 NA PBac{WH}Hr39f04827 NA PBac{WH}Hr39f06712 NA insertion of mobile activating element P{EP}Hr39EP2490 NA P{EP}Hr39EP2507 NA P{EPgy2}Hr39EY04579 NA P{GSV1}C277C277 NA P{Mae-UAS.6.11}B0799B0799 NA P{Mae-UAS.6.11}B1116B1116 NA P{Mae-UAS.6.11}B1501B1501 NA P{Mae-UAS.6.11}B2036b NA P{Mae-UAS.6.11}Hr39LA1.4 NA P{XP}Hr39d03582 NA P{XP}Hr39d05159 NA P{XP}Hr39d06230 NA P{XP}Hr39d09440 NA P{XP}Hr39d10907 NA insertion of enhancer trap binary system P{GawB}Hr39C318a No P{GawB}Hr39c739 No P{GawB}Hr39NP7329 No PBac{GAL4D,EYFP}Hr3980 No insertion of enhancer trap P{lacW}Hr39k13215 No P{PZ}Hr3903508 No P{PZ}Hr3904443 No P{PZ}Hr3907154 No
Gene Ontology: Function, Process & Cellular Component ( 16 unique terms )
Terms Based on Experimental Evidence ( 9 terms )
Molecular Function
CV term Evidence References
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from direct assay (Ohno et al., 1994) RNA polymerase II core promoter proximal region sequence-specific DNA binding inferred from direct assay (Ohno et al., 1994)
Biological Process
CV term Evidence References
activation of cysteine-type endopeptidase activity involved in apoptotic process inferred from mutant phenotype (Takemoto et al., 2007) ecdysone-mediated induction of salivary gland cell autophagic cell death inferred from mutant phenotype (Takemoto et al., 2007) female meiosis chromosome segregation inferred from mutant phenotype (Dobie et al., 2001) male courtship behavior, veined wing generated song production inferred from mutant phenotype (Moran and Kyriacou, 2009) regulation of gene silencing inferred from mutant phenotype (Schneiderman et al., 2010) spermathecum morphogenesis inferred from mutant phenotype (Allen and Spradling, 2008)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Ohno et al., 1994)
Terms Based on Predictions or Assertions ( 9 terms )
Molecular Function
CV term Evidence References
DNA binding non-traceable author statement (Swiss-Prot Project Members, 1996.6.1) ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from sequence or structural similarity with UniProtKB:P51128 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1996.6.1, Maglich et al., 2001) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:P51128 (FlyBase, 1992-) steroid hormone receptor activity inferred from electronic annotation with InterPro:IPR000536, InterPro:IPR001723, InterPro:IPR008946 (FlyBase Curators et al., 2004-) transcription cofactor activity non-traceable author statement (Swiss-Prot Project Members, 1996.6.1) zinc ion binding inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
regulation of transcription, DNA-dependent inferred from electronic annotation with InterPro:IPR000536, InterPro:IPR001628, InterPro:IPR001723, InterPro:IPR008946, InterPro:IPR013088 (FlyBase Curators et al., 2004-) non-traceable author statement (Swiss-Prot Project Members, 1996.6.1) steroid hormone mediated signaling pathway inferred from electronic annotation with InterPro:IPR000536, InterPro:IPR008946 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:P51128 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1996.6.1)
Sequence Ontology: Class of Gene
	gene   nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Hr39 - CG1532 anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based (Mintseris et al., 2009.11.23, Guruharsha et al., 2011) Hr39 - CG7049 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Hr39 - Ccs anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Hr39 - Pp1-87B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Hr39 - RpS21 anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based (Mintseris et al., 2009.11.23, Guruharsha et al., 2011)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Hr39 allele Gene References Hr39EP2490 pnr (Pena-Rangel et al., 2002)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 61349 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0261239 DroID - A comprehensive database of gene and protein interactions. • FBgn0261239 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35398
