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Gene Dmel\bap

General Information
Symbol	Dmel\bap	Species	D. melanogaster
Name	bagpipe	Annotation symbol	CG7902
Feature type	protein_coding_gene	FlyBase ID	FBgn0004862
Gene Model Status	Current	Stock availability	2 publicly available
Also Known As	NK-3, NK3
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	93D10-93D10	Sequence location	3R:17,214,602..17,216,171 [+]
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 bagpipe is referred to in FlyBase by the symbol Dmel\bap (CG7902, FBgn0004862). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: sequence-specific DNA binding; RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: regulation of transcription from RNA polymerase II promoter; mesoderm development. 23 alleles are reported. The phenotype of these alleles is annotated with: midgut muscle. It has one annotated transcript and one annotated polypeptide. Protein features are: Homeobox, conserved site; Homeodomain; Homeodomain, metazoa; 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 high levels in the following post-embryonic organs or tissues: adult crop. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult hindgut, adult heart. Comments on Affy2 ProbeSet: ProbeSet 1638565_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of bap. Gene sequence location is 3R:17214602..17216171.
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	NK3 (M. Nirenberg) Homeobox gene expressed transiently during embryonic development in some mesodermal cells (foregut and hindgut visceral muscle cells). NK3 poly A+ RNA was not detected in 0-3-hour embryos, but was found in low abundance in RNA from 3-6-hour embryos. The abundance was maximum in RNA from 6-12-hour embryos and then declined during further embryonic development.
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 93D10-93D10   Limits computationally determined from genome sequence between P{PZ}mod(mdg4)07038&P{lacW}mod(mdg4)L3101 and P{PZ}InR05545
Experimentally Determined Cytological Location
Cytogenetic map Notes References 93E1-93E1     (Kim, 1993) 93E1-93E3   (determined by in situ hybridisation)   (Kim and Nirenberg, 1989)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\bap 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 5.49
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) bap-RA FBtr0084087  NM_169958   1449   382
Additional Transcript Data & Comments
Reported size (kB)	1.55 (northern blot) (Azpiazu and Frasch, 1993)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein bap-PA   FBpp0083486   42.0   382   9.06     NP_732637   AAF55891
Additional Polypeptide Data & Comments
Reported size (kDa)	382 (aa) (Azpiazu and Frasch, 1993)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeodomain (IPR001356) Homeodomain-like (IPR009057) Homeobox, conserved site (IPR017970) Homeodomain, metazoa (IPR020479)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF55891   AY369088 AAQ73793   AY369089 AAQ73794   AY369090 AAQ73795   AY369091 AAQ73796   AY369092 AAQ73797   AY369093 AAQ73798   AY369094 AAQ73799   AY369095 AAQ73800   AY369096 AAQ73801   AY369097 AAQ73802   AY369098 AAQ73803   AY369099 AAQ73804   AY369100 AAQ73805   AY369101 AAQ73806   AY369102 AAQ73807   AY369103 AAQ73808   AY369104 AAQ73809   AY369105 AAQ73810   AY369106 AAQ73811   AY369107 AAQ73812   AY369108 AAQ73813   AY369109 AAQ73814   AY369110 AAQ73815   AY369111 AAQ73816   AY369112 AAQ73817   AY369113 AAQ73818   AY369114 AAQ73819   AY369115 AAQ73820   BI172041   BT001561 AAN71316   CO183405   L17133 AAC37165   M27291 AAA28618
UniProtKB/Swiss-Prot	P22809
UniProtKB/TrEMBL	Q53YH4
