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Gene Dmel\ems

General Information
Symbol	Dmel\ems	Species	D. melanogaster
Name	empty spiracles	Annotation symbol	CG2988
Feature type	protein_coding_gene	FlyBase ID	FBgn0000576
Gene Model Status	Current	Stock availability	7 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map	3-54.0
Cytogenetic map	88A2-88A2	Sequence location	3R:9,727,581..9,730,346 [+]
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 empty spiracles is referred to in FlyBase by the symbol Dmel\ems (CG2988, FBgn0000576). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding. There is experimental evidence that it is involved in the biological process: spiracle morphogenesis, open tracheal system; dendrite morphogenesis; embryonic development via the syncytial blastoderm; brain development; axonogenesis; neuroblast development; brain segmentation; open tracheal system development; ventral cord development. 18 alleles are reported. The phenotypes of these alleles are annotated with: organ system subdivision; organ system; cephalopharyngeal skeleton; late extended germ band embryo; larval head segment; non-connected developing system; sense organ; pharyngeal sclerite; spiracle; tracheal branch primordium. It has one annotated transcript and one annotated polypeptide. Protein features are: Homeobox, conserved site; Homeodomain; Homeodomain-like. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval trachea. Comments on Affy2 ProbeSet: ProbeSet 1628289_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of ems. Gene sequence location is 3R:9727581..9730346.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	ems: empty spiracles Embryonic lethal. Embryos display loss of filzorper in the posterior spiracles; posterior ends of longitudinal tracheal trunks incomplete. Failure of head involution; many cuticular structures that normally derive from the procephalic and mandibular lobes of the head missing; embryonic antennal organs missing. ems protein first appears as an anterior ring around the syncytial blastoderm at a position just anterior to that of Dfd; it is five to six cells wide dorsally and 10-12 cells wide ventrally; at gastrulation the ring is just anterior to the cephalic furrow. As gastrulation proceeds expression becomes patchy and confined to specific groups of cells. The protein is nuclear in localization. The metameric pattern of ems expression commences at the beginning of germ-band extension; protein first appears in a group of cells in each segment, which subsequently elongates and splits into two clusters of ems-positive cells in regions destined to give rise to tracheal pits, neuroblasts and epidermis. In the eighth abdominal segment, a large patch of ems-positive cells forms just posterior to the tracheal pit and presumably correspond to the primordia of the posterior spiracles and the filzkorper; a similar patch is formed anteriorly in embryos produced by bcd mothers. For a detailed discussion of the expression pattern see Dalton et al..
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 88A2-88A2   Limits computationally determined from genome sequence between P{PZ}flfl01949 and P{lacW}trxj14A6&P{PZ}trx00347
Experimentally Determined Cytological Location
Cytogenetic map Notes References 88A1-88A2   (determined by in situ hybridisation)   (Ranz et al., 1997) 88A-88A   (determined by in situ hybridisation)   (Walldorf and Gehring, 1990) 88A1-88A2   (determined by in situ hybridisation)   (Dalton et al., 1989)
Experimentally Determined Recombination Data
Location	3-54.0   3-53 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)	put (Jurgens et al., 1984)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\ems for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) ems-RA FBtr0082863  NM_169560   2476   494
Additional Transcript Data & Comments
Reported size (kB)	2.4 (northern blot) (Walldorf and Gehring, 1992) 2.3 (northern blot) (Dalton et al., 1989)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein ems-PA   FBpp0082326   53.4   494   7.60     NP_731868   AAF54999
Additional Polypeptide Data & Comments
Reported size (kDa)	497 (aa); 54 (kD predicted) (Walldorf and Gehring, 1992) 494 (aa) (Dalton et al., 1989)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeodomain (IPR001356) Homeodomain-like (IPR009057)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF54999   AF029219   BT021310 AAX33458   CO271454   CO271568   CO273433   CO301309   CO301384   CO310670   CO322723   CO325124   EC064716   EC215340   EC222947   EC223577   EC235348   EC243838   X51653 CAA35965   X66270 CAA46985
UniProtKB/Swiss-Prot	P18488
UniProtKB/TrEMBL	Q5BIB4