Orthologs
OrthoDB Orthologs (30) - 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 EOG6M0FM4 Dipteran inclusive ortholog search EOG6NKC3T Insect inclusive ortholog search EOG6GF29R Arthropod inclusive ortholog search EOG6MCVFX Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6M0FM4)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Hr39     Drosophila simulans   Dsim\GD24312 Y   Drosophila sechellia   Dsec\GM23404 Y   Drosophila erecta   Dere\GG21291 Y   Drosophila yakuba   Dyak\GE12908 Y   Drosophila ananassae   Dana\GF14318 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA21254 Y   Drosophila persimilis   Dper\GL26651 Y   Drosophila willistoni   Dwil\GK18731 Y   Drosophila virilis   Dvir\GJ18326 Y   Drosophila mojavensis   Dmoj\GI11193 Y   Drosophila grimshawi   Dgri\GH10687 Y
Orthologs in non-Drosophila Dipterans (EOG6NKC3T)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001304   Anopheles gambiae Malaria mosquito  Agam\AGAP009400   Anopheles gambiae Malaria mosquito  Agam\AGAP009399   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ802157
Orthologs in non-Dipteran Insects (EOG6GF29R)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB45414   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG007382   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH16165   Atta cephalotes Leafcutter ant  Acep\ACEP18350   Camponotus floridanus Florida carpenter ant  Cflo\CFLO16615   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL12408   Linepithema humile Argentine ant  Lhum\LH12534   Pogonomyrmex barbatus Red harvester ant  Pbar\PB21385   Solenopsis invicta Red fire ant  Sinv\SINV18006   Acyrthosiphon pisum Pea aphid  Apim\ACYPI006350   Bombyx mori Silkmoth  Bmor\BGIBMGA007914   Pediculus humanus Human body louse  Phum\PHUM318510   Tribolium castaneum Red flour beetle  Tcas\Hr39
Orthologs in non-Insect Arthropods (EOG6MCVFX)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_57218
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD24312 Drosophila sechellia Dsec\GM23404 Drosophila erecta Dere\GG21291 Drosophila yakuba Dyak\GE12908 Drosophila ananassae Dana\GF14318 Drosophila pseudoobscura pseudoobscura Dpse\GA21254 Drosophila persimilis Dper\GL26651 Drosophila willistoni Dwil\GK18731 Drosophila virilis Dvir\GJ18326 Drosophila mojavensis Dmoj\GI11193 Drosophila grimshawi Dgri\GH10687
Stocks & Reagents
Stocks Listed in FlyBase ( 30 )
Bloomington	10055 P{hsneo}Hr39neo8/CyO 12679 w1118; P{GT1}Hr39BG02396
Harvard	- P{XP}Hr39d03582 - P{XP}Hr39d05159 - P{XP}Hr39d06230 - P{XP}Hr39d09440 - P{XP}Hr39d10907 - PBac{RB}Hr39e02672 - PBac{WH}Hr39f00937 - PBac{WH}Hr39f06712
VDRC	v37694 w1118; P{GD4462}v37694 v37695 w1118; P{GD4462}v37695/CyO
	More stocks available...
Genomic Clones ( 1 )
	BACR34H23 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 349 )
	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	LD45021
Other clones	DPiM_LD45021
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH23566 LD15162 LD15320 LD35704 LD46342 RE13920 RE19837 RE20449 RE31929 SD03933 SD03961 SD06422