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 regulatory region FBsf0000435260 3R:17,217,194..17,220,837 evidence=Reporter construct (in vivo) (Lee and Frasch, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435331 3R:17,218,144..17,220,402 evidence=Reporter construct (in vivo) (Jakobsen et al., 2007, Halfon, 2012.6.19) regulatory region FBsf0000435363 3R:17,209,495..17,214,451 evidence=Reporter construct (in vivo) (Lee and Frasch, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435386 3R:17,216,987..17,217,167 evidence=Reporter construct (in vivo) (Lee and Frasch, 2005, Halfon, 2012.6.19) regulatory region FBsf0000435750 3R:17,216,931..17,217,197 evidence=Reporter construct (in vivo) (Lee and Frasch, 2005, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism | ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   organism | ubiquitous   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   head mesoderm   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) embryonic stage 10   hindgut visceral muscle primordium   (San Martin and Bate, 2001, Lee and Frasch, 2005) foregut visceral muscle primordium   (Lee and Frasch, 2005) visceral mesoderm   (Lee and Frasch, 2005) Comment:reference states trunk visceral mesoderm embryonic stage 11 -- 12   cephalic vascular primordium   (Fisher et al., 2012) procrystal cell   (Fisher et al., 2012) somatic muscle primordium   (Fisher et al., 2012) Comment:reported as muscle system primordium visceral muscle primordium   (Fisher et al., 2012) Comment:reported as muscle system primordium embryonic stage 13 -- 16   embryonic/larval muscle system   (Fisher et al., 2012) embryonic/larval somatic muscle   (Fisher et al., 2012) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Azpiazu and Frasch, 1993) mesoderm | dorsal   (Azpiazu and Frasch, 1993) embryonic stage 10 -- 11   visceral mesoderm of embryonic/larval midgut   (Azpiazu and Frasch, 1993) embryonic stage 11 -- 15   visceral mesoderm of embryonic/larval hindgut   (Azpiazu and Frasch, 1993) visceral mesoderm of embryonic/larval foregut   (Azpiazu and Frasch, 1993) embryonic stage 13 -- 17   cardioblast   (Azpiazu and Frasch, 1993)
Additional Descriptive Data
	bap is first expressed in 4-8hr embryos, peaks between 4 and 12 hours of embryogenesis and drops off dramatically subsequently. bap is expressed from embryonic stage 10 in the dorsal-most cells of the mesoderm. The bap expression occurs in patches along the anterior-posterior axis in the region corresponding to parasegments 2-12 of the epidermis which will give rise to the visceral mesoderm. Double staining for bap and en shows that the anterior border of each patch aligns with the anterior parasegmental borders. This expression is transient and disappears during stage 11. bap is also expressed in mesodermal cells at the proctodeum and stomodeum. These will develop into the visceral mesoderm of the hindgut and foregut and they continue bap expression until late embryogenesis. After stage 12, bap is also expressed in a subset of heart progenitors. (Azpiazu and Frasch, 1993)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 10   mesoderm | striped   (Lee and Frasch, 2000) embryonic stage 10 -- 11   visceral mesoderm | striped   (Weiss et al., 2001) embryonic stage 11   foregut primordium   (Zaffran et al., 2001) foregut visceral muscle primordium   (Zaffran et al., 2001) hindgut proper primordium   (Zaffran et al., 2001)
Additional Descriptive Data
	Stripes alternate with slp1. (Lee and Frasch, 2000) At embryonic stage 10 bap expressing cell clusters are interdigitated with jeb-expressing cell clusters. At embryonic stage 11, bap-expressing cells form stripes that are adjacent and dorsal to jeb-expressing cells. (Weiss et al., 2001)
Marker for
	visceral mesoderm
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (Reim and Frasch, 2005)
Expression Deduced from Reporters
Reporter: P{bap-GAL4.3} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   visceral mesoderm   (Hosono et al., 2003, Lee et al., 2003, Weiss et al., 2001) embryonic stage 10 -- 17   visceral mesoderm   (Stute et al., 2004) embryonic stage 11 -- 13   visceral mesoderm   (Zaffran et al., 2001) Reporter: P{bap-lacZ.3} Stage Tissue/Position (including subcellular localization) Reference embryonic stage 10   visceral mesoderm | dorsal   (Lee and Frasch, 2005) Comment:reference states trunk visceral mesoderm embryonic stage 10 -- 15   circular visceral muscle primordium | segmentally repeated   (Zaffran et al., 2001) embryonic stage 10 -- 17   visceral mesoderm | segmentally repeated   (Zaffran et al., 2001) circular visceral muscle primordium of midgut   (Zaffran et al., 2001) circular visceral muscle primordium | restricted   (Zaffran et al., 2001) midgut | restricted   (Zaffran et al., 2001) embryonic stage 11   myoblast   (Stute et al., 2004) visceral mesoderm   (Stute et al., 2004) embryonic stage 12   visceral mesoderm   (Zaffran and Frasch, 2002) embryonic stage 12 -- 13   visceral mesoderm   (Lee et al., 2003) embryonic stage 12 -- 15   trunk mesoderm   (Zaffran et al., 2001) embryonic stage 12 -- 16   visceral mesoderm | segmentally repeated   (Kolsch and Paululat, 2002) Reporter: P{bap-lacZ.4.5} Stage Tissue/Position (including subcellular localization) Reference embryonic stage   visceral mesoderm   (Azpiazu and Frasch, 1993)