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References protein binding site FBsf0000160144 3R:9,634,574..9,634,574 bound_moiety=Dfd-XP comment=The protein binding site maps to a XhoI-HindIII fragment. evidence=experimental linked_to=XhoI-HindIII_rfrag (Jones and McGinnis, 1993) protein binding site FBsf0000160696 3R:9,723,844..9,723,853 evidence=experimental bound_moiety=Abd-B-XP (Bergman et al., 2005, Taylor, 1998) protein binding site FBsf0000160697 3R:9,724,540..9,724,552 bound_moiety=ems-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) protein binding site FBsf0000160698 3R:9,723,844..9,723,856 bound_moiety=ems-XP evidence=experimental (Bergman et al., 2005, Taylor, 1998) protein binding site FBsf0000160699 3R:9,724,092..9,724,102 bound_moiety=Abd-B-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) protein binding site FBsf0000160700 3R:9,724,615..9,724,624 bound_moiety=Abd-B-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) protein binding site FBsf0000160701 3R:9,723,999..9,724,008 bound_moiety=Abd-B-XP evidence=experimental (Bergman et al., 2005, Taylor, 1998) protein binding site FBsf0000160702 3R:9,720,721..9,720,735 bound_moiety=tll-XP evidence=experimental (Bergman et al., 2005, Hartmann et al., 2001) protein binding site FBsf0000160703 3R:9,724,558..9,724,567 bound_moiety=Abd-B-XP evidence=experimental (Bergman et al., 2005, Taylor, 1998) protein binding site FBsf0000160704 3R:9,720,621..9,720,633 bound_moiety=tll-XP evidence=experimental (Hartmann et al., 2001, Bergman et al., 2005) protein binding site FBsf0000160705 3R:9,720,615..9,720,628 bound_moiety=bcd-XP evidence=experimental (Bergman et al., 2005, Hartmann et al., 2001) protein binding site FBsf0000160706 3R:9,720,583..9,720,598 bound_moiety=bcd-XP evidence=experimental (Bergman et al., 2005, Hartmann et al., 2001) protein binding site FBsf0000160707 3R:9,724,360..9,724,372 bound_moiety=ems-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) protein binding site FBsf0000160708 3R:9,723,807..9,723,816 bound_moiety=Abd-B-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) protein binding site FBsf0000160709 3R:9,724,527..9,724,536 bound_moiety=Abd-B-XP evidence=experimental (Taylor, 1998, Bergman et al., 2005) regulatory region FBsf0000161380 3R:9,728,514..9,729,763 comment=The ems upstream enhancer mediates embryonic expression in a dorsolateral patch in segment A8 (which includes the primordia of the posterior spiracles) in an Abd-B-dependent manner. An internal 1.0kb EcoRI-XhoI fragment is bound by a Dfd/Abd-B chimeric protein (containing the Abd-B homeodomain). evidence=experimental linked_to=EcoRI-EcoRI_rfrag (Jones and McGinnis, 1993) regulatory region FBsf0000435095 3R:9,736,092..9,738,152 evidence=Reporter construct (in vivo) (Perry et al., 2011, Halfon, 2012.6.19) regulatory region FBsf0000435305 3R:9,723,767..9,723,905 evidence=Reporter construct (in vivo) (Taylor, 1998, Halfon, 2012.6.19) regulatory region FBsf0000435324 3R:9,723,515..9,724,758 evidence=Reporter construct (in vivo) (Jones and McGinnis, 1993, Halfon, 2012.6.19) regulatory region FBsf0000435691 3R:9,720,485..9,721,653 evidence=Reporter construct (in vivo) (Hartmann et al., 2001, Halfon, 2012.6.19) regulatory region FBsf0000435742 3R:9,719,429..9,720,792 evidence=Reporter construct (in vivo) (Hartmann et al., 2001, Halfon, 2012.6.19) regulatory region FBsf0000436634 3R:9,720,485..9,720,788 evidence=Reporter construct (in vivo) (Hartmann et al., 2001, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4   organism | 70-90% egg length   (Walldorf and Gehring, 1992) Comment:70-89% egg length embryonic stage 4 -- 6   antennal anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi central brain anlage in statu nascendi   (Fisher et al., 2012) organism | gap expression pattern   (Fisher et al., 2012) dorsal head epidermis anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi visual anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi embryonic stage 5   organism | 70-80% egg length   (Rudolph et al., 1997) Comment:69-75% egg length organism | gap expression pattern   (Hauptmann, 2001) embryonic stage 6 -- 7   cephalic furrow | anterior to   (Rudolph et al., 1997) embryonic stage 7 -- 8   antennal anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage central brain anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage dorsal head epidermis anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage visual anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage clypeo-labral anlage   (Fisher et al., 2012) dorsal ectoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   antennal primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium central brain primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium visual primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium clypeo-labral primordium   (Fisher et al., 2012) dorsal ectoderm   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) Comment:reported as dorsal epidermis anlage gnathal primordium   (Fisher et al., 2012) Comment:reported as gnathal lobes anlage tracheal primordium   (Fisher et al., 2012) Comment:reported as tracheal system anlage embryonic stage 11   organism | segmentally repeated   (Jones and McGinnis, 1993) embryonic abdominal segment 8 | intense   (Jones and McGinnis, 1993) embryonic stage 11 -- 12   antennal primordium   (Fisher et al., 2012) atrium | precursor   (Fisher et al., 2012) Comment:reported as atrium primordium central brain primordium   (Fisher et al., 2012) clypeo-labral primordium   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as head epidermis primordium labial sensory complex primordium   (Fisher et al., 2012) maxillary sensory complex primordium   (Fisher et al., 2012) tracheal primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 12   embryonic optic lobe   (Walldorf and Gehring, 1992) embryonic stage 13 -- 16   atrium   (Fisher et al., 2012) embryonic antennal sense organ   (Fisher et al., 2012) embryonic brain   (Fisher et al., 2012) embryonic dorsal epidermis   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) lateral head epidermis   (Fisher et al., 2012) ventral head epidermis   (Fisher et al., 