Other clones	5963 28705 34901 40046 55664 64163 70742 81473 81807 82904 97140 97839 106104 107436 118975 119293 122049 160258 172781 214315.12 277113 521938 CK01.7D.B12 CK01.27C.G12 CK01.33C.B12 CK01.33D.G8 CK01.119C.B10 CK01.127D.C4 EC28793 EK010838 EK028440 EK030230 EK054859 EK058905 EK091237 EK098532 EK136539 EK153447 EK159201 EK165638 EK189923 EK191049 EK198441 EK215148 EK215449 EK216560 EK219433 EK220615 EK227939 EK229607 EK233340 EK238910 EK242145 EK263355 EK273422 EK291519 EK304410 EN00827 EP19839 EP20802 ESG0116c.B21_E02 RP003003003 RP003004112 RP003019015 RP003019640 RP003028086 RP003031368 RP003033158 RP003036498 RP003038067 RP003038591 RP003042138 RP003043361 RP003047187 RP003048380 RP003050493 RP003051494 RP003062796 RP003067941 RP003074883 RP003076487 RP003077954 RP003079763 RP003082787 RP003083905 RP003084590 RP003084659 RP003088029 RP003092933 RP003094089 RP003095406 RP003095589 RP003098626 RP003099048 RP003099962 RP003100881 RP003101369 RP003102579 RP003103624 RP003104755 RP003105279 RP003110232 RP003110286 RP003113112 RP003113620 RP003113640 RP003115516 RP003116565 RP003120198 RP003121110 RP003121560 RP003122185 RP003132283 RP003132662 RP003137848 RP003138761 RP003143974 RP003144015 RP003144328 RP003146232 RP003148323 RP003149629 RP003150586 RP003150686 RP003152053 RP003153959 RP003158557 RP003164295 RP003166012 RP003168544 RP003174777 RP003177028 RP003179229 RP003184054 RP003184128 RP003187629 RP003191282 RP003194705 RP003195562 RP003196534 RP003199211 RP003200184 RP003202811 RP003208724 RP003209972 RP003213714 RP003214610 RP003217142 RP003217655 RP003217908 RP003218054 RP003219497 RP003222086 RP003223475 RP003226399 RP003226655 RP003230385 RP003234390 RP003238076 RP003238734 RP003239031 RP003239861 RP003240152 RP003247658 RP003248692 RP003251445 RP003252819 RP003253917 RP003254415 RP003254548 RP003256289 RP003262977 RP003266875 RP003267726 RP003271456 RP003272524 RP003273632 RP003275940 RP003279011 RP003280867 RP003281577 RP003286762 RP003288618 RP003290046 RP003290910 RP003291131 RP003293277 RP003297108 RP003303661 RP003310134 RP003317769 RP003318132 RP003322366 RP003324506 RP003324569 RP003324751 RP003325451 RP003326184 RP003329051 RP003331420 RP003332583 RP003338992 RP003342295 RP003343124 RP003344595 RP003345008 RP003345235 RP003346639 RP003349911 RP003351052 RP003358079 RP003359610 RP003359848 RP003359864 RP003366039 RP003366065 RP003368815 RP003372178 RP003375214 RP003379664 RP003384354 RP003390438 RP003391047 RP003394377 RP003395775 RP003397595 RP003398991 RP003402691 RP003405314 RP003408814 RP003413910 RP003415405 RP003416797 RP003417633 RP003418724 RP003423250 RP003427269 RP003429686 RP003447384 RP003447696 RP003448287 RP003448671 RP003450397 RP003451051 RP003451509 RP003458458 RP003459635 RP003462181 RP003462924 RP003463723 RP003465335 RP003471604 RP003471616 RP003471650 RP003473313 RP003473456 RP003474343 RP003474682 RP003476812 RP003479083 RP003482533 RP003482544 RP003484311 RP003484631 RP003487448 RP003490551 RP003492584 RP003492741 RP003492856 RP003493988 RP003496157 RP003505101 RP003505321 RP003506148 RP003507716 RP003510039 RP003515103 RP003519381 RP003520089 RP003526027 RP003531098 RP003533742 RP003537953 RP003542302 RP003545953 RP003552421 RP003557307 RP003557457 RP003558754 RP003561411 RP003562981 RP003567729 RP003567797 RP003567811 RP003570352 RP003573851 RP003575600 RP003581284 RP003581797 RP003583735 RP003585522 RP003585540 RP003587986 RP003591916 RP003593356 RP003594494 RP003597040 RP003598951 RP003599436 RP003604102 RP003607191 RP003608539 RP003609076 RP003626318 RP003627277 RP003632601 RP003634311 RP003634433 RP003635311 RP003637343 RP003637627 RP003652183 RP003654741 RP003657987 RP003661071 RP003662611 RP003664474 RP003666714 RP003667057 RP003667230 RP003672677 RP003672826 RP003675961 RP003680775 RP003681377
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0261239 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35398