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 high levels in the following post-embryonic organs or tissues: adult crop. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult hindgut, adult heart. [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    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop  (584.8) Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop  584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    16.7 Larval Midgut    20.2 Larval Hindgut    140.1 Larval Malpighian Tubules    17.6 Larval Fat Body    13.7 Larval Salivary Gland    13.8 Larval Trachea    6.575 Larval Carcass    23.1 Adult Head    19.8 Adult Eye    1.45 Adult Brain    13.2 Adult Thoracic-Abdominal Ganglion    5.5 Adult Crop    584.8 Adult Midgut    20.5 Adult Hindgut    227.8 Adult Malpighian Tubules    6.3 Adult Fat Body    30.1 Adult Salivary Gland    13.3 Adult Heart    109.875 Adult VirginFemale Spermatheca    9.9 Adult InseminatedFemale Spermatheca    7.1 Adult Ovary    7.9 Adult Testis    10.2 Adult Male Accessory Gland    4.6 Adult Carcass    22.1 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    no informative data   NA  Eye    1.45   NA  Brain    no informative data   no informative data  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    5.5   NA  Crop    584.8   no informative data  Midgut    no informative data   140.1  Hindgut    227.8   no informative data  Malpighian Tubules    6.3   no informative data  Fat Body    no informative data   no informative data  Salivary Gland    no informative data   NA  Heart    109.875   6.575  Trachea    NA   NA  VirginFemale Spermatheca    9.9   NA  InseminatedFemale Spermatheca    7.1   NA  Ovary    7.9   NA  Testis    no informative data   NA  Male Accessory Gland    4.6   no informative data  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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 central nervous system, larvae L3    1 central nervous system, pupae P8    1 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    0 head, mated 1-day male    1 head, mated 4-day male    0 head, mated 20-day male    0 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    0 digestive system, 1-day adult    1 digestive system, 4-day adult    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    0 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    0 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr  (28) embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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 Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr  28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    0 embryo 02-04hr    3 embryo 04-06hr    20 embryo 06-08hr    28 embryo 08-10hr    7 embryo 10-12hr    7 embryo 12-14hr    6 embryo 14-16hr    8 embryo 16-18hr    6 embryo 18-20hr    5 embryo 20-22hr    3 embryo 22-24hr    4 larva L1    3 larva L2    2 larva L3 12hr old    1 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    1 white prepupae 24hr    1 pupae 2d postWPP    1 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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    1 cold shock, 4-day adult    1 heat shock, 4-day adult    0 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    0 Cadmium 100 mM 48 hrs, 4-day adult    0 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    0 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    0 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    0 Paraquat 10 mM 48 hrs, 4-day adult    1 Rotenone 2 μg 12 hrs, larvae L3    0 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_31 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • RE13967 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004862 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7902-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for bap Stages(s) 1-3 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal bap208 Other Phenotypes Allele wild-type bap+t11 Phenotype manifest in Allele embryonic/larval midgut | embryonic stage bap208 midgut muscle bap208
