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Gene Dmel\Hr4

General Information
Symbol	Dmel\Hr4	Species	D. melanogaster
Name	Hr4	Annotation symbol	CG43934
Feature type	protein_coding_gene	FlyBase ID	FBgn0264562
Gene Model Status	Current	Stock availability	37 publicly available
Also Known As	DHR4, CG16902, CG3600, EG:BACH61I5.1, EP1232, NR6A2, EG:133E12.2
Genomic Location
Chromosome (arm)	X	Recombination map
Cytogenetic map	2C1-2C1	Sequence location	X:1,835,973..1,901,989 [+]
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 Hr4 is referred to in FlyBase by the symbol Dmel\Hr4 (CG43934, FBgn0264562). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity. There is experimental evidence that it is involved in the biological process: growth; cellular response to hypoxia; regulation of developmental growth; intracellular steroid hormone receptor signaling pathway; pupariation. 61 alleles are reported. The phenotypes of these alleles are annotated with: eye; dorsocentral bristle; mesothoracic tergum; embryonic/larval fat body; tormogen cell; scutellar bristle; wing; ommatidium; anterior pupal spiracle; ring gland. It has 9 annotated transcripts and 9 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. Gene sequence location is X:1835973..1901989.
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.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02	Controlled Vocabulary Terms regulation of developmental growth
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 2C1-2C1   Limits computationally determined from genome sequence between P{EP}CG3600EP1232 and P{EP}EP427
Experimentally Determined Cytological Location
Cytogenetic map Notes References 2B16-2B18   (determined by in situ hybridisation)   (Abdelilah-Seyfried et al., 2000)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Hr4 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 5.43 Low-frequency RNA-Seq exon junction(s) not annotated. gene_with_stop_codon_read_through ; SO:0000697 Stop-codon suppression (UAG) postulated; FlyBase analysis. Gene model reviewed during 5.46 Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated Gene merge based on RNA-Seq junction and coverage data.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Hr4-RC FBtr0333341  NM_001038734   8403   1518 Hr4-RD FBtr0333340  NM_001272230   8596   1529 Hr4-RE FBtr0333339  NM_001272229   9374   1842 Hr4-RF FBtr0333338  NM_001272228   8417   1611 Hr4-RG FBtr0333337  NM_001272227   9386   1986 Hr4-RH FBtr0333342  NM_001272231   8406   1863 Hr4-RI FBtr0333343  NM_001272232   8338   2123 Hr4-RJ FBtr0333344  NM_001272233   9581   1843 Hr4-RK FBtr0333345  NM_001272234   12551   1843
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Hr4-PC   FBpp0305533   162.7   1518   8.70     NP_001033823   ABC67166 Hr4-PD   FBpp0305532   163.7   1529   8.70     NP_001259159   AGB95005 Hr4-PE   FBpp0305531   197.5   1842   8.03     NP_001259158   AGB95004 Hr4-PF   FBpp0305530   173.2   1611   9.67     NP_001259157   AGB95003 Hr4-PG   FBpp0305529   213.5   1986   8.17     NP_001259156   AGB95002 Hr4-PH   FBpp0305534   199.6   1863   8.66     NP_001259160   AGB95006 Hr4-PI   FBpp0305535   226.1   2123   9.05     NP_001259161   AGB95007 Hr4-PJ   FBpp0305536   197.5   1843   8.03     NP_001259162   AGB95008 Hr4-PK   FBpp0305537   197.5   1843   8.03     NP_001259163   AGB95009