Antibody Information
	polyclonal (Boulanger 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: Hr39 fs(2)neo8 fs(2)04443 (Allen and Spradling, 2008)
Additional comments
Other Comments
	Hr39 does not play an essential role during development. (Horner and Thummel, 1997) Temporal profile of gene expression is not altered in Eip74EF mutant background. (Fletcher and Thummel, 1995) Hr39 and Hr46 contribute to the regulatory hierarchy activated by the steroid hormone 20E at the onset of metamorphosis. (Horner et al., 1995) ftz-f1 and Hr39 bind as monomers to oligonucleotides corresponding to the ftz-f1 recognition element (F1RE) located within the zebra element of ftz promoter. Antagonism between the two receptors contributes to the net F1RE-dependent transcription of a reporter gene in cotransfection assays. Results suggest common target genes may be coregulated at the transcriptional level by a mechanism of competition between ftz-f1 and Hr39 monomers for binding to a common element. (Ohno et al., 1994) Hr39 cloned by screening an expression library with oligonucleotide probe corresponding to the positive element of the Adh adult enhancer: DNA sequence analysis showed Hr39 belongs to the steroid hormone receptor superfamily. Whereas ftz-f1, which binds to the same sequence, acts as an activator of distal Adh transcription, Hr39 acts to repress distal Adh transcription. (Ayer et al., 1993) Hr39 is a member of the nuclear receptor family which exhibit structural and functional properties similar to those of ftz-f1. A single copy gene. (Ohno and Petkovich, 1993)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057584 NM_057585 NM_134296 NM_165364 RefSeq (Proteins) • NP_476932 NP_476933 NP_599123 NP_724322 DDBJ / EMBL / GenBank • AAA28462 AAA28463 AAA28464 AAA28543 AAF53984 AAL39821 AAN11107 AAN11108 AAN11109 AC005811 AI512911 AQ254867 AW943758 AY069676 AZ300953 BH011498 CL705916 CZ473443 CZ473444 CZ474356 CZ474997 CZ474998 CZ476747 CZ477497 CZ480447 CZ483419 CZ487399 CZ489438 L06423 L07549 L07550 L07551 Entrez Gene - A searchable database of RefSeq genes. • 35398 UniProtKB/Swiss-Prot • Q05192
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Nuclear hormone receptor, ligand-binding, core (IPR000536) Zinc finger, nuclear hormone receptor-type (IPR001628) Steroid hormone receptor (IPR001723) Nuclear hormone receptor, ligand-binding (IPR008946) Zinc finger, NHR/GATA-type (IPR013088) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LD45021
Linkouts
	BioGRID - A database of protein and genetic interactions • 61349 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0261239 DroID - A comprehensive database of gene and protein interactions. • FBgn0261239 DRSC - Results from RNAi screens. • FBgn0261239 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0261239 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0261239 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35398 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35398 modMine - Data generated by the modENCODE project. • FBgn0261239 REDfly - A database of transcriptional regulatory elements. • FBgn0261239
Synonyms & Secondary IDs ( 24 )
Reported As