2012) embryonic stage 14   subesophageal ganglion   (Walldorf and Gehring, 1992) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic/larval posterior spiracle   (Walldorf and Gehring, 1992) antenno-maxillary complex   (Walldorf and Gehring, 1992) embryonic stage -- pupal stage     (Walldorf and Gehring, 1992) embryonic stage -- adult stage     (Dalton et al., 1989) embryonic stage 6 -- 7   cephalic furrow   (Walldorf and Gehring, 1992) embryonic stage 7 -- 17   procephalic segment   (Walldorf and Gehring, 1992) antennal segment   (Walldorf and Gehring, 1992) intercalary segment   (Walldorf and Gehring, 1992) embryonic stage 8 -- 17   organism | segment polarity expression pattern   (Walldorf and Gehring, 1992) embryonic stage 9 -- 17   mandibular segment   (Walldorf and Gehring, 1992) embryonic stage 13   presumptive embryonic/larval central nervous system | lateral   (Walldorf and Gehring, 1992)
Additional Descriptive Data
	ems transcripts are expressed at roughly 69-75% egg length in the cellular blastoderm embryo. Beginning at gastrulation, they are expressed in a set of stripes just anterior to the cephalic furrow. Expression of ems in the protocerebral domain of the head is mostly gone by stage 9. (Rudolph et al., 1997) ems transcripts are detected at all developmental stages except adult on northern blots. The peak of expression occurs between 6 and 12 hours of embryogenesis and a second smaller peak is seen in second instar larvae. Transcripts are first detected by in situ hybridization at the syncytial blastoderm stage in a stripe that extends from 70-76% egg length dorsally and 74-89% egg length ventrally. At the cellular blastoderm stage, expression fades in the ventral part of the stripe and to a lesser extent dorsally. At stages 6 and 7, @ems transcripts are expressed anterior to and along the cephalic furrow and in the anlagen for the intercalary and antennal segments and in part of the procephalic lobe. At stage 8, they are observed in lateral regions along the extending germ band and in an anterior dorsal patch at 85-90% egg length. During stage 9, expression is seen in 16 regions along the extended germ band and in the mandibular, intercalary, and antennal segments. By stage 10, staining in the gnathal segments corresponds to the anterior part of each segment and the staining in the abdominal segments occurs around the tracheal pits. Staining is also observed in the primordia of the posterior spiracles. Staining in the optic lobe primordium begins at stage 12. By stage 13, expression is seen in lateral cells of the CNS and in a row of cells immediately posterior to the forming segmental furrows. In stage 14, expression is restricted to the anterior part of the mandibular lobe, the antenno-maxillary complex, the subesophageal ganglion, and the posterior spiracles (Walldorf and Gehring, 1992) ems transcripts are expressed in all stages tested with a peak in 6-12 hr embryos, and high levels in 3rd instar larvae and pupae. (Dalton et al., 1989)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage   neuroblast   (Dalton et al., 1989) immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage   ectoderm   (Dalton et al., 1989) blastoderm stage   head   (Dalton et al., 1989) embryonic stage 6   cephalic furrow | anterior to   (Hartmann et al., 2001) Comment:single circumferential stripe of expression embryonic stage 9 -- 11   procephalic neurogenic region | restricted   (Urbach and Technau, 2003) protocerebral neuroblast | subset   (Urbach and Technau, 2003) tritocerebral neuroblast | subset   (Urbach and Technau, 2003) deuterocerebral neuroblast | subset   (Urbach and Technau, 2003) embryonic stage 10   organism | segmentally repeated   (Hartmann et al., 2001) embryonic intercalary segment   (Hartmann et al., 2001) embryonic antennal segment   (Hartmann et al., 2001) embryonic ocular segment   (Hartmann et al., 2001) embryonic stage 15   embryonic protocerebrum   (Hartmann et al., 2001) embryonic deuterocerebrum   (Hartmann et al., 2001) embryonic tritocerebrum   (Hartmann et al., 2001)
Additional Descriptive Data
	ems is expressed in two independently regulated patterns that are described in detail. The head specific pattern initiates prior to cellular blastoderm and continues to early germband extension. The metameric pattern initiates after gastrulation and includes expression in lateral neuroblasts, in ectodermal cells at the anterior lateral borders of each segment and in the filzkorper primordia. The region of ems expression in the head is anterior and adjacent to the Dfd expression stripe. In bcd mutants, the blastoderm head specific ems staining is absent while the later metameric pattern is unaffected. (Dalton et al., 1989) In stage 6 embryos, the ems protein expression domain is posterior to that of tll, with a 1-2 cell unlabled gap between. By embryonic stage 10, ems protein is distributed in a segmentally striped pattern. At this stage, ems expression colocalizes with tll in the intercalary segment, and is adjacent to tll in the antennal and ocular segments. At stage 15, ems expression is adjacent to tll expression in the embryonic brain. (Hartmann et al., 2001) ems protein is detected in discrete domains in the procephalic ectoderm of stage 9-11 embryos, including initially 3 domains between the anterior part of the mandibular segment and the posterior of the ocular segment. One of these domains further splits. Additional small domains of expression are observed in another region of the ocular segment and in a dorsal patch of procephalic ectoderm. Expression in procephalic neuroblasts stage 9-11: tritocerebrum - d6; deuterocerebrum - d3, d6, v3, v7; protocerebrum - cv5, pd2, pd5, pd8, pd10, pd15 (Urbach and Technau, 2003)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (Lichtneckert et al., 2007)