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Nuclear hormone receptor, ligand-binding (IPR008946) Steroid hormone receptor (IPR001723) Zinc finger, NHR/GATA-type (IPR013088) Zinc finger, nuclear hormone receptor-type (IPR001628) Nuclear hormone receptor, ligand-binding, core (IPR000536)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014298 ABC67166   AE014298 AGB95002   AE014298 AGB95003   AE014298 AGB95004   AE014298 AGB95005   AE014298 AGB95006   AE014298 AGB95007   AE014298 AGB95008   AE014298 AGB95009   AI542746   AL035245 CAA22835   AL035245 CAA22836   AQ254763   AY971884 AAX73355   BE976996   BI563637   BI565828   BI570488   BI571368   BI572990   BI590307   BT030119   CO155256   CO155629   CO177138   CO186301   CO187755   CO284677   CO287954   CO294008   CO294604   CO295064   CO296783   CO296794   CO299338   CO300315   CO307928   CO321273   CO321722   CO322555   CO322869   CO326427   CO340868   DQ327740   DQ327741   EC065011   EC066197   EC074532   EC195661   EC199477   EC201784   EC212692   EC218077   EC224389   EC224818   EC225385   EC244787   EC244791   EC246439   EC247311   EC259035   EL871652   EL871774   EL871775   EL875182   EL875183   EL875313   EL875314   EL882730   EL884043   EL884158   EL884159   GH889157
UniProtKB/Swiss-Prot	Q9W539
UniProtKB/TrEMBL	B7Z117 E1JJC9 O96835
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
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
nucleus inferred from direct assay (assigned by UniProtKB) (King-Jones et al., 2005)
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 (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 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    10 central nervous system, larvae L3    21 central nervous system, pupae P8    307 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8    177 carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    21 central nervous system, pupae P8  (307) head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae  (36) fat body, pupae P8  (177) carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    21 central nervous system, pupae P8  (307) head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8  (177) carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 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    10 central nervous system, larvae L3    21 central nervous system, pupae P8    307 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8    177 carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    21 central nervous system, pupae P8    307 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8    177 carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    21 central nervous system, pupae P8  (307) head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae  (36) fat body, pupae P8  (177) carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    21 central nervous system, pupae P8  (307) head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8  (177) carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 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    10 central nervous system, larvae L3    21 central nervous system, pupae P8    307 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    3 head, mated 1-day male    0 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    5 salivary gland, white prepupae    18 digestive system, larvae L3 wandering    8 digestive system, 1-day adult    0 digestive system, 4-day adult    1 digestive system, 20-day adult    0 fat body, larvae L3 wandering    4 fat body, white prepupae    36 fat body, pupae P8    177 carcass, larvae L3 wandering    24 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    0 ovary, virgin 4-day female    3 ovary, mated 4-day female    3 testis, mated 4-day male    0 accessory gland, mated 4-day male    5 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 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    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr  (37) embryo 12-14hr  (67) embryo 14-16hr  (83) embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9  (27) white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP  (65) pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 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    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr  (37) embryo 12-14hr  (67) embryo 14-16hr  (83) embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9  27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP  (65) pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 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    1 embryo 02-04hr    1 embryo 04-06hr    1 embryo 06-08hr    7 embryo 08-10hr    11 embryo 10-12hr    37 embryo 12-14hr    67 embryo 14-16hr    83 embryo 16-18hr    14 embryo 18-20hr    4 embryo 20-22hr    1 embryo 22-24hr    1 larva L1    1 larva L2    9 larva L3 12hr old    2 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    27 white prepupae new    21 white prepupae 12hr    8 white prepupae 24hr    4 pupae 2d postWPP    65 pupae 3d postWPP    13 pupae 4d postWPP    4 adult male 01day    1 adult male 05day    0 adult male 30day    0 adult female 01day    1 adult female 05day    1 adult female 30day    1 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 Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    1 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    2 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    0 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    0 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 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 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    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult  26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult  26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    24 cold shock, 4-day adult    26 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    0 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    3 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    6 Zinc 5 mM 12 hrs, larvae L3    7 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    0 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    3 Caffeine 25 mg/ml 48 hrs, 4-day adult    22 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (Graveley et al., 2011) mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal Hr417C9 lethal | pharate adult stage, with Hr41 Hr4Hsp70.PK lethal | pharate adult stage, with Hr4Hsp70.PK Hr41 lethal | prepupal stage Hr41 lethal | prepupal stage, with Scer\GAL4Cg.PA Hr4dsRNA.Scer\UAS lethal | pupal stage, with Scer\GAL4pnr-MD237 Hr4GD11026 lethal | recessive Hr4PL78 lethal | wandering third instar larval stage | heat sensitive Hr4Hsp70.PK partially lethal - majority die, with Scer\GAL4en-e16E Hr4EP1232 partially lethal - majority die | prepupal stage | heat sensitive Hr4dsRNA.hs partially lethal - majority die | pupal stage, with Hr41 Hr4Hsp70.PK partially lethal - majority die | pupal stage, with Hr4Hsp70.PK Hr41 partially lethal - majority die | pupal stage, with Scer\GAL4pnr-MD237 Hr4GD1464 partially lethal - majority die | pupal stage | heat sensitive Hr4dsRNA.hs Other Phenotypes Allele body color defective, with Scer\GAL4pnr-MD237 Hr4GD1464 developmental rate defective Hr41 developmental rate defective | first instar larval stage, with Scer\GAL4phm.PO Hr4Scer\UAS.cQa developmental rate defective | larval stage, with Scer\GAL4P0206 Hr4dsRNA.Scer\UAS developmental rate defective | prepupal stage Hr41 developmental rate defective | second instar larval stage, with Scer\GAL4Cg.PA Hr4Scer\UAS.cQa developmental rate defective | second instar larval stage, with Scer\GAL4P0206 Hr4Scer\UAS.cQa