Symbol Synonym	CG8676 (Norga et al., 2003, Battersby et al., 2003, Lee et al., 2003, Molnar et al., 2006, Grieder et al., 2007, Perkins et al., 2009.3.31, Schneiderman et al., 2010, Ni et al., 2010.12.1) dFTZ-F1β (Laudet and Adelmant, 1995) DHR30 (Schwartz et al., 2001) DHR39 (Li and White, 2003, Richards et al., 1999, Nuclear Receptors Nomenclature Committee, 1999, Schwartz et al., 1999, Ueda et al., 1998, Furia et al., 1998, Crispi et al., 1998, Horner and Thummel, 1997, Schaefer and Taghert, 1995, Henrich and Brown, 1995, Fisk and Thummel, 1995, Horner et al., 1995, Huet et al., 1995, Fletcher and Thummel, 1995, Jindra, 1994, Palanker et al., 2006, King-Jones and Thummel, 2005, Zeitouni et al., 2007, Beckstead et al., 2005, Dubrovsky et al., 2011, Akagi et al., 2013) DHR39/Ftz-F1β (Yu et al., 1999) EP(2)2490 (Pena-Rangel et al., 2002) fs(2)04443   fs(2)neo8   ftz-F1 (Karlin and Burge, 1996, Fisk and Thummel, 1995) FTZ-F1 (Pankratz and Jaeckle, 1993) FTZ-F1B (Ohno, 1993.3.25) ftz-F1β (Segraves, 1994, Ohno et al., 1994, ) ftz-f1β (Petkovich et al., 1993, ) FTZ-F1β (Ohno and Petkovich, 1993, ) Hr39 (Spokony, 2012.12.12, Moran and Kyriacou, 2009, Abramov et al., 2011, Allen and Spradling, 2008, Buszczak et al., 2007, Zhang et al., 2007, Molnar et al., 2006, Grieder et al., 2007, Liebl et al., 2006, Zeitouni et al., 2007, Allen and Spradling, 2008, Prokupek et al., 2009, Shalaby et al., 2009, Spokony and White, 2012.5.22, Boulanger et al., 2011, Spradling et al., 2011, Japanese National Institute of Genetics, 2012.5.21, Sun and Spradling, 2012) HR39 (Bates et al., 2010, Schneiderman et al., 2010) i70 (Battersby et al., 2003) NR5B1 (Nuclear Receptors Nomenclature Committee, 1999, King-Jones and Thummel, 2005) unnamed (Guichet et al., 1996, Cooley et al., 1988) βFTZ-E1 (Zeitouni et al., 2007) βFTZ-F1 (D'Avino and Thummel, 1998, Thummel, 1997, Baehrecke, 1996, Takemoto et al., 2007)
Name Synonym	fs(2)04443   fs(2)neo8   Hormone receptor-like in 39 (Zeitouni et al., 2007, Davis et al., 2011) hormone receptor-like in 39 (Bates et al., 2010) NR5A-class nuclear hormone receptor (Sun and Spradling, 2012)
Secondary FlyBase IDs
	FBgn0010229 FBgn0013458 FBgn0014175 FBgn0026243
References ( 102 )
Generate a list of	All references relating to this gene ( 102 )
List References by type	Research paper  ( 50 ) Supplementary material  ( 8 ) Review  ( 11 ) Personal communication to FlyBase  ( 15 ) Abstract  ( 8 ) FlyBase analysis  ( 3 ) DNA/RNA sequence record  ( 2 ) Stock list  ( 1 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 8 )
	Akagi et al., 2013, J. Mol. Biol. 425(1): 71--81 The Binding of Multiple Nuclear Receptors to a Single Regulatory Region Is Important for the Proper Expression of EDG84A in Drosophila melanogaster. [FBrf0220406] Sun and Spradling, 2012, Curr. Biol. 22(10): 862--871 NR5A Nuclear Receptor Hr39 Controls Three-Cell Secretory Unit Formation in Drosophila Female Reproductive Glands. [FBrf0218434] Abramov et al., 2011, Dokl. Biochem. Biophys. 437(1): 72--76 Genetic and molecular analysis of gene trans-inactivation caused by homologous eu-heterochromatic chromosome rearrangement in Drosophila melanogaster. [FBrf0213780] Ambegaokar and Jackson, 2011, Hum. Mol. Genet. 20(24): 4947--4977 Functional genomic screen and network analysis reveal novel modifiers of tauopathy dissociated from tau phosphorylation. [FBrf0217690] Boulanger et al., 2011, Nat. Neurosci. 14(1): 37--44 ftz-f1 and Hr39 opposing roles on EcR expression during Drosophila mushroom body neuron remodeling. [FBrf0212642] Davis et al., 2011, BMC Dev. Biol. 11: 66 Identification of common and cell type specific LXXLL motif EcR cofactors using a bioinformatics refined candidate RNAi screen in Drosophila melanogaster cell lines. [FBrf0216830] Dubrovsky et al., 2011, J. Biol. Chem. 286(38): 33689--33700 The Drosophila FTZ-F1 Nuclear Receptor Mediates Juvenile Hormone Activation of E75A Gene Expression through an Intracellular Pathway. [FBrf0215576] Spradling et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(38): 15948--15953 Drosophila P elements preferentially transpose to replication origins. [FBrf0215815] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...