Expression Deduced from Reporters
Reporter: P{ems-lacZ.IV} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 6   ventral neurectoderm | restricted   (Hartmann et al., 2001) head | restricted   (Hartmann et al., 2001) ventral neurectoderm of head | restricted   (Hartmann et al., 2001) embryonic stage 9   head | restricted   (Hartmann et al., 2001) embryonic stage 15   deuterocerebrum | restricted   (Hartmann et al., 2001) protocerebrum | restricted   (Hartmann et al., 2001) embryonic tritocerebrum | restricted   (Hartmann et al., 2001)
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval trachea. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    33.35 Larval Midgut    11.9 Larval Hindgut    8.8 Larval Malpighian Tubules    8.7 Larval Fat Body    16.6 Larval Salivary Gland    6.7 Larval Trachea    240.325 Larval Carcass    34.6 Adult Head    21.4 Adult Eye    11.875 Adult Brain    9.9 Adult Thoracic-Abdominal Ganglion    26.6 Adult Crop    7.8 Adult Midgut    6.8 Adult Hindgut    8 Adult Malpighian Tubules    5 Adult Fat Body    11.9 Adult Salivary Gland    9 Adult Heart    55.325 Adult VirginFemale Spermatheca    6.3 Adult InseminatedFemale Spermatheca    8.6 Adult Ovary    1.9 Adult Testis    5.7 Adult Male Accessory Gland    12 Adult Carcass    30 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    21.4   NA  Eye    11.875   NA  Brain    9.9   33.35  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    26.6   NA  Crop    7.8   no informative data  Midgut    6.8   8.8  Hindgut    8   8.7  Malpighian Tubules    5   no informative data  Fat Body    no informative data   6.7  Salivary Gland    9   NA  Heart    55.325   240.325  Trachea    NA   NA  VirginFemale Spermatheca    6.3   NA  InseminatedFemale Spermatheca    8.6   NA  Ovary    1.9   NA  Testis    5.7   NA  Male Accessory Gland    no informative data   34.6  Carcass    no informative data 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    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (35) central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering  (35) central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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    35 central nervous system, larvae L3    6 central nervous system, pupae P8    1 head, virgin 1-day female    2 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    1 head, mated 20-day female    1 head, mated 1-day male    2 head, mated 4-day male    2 head, mated 20-day male    2 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    1 fat body, white prepupae    3 fat body, pupae P8    2 carcass, larvae L3 wandering    17 carcass, 1-day adult    2 carcass, 4-day adult    2 carcass, 20-day adult    2 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    0 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 very low expression. Peak expression observed within 00-12 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    18 embryo 04-06hr  (33) embryo 06-08hr  (39) embryo 08-10hr  (30) embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 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    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 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    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    18 embryo 04-06hr  (33) embryo 06-08hr  (39) embryo 08-10hr  30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 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    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 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    18 embryo 04-06hr    33 embryo 06-08hr    39 embryo 08-10hr    30 embryo 10-12hr    17 embryo 12-14hr    14 embryo 14-16hr    9 embryo 16-18hr    5 embryo 18-20hr    7 embryo 20-22hr    5 embryo 22-24hr    4 larva L1    3 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    7 white prepupae new    7 white prepupae 12hr    7 white prepupae 24hr    12 pupae 2d postWPP    4 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    1 adult female 05day    0 adult female 30day    0 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 Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    3 Cadmium 50 mM 48 hrs, 4-day adult    2 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    1 Zinc 5 mM 12 hrs, larvae L3    5 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    0 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    1 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_11 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • RE15812 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000576 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2988-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage | recessive emsunspecified viable, with Scer\GAL4pnr-MD237 emsGD1435 Other Phenotypes Allele increased cell death | somatic clone ems3 neuroanatomy defective ems2 neuroanatomy defective | adult stage | somatic clone ems3 neuroanatomy defective | adult stage | somatic clone, with Scer\GAL4GH146 emsScer\UAS.cRa neuroanatomy defective | larval stage | somatic