Classical Alleles ( 16 )
For All Classical Alleles Show
Allele of bap Class Mutagen Stocks Known lesion bap208 loss of function allele ethyl methanesulfonate 0 -- bapF-274F natural population 0 Yes bapF-611F natural population 0 Yes bapF-775F natural population 0 Yes bapF-96S natural population 0 Yes bapS-1224F natural population 0 Yes bapS-26F natural population 0 Yes bapS-377F natural population 0 Yes bapS-438S natural population 0 Yes bapS-510S natural population 0 Yes bapS-512F natural population 0 Yes bapS-521S natural population 0 Yes bapS-549S natural population 0 Yes bapS-565F natural population 0 Yes bapS-968F natural population 0 Yes bapUS-255F natural population 0 Yes
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of bap Class Mutagen Stocks Known lesion bapJF02404 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes bapKK108567 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes bap+t11 in vitro construct - genomic fragment 0 Yes bapGD1383 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes baphs.PP in vitro construct - regulatory fusion 0 Yes bapScer\UAS.cRa in vitro construct - regulatory fusion 0 Yes bapScer\UAS.cZa in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)e-BS2 (Jagla et al., 1997) Df(3R)e-D7 (Lo and Frasch, 1998, Azpiazu and Frasch, 1993) Df(3R)e-F1 (Jagla et al., 1997)
Partially disrupted in	Df(3R)e-F1 (De Graeve et al., 2004) Df(3R)lb (De Graeve et al., 2004)
Not disrupted in	Df(2R)gsb (Azpiazu et al., 1996) Df(3R)e-Gp4 (Jagla et al., 1997) Df(3R)GC14 (Bodmer, 1993, Azpiazu and Frasch, 1993, Jagla et al., 1997)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{bap-lacZ.1} No P{bap-lacZ.2} No P{bap-lacZ.3.1} No P{bap-lacZ.3.2.1} No P{bap-lacZ.3.2.1-bap-m} No P{bap-lacZ.3.2.1-C1-m} No P{bap-lacZ.3.2.1-slp-m1} No P{bap-lacZ.3.2.1-slp-m2} No P{bap-lacZ.3.2.1-slp-m4} No P{bap-lacZ.3.2.1-slp-m5} No P{bap-lacZ.3.2.1-Smad1-m} No P{bap-lacZ.3.2.1-Smad2-m} No P{bap-lacZ.3.2.1-Smad3,4-d} No P{bap-lacZ.3.2.1-Smad5-d} No P{bap-lacZ.3.2.1-tinD1.3'} No P{bap-lacZ.3.2.1-tinD1.5'} No P{bap-lacZ.3.2.1-tin-m} No P{bap-lacZ.3.2} No P{bap-lacZ.3.2R1-3mut} No P{bap-lacZ.3.2ΔR3} No P{bap-lacZ.3} No P{bap-lacZ.4.5} No P{bap-lacZ.DS3.5} No P{bap-lacZ.H2-1.2} No UAS construct P{GD1383} NA P{KK108567} NA P{TRiP.JF02404} NA P{UAS-bap.R} NA P{UAS-bap.Z} NA heat-shock construct P{hs-bap.P} NA characterization construct P{bap-GAL4.3} NA P{bap-RFP.3} NA P{CaSperRe3} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 13 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function
CV term Evidence References
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity inferred from genetic interaction with βTub60D (Zaffran and Frasch, 2002) sequence-specific DNA binding inferred from direct assay (Zaffran and Frasch, 2002)
Biological Process
CV term Evidence References
mesoderm development inferred from expression pattern (Furlong et al., 2001) regulation of transcription from RNA polymerase II promoter inferred from mutant phenotype (Zaffran and Frasch, 2002)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Reim and Frasch, 2005)
Terms Based on Predictions or Assertions ( 9 terms )
Molecular Function
CV term Evidence References
DNA binding non-traceable author statement (Swiss-Prot Project Members, 1991.8.1) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with EMBL:AF138905 (FlyBase, 1992-)
Biological Process
CV term Evidence References
cell fate commitment non-traceable author statement (Swiss-Prot Project Members, 1991.8.1) heart development non-traceable author statement (Cripps and Olson, 2002) mesodermal cell fate commitment traceable author statement (Cripps and Olson, 2002) mesodermal cell fate specification traceable author statement (Jagla et al., 2001) midgut development traceable author statement (Jagla et al., 2001) visceral muscle development non-traceable author statement (Furlong et al., 2001)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with mouse Bapx1 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1991.8.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