developmental rate defective | third instar larval stage Hr41 large body | first instar larval stage, with Scer\GAL4P0206 Hr4Scer\UAS.cQa small body Hr41 small body | adult stage | heat sensitive Hr4dsRNA.hs small body | prepupal stage, with Scer\GAL4P0206 Hr4dsRNA.Scer\UAS small body | pupal stage | heat sensitive Hr4dsRNA.hs small body | second instar larval stage | heat sensitive Hr4dsRNA.hs visible, with Scer\GAL4en-e16E Hr4EP1232 visible, with Scer\GAL4ey.PH Hr4EP1232 visible, with Scer\GAL4GMR.PF Hr4EP1232 visible, with Scer\GAL4hs.2sev Hr4EP1232 visible, with Scer\GAL4pnr-MD237 Hr4GD1464 visible, with Scer\GAL4sca-537.4 Hr4EP1232 wild-type, with Scer\GAL4ap-md544 Hr4EP1232 Phenotype manifest in Allele anterior pupal spiracle, with Scer\GAL4Cg.PA Hr4dsRNA.Scer\UAS chaeta | supernumerary, with Scer\GAL4pnr-MD237 Hr4GD1464 dorsocentral bristle, with Scer\GAL4sca-537.4 Hr4EP1232 embryonic/larval fat body, with Scer\GAL4P0206 Hr4Scer\UAS.cQa eye, with Scer\GAL4ey.PH Hr4EP1232 eye, with Scer\GAL4GMR.PF Hr4EP1232 eye, with Scer\GAL4hs.2sev Hr4EP1232 mesothoracic tergum, with Scer\GAL4pnr-MD237 Hr4GD1464 ommatidium, with Scer\GAL4hs.2sev Hr4EP1232 ring gland, with Scer\GAL4P0206 Hr4Scer\UAS.cQa scutellar bristle, with Scer\GAL4sca-537.4 Hr4EP1232 tormogen cell, with Scer\GAL4sca-537.4 Hr4EP1232 wing, with Scer\GAL4en-e16E Hr4EP1232
Classical Alleles ( 47 )
For All Classical Alleles Show
Allele of Hr4 Class Mutagen Stocks Known lesion Hr45-HA-1598 1 -- Hr45-SZ-3682 1 -- Hr45-SZ-4091 1 -- Hr4BG01273 1 -- Hr4BG01752 1 -- Hr4c03178 1 -- Hr4c05577 1 -- Hr4d00604 1 -- Hr4d01238 1 -- Hr4d03978 1 -- Hr4d05558 1 -- Hr4d05930 1 -- Hr4d09591 1 -- Hr4d11108 1 -- Hr4e01886 1 -- Hr4EP1232 P-element activity 1 -- Hr4EY20645 1 -- Hr4f02909 1 -- Hr4f06490 1 -- Hr4G0257b 1 -- Hr4KG00928 1 -- Hr4NP3258 1 -- Hr4NP3383 1 -- Hr4NP3468 1 -- Hr4NP5906 1 -- Hr4NP6011 1 -- Hr417C9 0 -- Hr41 Delta2-3 0 Yes Hr45-HA-2104 0 -- Hr45-HA-2120 0 -- Hr45-HA-2624 0 -- Hr4d01059 0 -- Hr4d04793 0 -- Hr4d05310 0 -- Hr4d05936 0 -- Hr4d06495 0 -- Hr4d07038 0 -- Hr4d07833 0 -- Hr4d09433 0 -- Hr4d11610 0 -- Hr4EP1549 0 -- Hr4GG01181 0 -- Hr4GG01378 0 -- Hr4GG01571 0 -- Hr4GG01619 0 -- Hr4NP7262 0 -- Hr4PL78 Delta2-3 0 --
Alleles Carried on Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Hr4 Class Mutagen Stocks Known lesion Hr4GD11026 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Hr4GD1464 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Hr4hs.T:Scer\GAL4.T:Ivir\HA1 in vitro construct - regulatory fusion in vitro construct - coding region fusion 2 Yes Hr4HM05260 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr4KK110027 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr4KK110718 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr4KK111562 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Hr4T:Avic\GFP-EGFP,T:Zzzz\TC,T:Zzzz\StrepII,T:Zzzz\TEV.CS,T:Zzzz\FLAG in vitro construct - coding region fusion 1 Yes Hr4dsRNA.hs 0 Yes Hr4dsRNA.Scer\UAS in vitro construct - regulatory fusion in vitro construct - RNAi 0 Yes Hr4Hsp70.PK in vitro construct - regulatory fusion 0 Yes Hr4NIG.16902R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes Hr4Scer\UAS.cQa in vitro construct - regulatory fusion 0 Yes Hr4tCH322-137G06 in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD1464} NA P{KK110718} NA P{KK111562} NA P{NIG.16902R} NA P{TRiP.HM05260} NA P{UAS-Hr4-RNAi} NA heat-shock construct P{hs-GAL4-DHR4.LBD.HA} NA P{hs-Hr4.RNAi} NA P{Hsp70-Hr4.PK} NA GAL4 construct P{hs-GAL4-DHR4.LBD.HA} No characterization construct PBac{CH322-137G06} NA PBac{Hr4-GFP.FSTF} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}EP427 NA P{EP}Hr41 NA P{EP}Hr4EP1232 NA P{EP}Hr4EP1549 NA