clone ems3 neuroanatomy defective | somatic clone ems3 Phenotype manifest in Allele adult antennal lobe projection neuron DL1 adPN | somatic clone, with Scer\GAL4GH146 emsScer\UAS.cRa adult antennal lobe projection neuron VA1v adPN | somatic clone ems3 adult antennal lobe projection neuron VA3 adPN | somatic clone ems3 adult antennal lobe projection neuron VM2 adPN | somatic clone ems3 adult brain | somatic clone ems3 antennal lobe | somatic clone ems3 antennal lobe projection neuron adPN | somatic clone ems3 antennal lobe projection neuron adPN | somatic clone, with Scer\GAL4GH146 emsScer\UAS.cRa antennal lobe projection neuron lPN | somatic clone ems3 antennal segment ems3 antennal sense organ ems3 ems4 associated organ ems3 Bolwig organ ems3 central nervous system emshs.PH cephalopharyngeal skeleton emsbtd.PS cervical connective ems1 deuterocerebral neuromere ems1 ems10D29 ems2 dorsal branch primordium ems2 dorsal bridge ems4 dorsolateral papilla | ectopic emsbtd.PS dorsomedial papilla ems3 embryonic/larval antennal segment sensillum | embryonic stage emsunspecified embryonic/larval brain | somatic clone ems3 embryonic/larval optic lobe ems1 embryonic/larval optic lobe | embryonic stage ems3 embryonic/larval pharynx | embryonic stage ems4 embryonic deuterocerebrum ems2 embryonic head emsunspecified embryonic head epidermis ems2 embryonic mandibular segment emsbtd.PS embryonic tritocerebrum ems2 fascicle | somatic clone ems3 filzkorper ems1 ems2 ems3 ems4 emsunspecified ganglionic branch primordium ems2 hypocerebral ganglion ems3 intercalary segment ems3 lateral process ems4 local interneuron of larval antennal lobe | somatic clone ems3 longitudinal connective ems2 mandibular segment ems3 maxillary lobe ems1 neurite | cell autonomous | somatic clone ems3 neuroblast | somatic clone ems3 ocular segment ems3 spiracular chamber ems2 ems3 stigmatophore ems2 ems3 tracheal primordium ems2 tritocerebral neuromere ems1 ems10D29 ems2 ventral nerve cord ems2 ventral nerve cord commissure ems2 vertical bridge ems4 visceral branch primordium ems2
Classical Alleles ( 8 )
For All Classical Alleles Show
Allele of ems Class Mutagen Stocks Known lesion ems1 ethyl methanesulfonate 2 Yes ems4 hypomorphic allele - genetic evidence ethyl methanesulfonate 1 Yes ems2 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes ems3 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes ems10D29 0 -- ems7099 0 -- ems9Q84 0 -- emsunspecified 0 --
Alleles Carried on Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Allele of ems Class Mutagen Stocks Known lesion emsGD1435 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes emshs.PJ in vitro construct - regulatory fusion 1 Yes emsJF03153 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes ems-hp.Scer\UAS in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes emsbtd.PS in vitro construct - regulatory fusion 0 Yes emshs.PH in vitro construct - regulatory fusion 0 Yes emsScer\UAS.cRa in vitro construct - regulatory fusion 0 Yes emsScer\UAS.cSa in vitro construct - regulatory fusion 0 Yes emsT:Avic\GFP-EGFP in vitro construct - coding region fusion 0 Yes emstCH322-143M02 in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)293γ5 (Jarman and Collett, 1998, Dalton et al., 1989) Df(3R)293γ7 (Jarman and Collett, 1998) Df(3R)ED5622 (Ryder and Roote, 2004.11.10) Df(3R)ED5642 (Ryder and Roote, 2004.11.10) Df(3R)Exel6171 (Ryder, 2004.4.26) Df(3R)Exel6288 (Ryder, 2004.4.26) Df(3R)kar5l (Jurgens et al., 1984) Df(3R)red1 (Dalton et al., 1989) Df(3R)red3l (Jarman and Collett, 1998, Jurgens et al., 1984, Tearle and Nusslein-Volhard, 1987, Dalton et al., 1989, Harbecke and Lengyel, 1995) Df(3R)ry506-85C (Harbecke and Lengyel, 1995)
Not disrupted in	Df(3R)l26c (Jarman and Collett, 1998) Df(3R)M36 (Jarman and Collett, 1998) Df(3R)M49 (Jarman and Collett, 1998) Df(3R)red-P1 (Jarman and Collett, 1998) Df(3R)red-P52 (Jarman and Collett, 1998, Dalton et al., 1989) Df(3R)red-P93 (Tearle and Nusslein-Volhard, 1987) Df(3R)ry85 (Dalton et al., 1989) Df(3R)su(Hw)7 (Jarman and Collett, 1998) Df(3R)urd (Jarman and Collett, 1998)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{ems-lacZ.1.0D} No P{ems-lacZ.1.2} No P{ems-lacZ.2.6D} No P{ems-lacZ.3.3} No P{ems-lacZ.4.6} No P{ems-lacZ.4xA} No P{ems-lacZ.4xB} No P{ems-lacZ.4xC} No P{ems-lacZ.5.6} No P{ems-lacZ.8.2} No P{ems-lacZ.IV} No P{ems-lacZ.mutBCD} No P{ems-lacZ.mutTLL} No P{ems-lacZ.W} No heat-shock construct P{hs-ems} NA P{hsp70-ems} NA UAS construct P{GD1435} NA P{TRiP.JF03153} NA P{UAS-ems.R} NA P{UAS-ems.S} NA characterization construct P{btd-ems.S} NA P{ems-GAL4.HRE} NA PBac{CH322-143M02} NA PBac{ems-EGFP.S} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 17 unique terms )
Terms Based on Experimental Evidence ( 11 terms )
Molecular Function
CV term Evidence References
RNA polymerase II distal enhancer sequence-specific DNA binding inferred from direct assay (Taylor, 1998)
Biological Process
CV term Evidence References
axonogenesis inferred from mutant phenotype (Hartmann et al., 2000) brain development inferred from mutant phenotype (Lichtneckert et al., 2007, Hartmann et al., 2000) brain segmentation inferred from mutant phenotype (Hirth et al., 1995) dendrite morphogenesis inferred from mutant phenotype (Lichtneckert et al., 2008) embryonic development via the syncytial blastoderm inferred from mutant phenotype (Hirth et al., 1995, Hartmann et al., 2000) neuroblast development inferred from mutant phenotype (Lichtneckert et al., 2007) open tracheal system development inferred from expression pattern AND inferred from mutant phenotype (Ebner et al., 2002) spiracle morphogenesis, open tracheal system inferred from mutant phenotype (Hu and Castelli-Gair, 1999) ventral cord development inferred from mutant phenotype (Hartmann et al., 2000)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Lichtneckert et al., 2007)