bap - BCAS2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG11266 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG17454 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG1785 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG3817 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG4619 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG6084 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG6724 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG7878 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG8043 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG8545 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CG8963 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Cdc5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - CkIIα anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Cyt-c-p anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - DnaJ-1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Eb1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Gp210 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Hsc70-1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Imp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - LRP1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Mtr3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - NHP2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Nop56 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - P32 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Pgam5 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rbp1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rbp1-like anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rlb1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - RpL35A anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - RpLP0 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rpt2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rrp4 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rrp40 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Rrp46 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Saf-B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - Sec23 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - U4-U6-60K anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - l(3)72Ab anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL13 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL4 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL44 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL52 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpL54 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpS24 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - mRpS33 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - nonA-l anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) bap - pont 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 bap allele Gene References
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0004862 DroID - A comprehensive database of gene and protein interactions. • FBgn0004862 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42537 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P22809
Orthologs
OrthoDB Orthologs (39) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6TTH3Z Dipteran inclusive ortholog search EOG618BX5 Insect inclusive ortholog search EOG67H4KR Arthropod inclusive ortholog search EOG6GHX4T Metazoa inclusive ortholog search EOG622PFD
Orthologs in Drosophila Species (EOG6TTH3Z)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\bap     Drosophila simulans   Dsim\bap Y   Drosophila sechellia   Dsec\bap Y   Drosophila erecta   Dere\GG24598 Y   Drosophila yakuba   Dyak\GE25732 Y   Drosophila ananassae   Dana\GF18600 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA20672 Y   Drosophila persimilis   Dper\GL27337 Y   Drosophila willistoni   Dwil\GK14503 Y   Drosophila virilis   Dvir\GJ14311 Y   Drosophila grimshawi   Dgri\GH22032 Y
Orthologs in non-Drosophila Dipterans (EOG618BX5)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL006597   Anopheles gambiae Malaria mosquito  Agam\AGAP003671   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ004109