P{EPgy2}Hr4EY20645 NA P{Mae-UAS.6.11}B2007B2007 NA P{Mae-UAS.6.11}GG01274GG01274 NA P{Mae-UAS.6.11}GG01510GG01510 NA P{Mae-UAS.6.11}Hr4GG01181 NA P{Mae-UAS.6.11}Hr4GG01378 NA P{Mae-UAS.6.11}Hr4GG01571 NA P{Mae-UAS.6.11}Hr4GG01619 NA P{XP}Hr4d00604 NA P{XP}Hr4d01059 NA P{XP}Hr4d01238 NA P{XP}Hr4d03978 NA P{XP}Hr4d04793 NA P{XP}Hr4d05310 NA P{XP}Hr4d05558 NA P{XP}Hr4d05930 NA P{XP}Hr4d05936 NA P{XP}Hr4d06495 NA P{XP}Hr4d07038 NA P{XP}Hr4d07833 NA P{XP}Hr4d09433 NA P{XP}Hr4d09591 NA P{XP}Hr4d11108 NA P{XP}Hr4d11610 NA miscellaneous insertions P{GT1}Hr4BG01273 NA P{GT1}Hr4BG01752 NA P{RS5}Hr45-HA-1598 NA P{RS5}Hr45-HA-2104 NA P{RS5}Hr45-HA-2120 NA P{RS5}Hr45-HA-2624 NA P{RS5}Hr45-SZ-3682 NA P{RS5}Hr45-SZ-4091 NA P{SUPor-P}Hr4KG00928 NA PBac{PB}Hr4c03178 NA PBac{PB}Hr4c05577 NA PBac{RB}Hr4e01886 NA PBac{WH}Hr4f02909 NA PBac{WH}Hr4f06490 NA insertion of enhancer trap binary system P{GawB}Hr4NP3258 No P{GawB}Hr4NP3383 No P{GawB}Hr4NP3468 No P{GawB}Hr4NP5906 No P{GawB}Hr4NP6011 No P{GawB}Hr4NP7262 No insertion of enhancer trap P{lacW}Hr4G0257b No P{lacW}Hr4PL78 No
Gene Ontology: Function, Process & Cellular Component ( 13 unique terms )
Terms Based on Experimental Evidence ( 7 terms )
Molecular Function
CV term Evidence References
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from mutant phenotype (assigned by UniProtKB) (King-Jones et al., 2005)
Biological Process
CV term Evidence References
cellular response to hypoxia inferred from mutant phenotype (Lee et al., 2008) growth inferred from mutant phenotype (assigned by UniProtKB) (King-Jones et al., 2005) intracellular steroid hormone receptor signaling pathway inferred from mutant phenotype (assigned by UniProtKB) (King-Jones et al., 2005) pupariation inferred from mutant phenotype (assigned by UniProtKB) (King-Jones et al., 2005) regulation of developmental growth inferred from mutant phenotype (Ou et al., 2011)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (assigned by UniProtKB) (King-Jones et al., 2005)
Terms Based on Predictions or Assertions ( 8 terms )
Molecular Function
CV term Evidence References
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q64249 (FlyBase, 1992-) non-traceable author statement (Maglich et al., 2001) sequence-specific DNA binding inferred from electronic annotation with InterPro:IPR001628 (FlyBase Curators et al., 2004-) steroid hormone receptor activity inferred from electronic annotation with InterPro:IPR000536, InterPro:IPR001723, InterPro:IPR008946 (FlyBase Curators et al., 2004-) zinc ion binding inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
metamorphosis non-traceable author statement (King-Jones and Thummel, 2002) 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-) 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:Q64249 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	gene_with_stop_codon_read_through (FlyBase Genome Annotators, 2012) nuclear_gene (FlyBase Genome Annotators, 2008) protein_coding_gene (FlyBase Genome Annotators, 2008)
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 Hr4 allele Gene References CG3600EP1232 pnr (Pena-Rangel et al., 2002) unspecified grim (Mueller et al., 2005) H (Mueller et al., 2005) p53 (Mueller et al., 2005) rpr (Mueller et al., 2005) W (Mueller et al., 2005)
External Data
Linkouts
Orthologs
OrthoDB Orthologs (29) - 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 EOG6XWGHM Dipteran inclusive ortholog search EOG6CRM7M Insect inclusive ortholog search EOG6H44ZR Arthropod inclusive ortholog search EOG69P8DG Metazoa inclusive ortholog search EOG6ZKXD5