Terms Based on Predictions or Assertions ( 8 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q04743 (FlyBase, 1992-)
Biological Process
CV term Evidence References
anterior head segmentation traceable author statement (Peel, 2004) brain development non-traceable author statement (Ball et al., 2004) pattern specification process non-traceable author statement (Ball et al., 2004) regulation of transcription, DNA-dependent inferred from sequence or structural similarity with UniProtKB:Q04743 (FlyBase, 1992-) specification of segmental identity, antennal segment non-traceable author statement (Swiss-Prot Project Members, 1990.11.1) specification of segmental identity, mandibular segment non-traceable author statement (Swiss-Prot Project Members, 1990.11.1)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:Q04743 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
ems - CG11266 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - CG15220 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - CG8778 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - Gnf1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - Imp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - Irbp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - Ku80 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) ems - RPA2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions ems allele Gene References unspecified tor (Strecker et al., 1992)
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0000576 DroID - A comprehensive database of gene and protein interactions. • FBgn0000576
Orthologs
OrthoDB Orthologs (49) - 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 EOG6WH96D Dipteran inclusive ortholog search EOG6B5PFQ Insect inclusive ortholog search EOG64J1GB Arthropod inclusive ortholog search EOG6JH9ZZ Metazoa inclusive ortholog search EOG6SBSV6
Orthologs in Drosophila Species (EOG6WH96D)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\ems     Drosophila simulans   Dsim\GD18937 Y   Drosophila sechellia   Dsec\GM24141 Y   Drosophila erecta   Dere\GG19873 Y   Drosophila yakuba   Dyak\GE26304 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA15560 Y   Drosophila persimilis   Dper\GL24224 Y   Drosophila willistoni   Dwil\GK22678 Y
Orthologs in non-Drosophila Dipterans (EOG6B5PFQ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL003506 Y Aedes aegypti Yellow fever mosquito  Aaeg\AAEL003504 Y Anopheles gambiae Malaria mosquito  Agam\AGAP001618 Y Anopheles gambiae Malaria mosquito  Agam\AGAP001619 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ009087 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ009088 Y
Orthologs in non-Dipteran Insects (EOG64J1GB)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB52912 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG001943 Y Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH16580 Y Atta cephalotes Leafcutter ant  Acep\ACEP22767 Y Atta cephalotes Leafcutter ant  Acep\ACEP22765 Y Camponotus floridanus Florida carpenter ant  Cflo\CFLO11975 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL11817 Y Linepithema humile Argentine ant  Lhum\LH18117 Y Linepithema humile Argentine ant  Lhum\LH18118 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB25301 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB25305 Y Solenopsis invicta Red fire ant  Sinv\SINV22974 Y Acyrthosiphon pisum Pea aphid  Apim\ACYPI006661 Y Bombyx mori Silkmoth  Bmor\BGIBMGA010749 Y Bombyx mori Silkmoth  Bmor\BGIBMGA010750 Y Pediculus humanus Human body louse  Phum\PHUM205160 Y Tribolium castaneum Red flour beetle  Tcas\ems Y
Orthologs in non-Insect Arthropods (EOG6JH9ZZ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\ZNF280D Y Daphnia pulex Water flea  Dpux\p15 Y Ixodes scapularis Deer tick  Isca\ISCW012144 Y
Orthologs in non-Arthropod Metazoa (EOG6SBSV6)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\ceh-2 Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_002592gn Y Danio rerio Zebrafish  Drer\emx2 Y Danio rerio Zebrafish  Drer\emx1 Y Danio rerio Zebrafish  Drer\emx3 Y Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000033848 Y Xenopus tropicalis Western clawed frog  Xtro\emx2 Y Xenopus tropicalis Western clawed frog  Xtro\emx1.2 Y Gallus gallus Domestic chicken  Ggal\EMX2 Y Gallus gallus Domestic chicken  Ggal\EMX1 Y Mus musculus House mouse  Mmus\Emx1 Y Mus musculus House mouse  Mmus\Emx2 Y Rattus norvegicus Norway rat  Rnor\Emx1 Y Rattus norvegicus Norway rat  Rnor\Emx2 Y Homo sapiens Human  Hsap\EMX2 Y
Human Orthologs (1)
Gene OMIM HGNC Hsap\EMX2
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD18937 Drosophila sechellia Dsec\GM24141 Drosophila erecta Dere\GG19873 Drosophila yakuba Dyak\GE26304 Drosophila ananassae Dana\GF16103 Drosophila pseudoobscura pseudoobscura Dpse\GA15560 Drosophila persimilis Dper\GL24224 Drosophila willistoni Dwil\GK22678 Drosophila virilis Dvir\GJ22569 Drosophila mojavensis Dmoj\GI10044 Drosophila grimshawi Dgri\GH14408
Stocks & Reagents