Orthologs in non-Dipteran Insects (EOG67H4KR)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\LOC100577942   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH11497   Atta cephalotes Leafcutter ant  Acep\ACEP23863   Camponotus floridanus Florida carpenter ant  Cflo\CFLO21169   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL13863   Linepithema humile Argentine ant  Lhum\LH25158   Pogonomyrmex barbatus Red harvester ant  Pbar\PB10986   Pogonomyrmex barbatus Red harvester ant  Pbar\PB10984   Solenopsis invicta Red fire ant  Sinv\SINV22315   Solenopsis invicta Red fire ant  Sinv\SINV24651   Bombyx mori Silkmoth  Bmor\BGIBMGA010706   Pediculus humanus Human body louse  Phum\PHUM439840   Tribolium castaneum Red flour beetle  Tcas\TC012743
Orthologs in non-Insect Arthropods (EOG6GHX4T)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Ixodes scapularis Deer tick  Isca\ISCW014989
Orthologs in non-Arthropod Metazoa (EOG622PFD)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_013047gn   Danio rerio Zebrafish  Drer\nkx3.2   Danio rerio Zebrafish  Drer\nkx3.3   Xenopus tropicalis Western clawed frog  Xtro\bapx   Xenopus tropicalis Western clawed frog  Xtro\nkx3-2   Xenopus tropicalis Western clawed frog  Xtro\nkx3-1   Mus musculus House mouse  Mmus\Nkx3-1   Mus musculus House mouse  Mmus\Nkx3-2   Rattus norvegicus Norway rat  Rnor\Nkx3-1   Homo sapiens Human  Hsap\NKX3-2   Homo sapiens Human  Hsap\NKX3-1
Human Orthologs (2)
Gene OMIM HGNC Hsap\NKX3-2     Hsap\NKX3-1
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\bap Drosophila sechellia Dsec\bap Drosophila erecta Dere\GG24598 Drosophila yakuba Dyak\GE25732 Drosophila ananassae Dana\GF18600 Drosophila pseudoobscura pseudoobscura Dpse\GA20672 Drosophila persimilis Dper\GL27337 Drosophila willistoni Dwil\GK14503 Drosophila virilis Dvir\GJ14311 Drosophila mojavensis Dmoj\GI21951 Drosophila grimshawi Dgri\GH22032
Stocks & Reagents
Stocks Listed in FlyBase ( 2 )
Bloomington	27061 y1 v1; P{TRiP.JF02404}attP2
VDRC	v101354 P{KK108567}VIE-260B
Genomic Clones ( 2 )
	BACR06L13 BACR34E13 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 3 )
	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	RE13967
Other clones	DPiM_RE13967
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	EC25665
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0004862 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42537
Antibody Information
	polyclonal (Lee and Frasch, 2000)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments	The suggestion that bap and prd9 are the same is incorrect (Frasch, pers. comm. to FlyBase 24th March 1995) (Kim and Nirenberg, 1989)
Other Comments
	bap and bin are required for activation of βTub60D in the visceral mesoderm. (Zaffran and Frasch, 2002) vimar is one of the bap target genes that are required for normal development and differentiation of the midgut visceral mesoderm. (Lo and Frasch, 1998) hh is required for the normal activation of bap and srp in anterior portions of each parasegment, whereas wg is required to suppress bap and srp expression in posterior portions. hh and wg play opposing roles in mesoderm segmentation. (Azpiazu et al., 1996) hh and wg activities in the gut epithelial cells are required for the expression of the homeobox gene bap in the ensheathing visceral mesoderm. (Hoch and Pankratz, 1996) The bap gene product is required for the specification of the visceral mesoderm. (Azpiazu and Frasch, 1993) Homeobox gene expressed transiently during embryonic development in some mesodermal cells (foregut and hindgut visceral muscle cells). bap poly(A)+ RNA was not detected in 0-3-hour embryos, but was found in low abundance in RNA from 3-6-hour embryos. The abundance was maximum in RNA from 6-12-hour embryos and then declined during further embryonic development.