Orthologs in Drosophila Species (EOG6XWGHM)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Hr4     Drosophila sechellia   Dsec\GM19185     Drosophila sechellia   Dsec\GM19186 Y   Drosophila erecta   Dere\GG12896 Y   Drosophila willistoni   Dwil\GK25182 Y   Drosophila virilis   Dvir\GJ14872 Y   Drosophila mojavensis   Dmoj\GI15166 Y   Drosophila grimshawi   Dgri\GH12110 Y
Orthologs in non-Drosophila Dipterans (EOG6CRM7M)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\hr4   Anopheles gambiae Malaria mosquito  Agam\AGAP004693   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ005424
Orthologs in non-Dipteran Insects (EOG6H44ZR)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG009841   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG009846   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH23423   Atta cephalotes Leafcutter ant  Acep\ACEP11972   Atta cephalotes Leafcutter ant  Acep\ACEP11971   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL13156   Linepithema humile Argentine ant  Lhum\LH13418   Linepithema humile Argentine ant  Lhum\LH13413   Pogonomyrmex barbatus Red harvester ant  Pbar\PB18811   Solenopsis invicta Red fire ant  Sinv\SINV11105   Acyrthosiphon pisum Pea aphid  Apim\ACYPI008092   Bombyx mori Silkmoth  Bmor\BGIBMGA007888   Pediculus humanus Human body louse  Phum\PHUM195250   Tribolium castaneum Red flour beetle  Tcas\Hr4
Orthologs in non-Insect Arthropods (EOG69P8DG)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_203579   Ixodes scapularis Deer tick  Isca\ISCW023325
Orthologs in non-Arthropod Metazoa (EOG6ZKXD5)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\nhr-91   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_013305gn
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD16580 Drosophila sechellia Dsec\GM19186 Drosophila erecta Dere\GG12895 Drosophila erecta Dere\GG12896 Drosophila ananassae Dana\GF22191 Drosophila pseudoobscura pseudoobscura Dpse\GA22933 Drosophila persimilis Dper\GL15259 Drosophila willistoni Dwil\GK25182 Drosophila virilis Dvir\GJ14872 Drosophila mojavensis Dmoj\GI15166 Drosophila grimshawi Dgri\GH12110
Stocks & Reagents
Stocks Listed in FlyBase ( 37 )
Harvard	- P{XP}Hr4d00604 - P{XP}Hr4d01238 - P{XP}Hr4d03978 - P{XP}Hr4d05558 - P{XP}Hr4d05930 - P{XP}Hr4d09591 - P{XP}Hr4d11108 - PBac{PB}Hr4c03178 - PBac{PB}Hr4c05577
VDRC	v101865 P{KK110027}VIE-260B v102096 P{KK110718}VIE-260B v102361 P{KK111562}VIE-260B
	More stocks available...
Genomic Clones ( 2 )
	BACR05N09 BACR33I18 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 54 )
	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
Other clones	IP12727
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RH02831 RH03910 RH06248 RH08569 RH34310 RH63654 SD09196
Other clones	34219 34283 42863 62111 62609 75171 75267 76284 81497 81607 103625 104372 153075 214545.48 bs58f10 CK01.38D.E6 CK01.66C.E11 EK018559 EK032751 EK052618 EK067410 EK166534 EK175124 EK177928 EK186244 EK188360 EK189112 EK205358 EK207261 EK208520 EK215145 EK215160 EK256216 EK290621 EN05725 EN06443 EP03908 EP11501 IP03726 IP03826 IP12427 IP15213 IP15313 IP15413 IP15513 RP003552118
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Hr4 EG:133E12.2 (King-Jones, 2001.3.12)
Source for database merge of	Source for merge of: CG3600 EP1232 (Mueller et al., 2005) Source for merge of: CG42527 Hr4 (FlyBase Genome Annotators, 2012) Source for merge of: Hr4 CG3600 (FlyBase Genome Annotators, 2012)
Additional comments	Annotations CG42527 and CG43692 merged as CG43934 in release 5.46 of the genome annotation. Merge supported by RNA-seq junction data. (FlyBase Genome Annotators, 2012) Annotations CG16902 and CG3600 merged as CG43692 in release 5.43 of the genome annotation. (FlyBase Genome Annotators, 2012) One or more of the processed transcripts for these genes contain two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG42527 (FBgn0260432) and CG16902, Hr4 (FBgn0023546). (FlyBase Genome Annotators, 2008) One or more of the processed transcripts for these genes contain two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG42527 (FBgn0260432), CG16902, Hr4 (FBgn0023546). (FlyBase Genome Annotators, 2008)