Stocks Listed in FlyBase ( 7 )
Bloomington	7438 P{hsp70-ems}1; cn1; ry506 28726 y1 v1; P{TRiP.JF03153}attP2 34503 st1 ems4 e1/TM3, Sb1 3349 ru1 h1 th1 st1 cu1 ems1 sr1 es ca1/TM3, Sb1 Ser1
Kyoto	106996 ru1 h1 th1 st1 cu1 ems1 sr1 es ca1/TM3, Sb1 Ser1
VDRC	v9417 w1118; P{GD1435}v9417 v9419 w1118; P{GD1435}v9419/TM3
Genomic Clones ( 1 )
	BACR25B05 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 16 )
	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	RE15812
Other clones	DPiM_RE15812
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	10832 54805 63188 67590 99838 161585 EK103506 EK103906 EK110937 EK180704 EK180842 EK188732 EK195642 EK222247
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0000576 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 41697
Antibody Information
	polyclonal (Ando et al., 2011, Dalton et al., 1989)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	ems is essential for correct post-embryonic projection neuron development in the olfactory system. (Lichtneckert et al., 2008) In the posterior brain and the ventral nerve cord, ems is necessary for correct axonal pathfinding of specific interneurons. (Hartmann et al., 2000) Mis-expression of ems in the head transforms segment identity in a btd-dependent manner. (Schock et al., 2000) ems and btd gene products interact in vitro. (Schock et al., 2000) ems is able to specify head identity when acting in concert with btd. (Schock et al., 2000) In ems mutants, invagination of the spiracle cells adjacent to the trachea does not occur, though more posterior cells of the spiracle invaginate normally, producing a spiracle without a lumen. (Hu and Castelli-Gair, 1999) In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes. (Kliman and Eyre-Walker, 1998) Psc protein is associated with an upstream fragment of ems. (Strutt and Paro, 1997) Probes labelled with digoxigenin, fluorescein and biotin allow detection of RNA of three different genes in three different colours. (Hauptmann and Gerster, 1996) ems is the gene responsible for sclerotic plate formation in larvae lacking all thoracic and abdominal homeotic genes and is phenotypically suppressed by the homeotic genes in normal development. (Macias and Morata, 1996) oc and ems are required for brain segmentation in the embryo. (Hirth et al., 1995) Heat shock induced expression of mouse Hox genes in Drosophila embryos deficient for homeotic genes demonstrates that functional hierarchy is a universal property of the homeobox genes. Correlations exist between the expression patterns of the mouse Hox genes along the antero-posterior body axis of mice and the extent of their effect along the antero-posterior body axis of flies. (Bachiller et al., 1994) ems, a head-specific gap gene, may function as a co-repressor of dl, thereby linking the anteroposterior and dorsoventral systems st the molecular level. (Grossniklaus et al., 1994) Expression of the trn pair rule stripes requires ftz and ems. (Chang et al., 1993) ems is a downstream gene that is transcriptionally regulated by Abd-B gene products. Genetic epistasis tests suggest that both ems and Abd-B gene products are required in combination for the specification of the filzkorper primordia. (Jones and McGinnis, 1993) One of the homeodomain loci identified in a screen for genes encoding DNA binding proteins capable of binding to a consensus Engrailed binding site. (Kalionis and O'Farrell, 1993) The role of ems in the regulation of run mRNA expression in the early embryo has been investigated. (Klingler and Gergen, 1993) Isolated by cross-homology to a Dr probe. Stated to be at 88A: no further details given. (Walldorf and Gehring, 1992) ems has been cloned and sequenced and shown to be a homeobox-containing gene. Its expression pattern and mutant phenotype suggest it is a gap gene. (Walldorf and Gehring, 1992) ems has a gap-gene-like role in mediating the development of head structures. In ems mutant embryos gt stripe 1 is normal but stripes 1 and 2 fail to sharpen and separate at cellular blastoderm. ems is positively regulated by bcd. (Eldon and Pirrotta, 1991) Mutations in zygotic gene ems do not interact with RpII140wimp. (Parkhurst and Ish-Horowicz, 1991) btd, ems and oc are required to establish contiguous blocks of segments and may behave like gap genes that mediate bcd function in the embryonic head. (Cohen and Jurgens, 1990) ems is required for the development of structures that derive from the most anterior head segments of the embryo. (Dalton et al., 1989) ems mutants display spiracles devoid of filzkorper, no antenna and an open head. (Jurgens et al., 1984) Embryonic lethal. Embryos display loss of filzkorper in the posterior spiracles; posterior ends of longitudinal tracheal trunks incomplete. Failure of head involution; many cuticular structures that normally derive from the procephalic and mandibular lobes of the head missing; embryonic antennal organs missing. ems protein first appears as an anterior ring around the syncytial blastoderm at a position just anterior to that of Dfd; it is five to six cells wide dorsally and 10-12 cells wide ventrally; at gastrulation the ring is just anterior to the cephalic furrow. As gastrulation proceeds expression becomes patchy and confined to specific groups of cells. The protein is nuclear in localization. The metameric pattern of ems expression commences at the beginning of germ-band extension; protein first appears in a group of cells in each segment, which subsequently elongates and splits into two clusters of ems-positive cells in regions destined to give rise to tracheal pits, neuroblasts and epidermis. In the eighth abdominal segment, a large patch of ems-positive cells forms just posterior to the tracheal pit and presumably correspond to the primordia of the posterior spiracles and the filzkorper; a similar patch is formed anteriorly in embryos produced by bcd mothers. For a detailed discussion of the expression pattern see Dalton et al.