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_169958 RefSeq (Proteins) • NP_732637 DDBJ / EMBL / GenBank • AAA28618 AAC37165 AAF55891 AAN71316 AAQ73793 AAQ73794 AAQ73795 AAQ73796 AAQ73797 AAQ73798 AAQ73799 AAQ73800 AAQ73801 AAQ73802 AAQ73803 AAQ73804 AAQ73805 AAQ73806 AAQ73807 AAQ73808 AAQ73809 AAQ73810 AAQ73811 AAQ73812 AAQ73813 AAQ73814 AAQ73815 AAQ73816 AAQ73817 AAQ73818 AAQ73819 AAQ73820 AY369088 AY369089 AY369090 AY369091 AY369092 AY369093 AY369094 AY369095 AY369096 AY369097 AY369098 AY369099 AY369100 AY369101 AY369102 AY369103 AY369104 AY369105 AY369106 AY369107 AY369108 AY369109 AY369110 AY369111 AY369112 AY369113 AY369114 AY369115 BI172041 BT001561 L17133 M27291 Entrez Gene - A searchable database of RefSeq genes. • 42537 UniProtKB/Swiss-Prot • P22809 UniProtKB/TrEMBL • Q53YH4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeodomain (IPR001356) Homeodomain-like (IPR009057) Homeobox, conserved site (IPR017970) Homeodomain, metazoa (IPR020479) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE13967
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0004862 DroID - A comprehensive database of gene and protein interactions. • FBgn0004862 DRSC - Results from RNAi screens. • FBgn0004862 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004862 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7902-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004862 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42537 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /gene/bagpipe.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42537 modMine - Data generated by the modENCODE project. • FBgn0004862 REDfly - A database of transcriptional regulatory elements. • FBgn0004862 SignaLink - A protein-protein and protein-miRNA interaction database with multi-layered structure and multiple confidence scores. • P22809
Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	bap (Williams et al., 2010, Jakobsen et al., 2007, Steiner et al., 2012, Zaffran and Frasch, 2005, Nègre et al., 2011, Biehs et al., 2010, Nekrasov et al., 2007, Sandmann et al., 2006, McDermott and Kliman, 2008, Liu et al., 2009, Popichenko et al., 2007, Bantignies et al., 2011, Copley, 2005, Wolfstetter et al., 2009, Zeitlinger et al., 2007, Zaffran and Frasch, 2002, Yan et al., 2010, Zhai et al., 2010, Reim et al., 2012) Bap (Goldstein et al., 2005, Zinzen et al., 2009, Hazelett et al., 2009) bgp (Xu et al., 1996, ) CG7902 (Perkins et al., 2009.3.31, Keleman et al., 2009.8.5, Hazelett et al., 2009) dNK-3 (Nakagoshi et al., 1998) NK-3 (Kim et al., 1998, Walldorf and Gehring, 1992, Webber et al., 1990) NK3 (Lints et al., 1993, Fyrberg et al., 1994, Bodmer, 1993, ) nk-3 (Bodmer et al., 1990)
Name Synonym	bagpipe (Kim, 1993, Morrell et al., 2006, Williams et al., 2010, Jakobsen et al., 2007, Nekrasov et al., 2007, Wolfstetter et al., 2009, Yan et al., 2010, Hazelett et al., 2009, Zhai et al., 2010, Reim et al., 2012) Bagpipe (Cho et al., 2005, Goldstein et al., 2005, Wilczyński and Furlong, 2010, Nègre et al., 2011, Popichenko et al., 2007, Rivas et al., 2008, Zinzen et al., 2009)
Secondary FlyBase IDs
	FBgn0002943
References ( 152 )
Generate a list of	All references relating to this gene ( 152 )
List References by type	Research paper  ( 102 ) Supplementary material  ( 4 ) Review  ( 21 ) Personal communication to FlyBase  ( 7 ) Abstract  ( 10 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Protein sequence record  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 ) Book  ( 1 )
Recent research papers ( 7 )
	Schaub and Frasch, 2013, Dev. Biol. 376(2): 245--259 Org-1 is required for the diversification of circular visceral muscle founder cells and normal midgut morphogenesis. [FBrf0221030] Busser et al., 2012, Development 139(6): 1164--1174 Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. [FBrf0217483] Reim et al., 2012, Dev. Biol. 368(1): 28--43 The FGF8-related signals Pyramus and Thisbe promote pathfinding, substrate adhesion, and survival of migrating longitudinal gut muscle founder cells. [FBrf0218673] Steiner et al., 2012, Genome Res. 22(4): 766--777 Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. [FBrf0217906] Stojnic et al., 2012, PLoS Comput. Biol. 8(11): e1002725 A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles. [FBrf0219905] Bantignies et al., 2011, Cell 144(2): 214--226 Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila. [FBrf0212775] Nègre et al., 2011, Nature 471(7339): 527--531 A cis-regulatory map of the Drosophila genome. [FBrf0213303] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...