Other Comments
	Hr4 oscillates between the nucleus and cytoplasm of cells in the prothoracic gland. Hr4 is absent from nuclei at developmental times when low titre ecdysone pulses occur. (Ou et al., 2011) Hr4 acts as a transcriptional repressor of Cyp6t3. (Ou et al., 2011) New annotation (CG42527) in release 5.14 of the genome annotation. (FlyBase Genome Annotators, 2008) RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_001038734 NM_001272227 NM_001272228 NM_001272229 NM_001272230 NM_001272231 NM_001272232 NM_001272233 NM_001272234 RefSeq (Proteins) • NP_001033823 NP_001259156 NP_001259157 NP_001259158 NP_001259159 NP_001259160 NP_001259161 NP_001259162 NP_001259163 DDBJ / EMBL / GenBank • AAF45701 AAF45702.3 AAS65249.1 AAX73355 ABC67166 ACL82879 ACL82880 ACZ95180 AGB95002 AGB95003 AGB95004 AGB95005 AGB95006 AGB95007 AGB95008 AGB95009 AL035245 AQ254763 AY971884 CAA22835 CAA22836 DQ327740 DQ327741 Entrez Gene - A searchable database of RefSeq genes. • 31161 31162 8674057 UniProtKB/Swiss-Prot • Q9W539 UniProtKB/TrEMBL • B7Z117 E1JJC9 O96835
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Nuclear hormone receptor, ligand-binding (IPR008946) Steroid hormone receptor (IPR001723) Zinc finger, NHR/GATA-type (IPR013088) Zinc finger, nuclear hormone receptor-type (IPR001628) Nuclear hormone receptor, ligand-binding, core (IPR000536)
Linkouts
Synonyms & Secondary IDs ( 14 )
Reported As
Symbol Synonym	CG3600 (Manak et al., 2006, Manak et al., 2006, Keleman et al., 2009.8.5, Comet et al., 2006, Grieder et al., 2007, ) CG16902 (Mosallanejad et al., 2010, Perkins et al., 2009, Keleman et al., 2009.8.5, Lee et al., 2008, Benos, 2000.12.13, King-Jones, 2001.3.12, Bourbon et al., 2002) CG42527 (FlyBase Genome Annotators, 2008) CG43692 (FlyBase Genome Annotators, 2012, ) CG43934 (FlyBase Genome Annotators, 2012) DHR4 (Ou et al., 2011, Dubrovsky et al., 2011, de Rosny et al., 2008, Kozlova et al., 2009, Stabell et al., 2007, King-Jones and Thummel, 2005, Palanker et al., 2006, King-Jones et al., 2001, King-Jones and Thummel, 2002, Sullivan and Thummel, 2003, King-Jones et al., 2004, Shingleton, 2005) EG:133E12.2 (Benos et al., 2001, Boutros et al., 2004) EG:BACH61I5.1 (Benos et al., 2001, Ringrose et al., 2003) EP1232 (Abdelilah-Seyfried et al., 2000, Tseng and Hariharan, 2002) EP(X)1232 (Pena-Rangel et al., 2002) GRF (Laudet, 2004.6.14) Hr4 (Spokony and White, 2012.5.22, Gauhar et al., 2009, Venken et al., 2009, Lee et al., 2008, Comet et al., 2006, Japanese National Institute of Genetics, 2012.5.21, FlyBase Genome Annotators, 2008, FlyBase Genome Annotators, 2012) NR6A2 (King-Jones and Thummel, 2005, Laudet, 2004.6.14) null
Name Synonym	Hr4
Secondary FlyBase IDs
	FBgn0023546 FBgn0026087 FBgn0043372 FBgn0260432 FBgn0263775
References ( 50 )
Generate a list of	All references relating to this gene ( 50 )
List References by type	Research paper  ( 21 ) Supplementary material  ( 6 ) Review  ( 2 ) Personal communication to FlyBase  ( 9 ) Abstract  ( 4 ) FlyBase analysis  ( 5 ) Stock list  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 2 )
	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] Ou et al., 2011, PLoS Biol. 9(9): e1001160 Nuclear Receptor DHR4 Controls the Timing of Steroid Hormone Pulses During Drosophila Development. [FBrf0216318] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...