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_169560 RefSeq (Proteins) • NP_731868 DDBJ / EMBL / GenBank • AAF54999 AAX33458 AF029219 BT021310 CAA35965 CAA46985 X51653 X66270 Entrez Gene - A searchable database of RefSeq genes. • 41697 UniProtKB/Swiss-Prot • P18488 UniProtKB/TrEMBL • Q5BIB4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeodomain (IPR001356) Homeodomain-like (IPR009057) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE15812
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0000576 DroID - A comprehensive database of gene and protein interactions. • FBgn0000576 DRSC - Results from RNAi screens. • FBgn0000576 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000576 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2988-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0000576 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 41697 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /segment/emptyspi.htm modMine - Data generated by the modENCODE project. • FBgn0000576 REDfly - A database of transcriptional regulatory elements. • FBgn0000576
Synonyms & Secondary IDs ( 13 )
Reported As
Symbol Synonym	ant   CG2988 (Perkins et al., 2009) E4 (Dalton et al., 1989) ems (Urbach et al., 2006, Krattinger et al., 2007, Scholtz, 2006, Lovegrove et al., 2006, Venken et al., 2009, Hueber et al., 2007, Lichtneckert et al., 2007, Sprecher and Hirth, 2006, Bellen et al., 2011, Perry et al., 2011, Stöbe et al., 2009, Kumar et al., 2009, DeFalco et al., 2008, Das et al., 2008, Lichtneckert et al., 2008, Sotillos et al., 2008, Ochoa-Espinosa et al., 2009, Nanda et al., 2009, Immonen and Ritchie, 2012, Copley, 2005, Seibert et al., 2009, Löhr et al., 2009, Venken et al., 2009, Grad et al., 2004, Magalhaes et al., 2007, Hartmann et al., 2010, Maurel-Zaffran et al., 2010, Blanco and Gehring, 2008, Yassin et al., 2010, Hauptmann, 2001, Zhai et al., 2010, Kazemian et al., 2010, Sprecher et al., 2007, Andrioli et al., 2012, Lovegrove et al., 2006, Zhai et al., 2011, He et al., 2012, Nikulova et al., 2012) Ems (Goldstein et al., 2005, Noyes et al., 2008) EMS (Kim et al., 2010) W13
Name Synonym	antenna   empty-spiracle (Andrioli et al., 2012) empty spiracles (Taylor, 1997.10.7, Schwartz and Pirrotta, 2007, Yucel and Small, 2006, Scholtz, 2006, Hueber et al., 2007, Lichtneckert et al., 2007, Sprecher and Hirth, 2006, Kumar et al., 2009, DeFalco et al., 2008, Lichtneckert et al., 2008, Ochoa-Espinosa et al., 2009, Rehmsmeier et al., 2004, Seibert et al., 2009, Löhr et al., 2009, Hartmann et al., 2010, Blanco and Gehring, 2008, Das et al., 2008, Zhai et al., 2010, Zhai et al., 2011) Empty spiracles (Goldstein et al., 2005, Nanda et al., 2009) Empty Spiracles (Kim et al., 2010) empty-spiracles (Ishihara and Shibata, 2008, Coiffier et al., 2008)
Secondary FlyBase IDs
	FBgn0000145
References ( 225 )
Generate a list of	All references relating to this gene ( 225 )
List References by type	Research paper  ( 136 ) Supplementary material  ( 5 ) Review  ( 41 ) Personal communication to FlyBase  ( 10 ) Abstract  ( 23 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Stock list  ( 1 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 ) Conference report  ( 1 ) Book  ( 1 )
Recent research papers ( 10 )
	Andrioli et al., 2012, Dev. Biol. 361(1): 177--185 Huckebein is part of a combinatorial repression code in the anterior blastoderm. [FBrf0216872] He et al., 2012, Mol. Biol. Evol. 29(3): 1059--1070 Evolutionary origins of transcription factor binding site clusters. [FBrf0217421] Immonen and Ritchie, 2012, Proc. Biol. Sci. 279(1732): 1359--1365 The genomic response to courtship song stimulation in female Drosophila melanogaster. [FBrf0217554] Nikulova et al., 2012, Nucleic Acids Res. 40(12): e93 CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. [FBrf0218757] Weber et al., 2012, PLoS ONE 7(4): e34745 Genome-Wide Association Analysis of Oxidative Stress Resistance in Drosophila melanogaster. [FBrf0218073] Ando et al., 2011, Dev. Biol. 358(1): 122--136 TALE-class homeodomain transcription factors, homothorax and extradenticle, control dendritic and axonal targeting of olfactory projection neurons in the Drosophila brain. [FBrf0215261] Bellen et al., 2011, Genetics 188(3): 731--743 The Drosophila gene disruption project: progress using transposons with distinctive site specificities. [FBrf0214229] Gabilondo et al., 2011, Mech. Dev. 128(3-4): 208--221 A targeted genetic screen identifies crucial players in the specification of the Drosophila abdominal Capaergic neurons. [FBrf0213290] Perry et al., 2011, Proc. Natl. Acad. Sci. U.S.A. 108(33): 13570--13575 Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. [FBrf0214713] Zhai et al., 2011, Biochem. Biophys. Res. Commun. 414(4): 761--766 Functional dissection of the Hox protein Abdominal-B in Drosophila cell culture. [FBrf0216579] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...