• Home
• Tools
  • Tools Overview
  • Query Tools

    
    • QuickSearch
    • QueryBuilder
    • TermLink
    • CytoSearch
    • RNA-Seq Search
    • Interactions Browser
    • ImageBrowse
    • Find A Person
    • Google™ FlyBase
  • Genomic/Map Tools

    
    • BLAST
    • GBrowse
    • GBrowse 2 Beta
    • CytoSearch
    • Feature Mapper
    • Aberrations Maps
    • Chromosome Maps
    • Coordinates Converter
  • Retrieve/Convert

    
    • Batch Download
    • Coordinates Converter
    • ID Converter
  • Data Submission

    
    • Fast-Track Your Paper
    • Submit Personal Comm
    • Add A New Person
    • Update Person Info
  • People

    
    • Find A Person
    • Add A New Person
    • Update Person Info
• Files
  • Files Overview
  • Current release
  • Archived releases
  • Map Conversion
  • FTP site:
  • Releases (FTP)
  • Genomes (FTP)
• Species
  • Phylogeny
  • Sequenced Species
  • Synteny Table
  • Color Illustrations
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All Resources
  • Model Organisms
  • Stock Collections
  • Vectors & Constructs
  • Other links:
  • BDGP
  • DGRC
  • DIS by issue
  • FlyExpress
  • Interactive Fly
  • modENCODE
  • Textpresso for Fly
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • FlyBase Guides
  • Video Tutorials
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Contact FlyBase
• Archives
  • Prior Release
  • Other Archives
  • Coordinate Converter

Gene Dmel\byn

General Information
Symbol	Dmel\byn	Species	D. melanogaster
Name	brachyenteron	Annotation symbol	CG7260
Feature type	protein_coding_gene	FlyBase ID	FBgn0011723
Gene Model Status	Current	Stock availability	3 publicly available
Also Known As	Trg
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	68E3-68E3	Sequence location	3L:11,920,793..11,929,019 [+]
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 brachyenteron is referred to in FlyBase by the symbol Dmel\byn (CG7260, FBgn0011723). 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 transcription factor activity; protein homodimerization activity. There is experimental evidence that it is involved in the biological process: hindgut morphogenesis; Malpighian tubule morphogenesis; positive regulation of transcription from RNA polymerase II promoter; midgut development. 14 alleles are reported. The phenotypes of these alleles are annotated with: organ system; multicellular structure; non-connected developing system; anatomical structure; portion of tissue; extended germ band embryo; organ system subdivision; ISN innervated muscle of A1-7; ectoderm derivative; late extended germ band embryo. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: Transcription factor, Brachyury; Transcription factor, T-box; Transcription factor, T-box, conserved site; p53-like transcription factor, DNA-binding. 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 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult hindgut. Expression at moderate levels in the following post-embryonic organs or tissues: larval hindgut. Comments on Affy2 ProbeSet: ProbeSet 1639885_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of byn. Gene sequence location is 3L:11920793..11929019.
User Contributed Data
	Beta version, feedback welcome
External Summaries
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
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 68E3-68E3   Limits computationally determined from genome sequence between P{PZ}CycA02461&P{PZ}CycA03946 and P{PZ}rols08232&P{lacW}l(3)j2D3j2D3
Experimentally Determined Cytological Location
Cytogenetic map Notes References 68D-68E   (determined by in situ hybridisation)   (Murakami et al., 1995) 68D-68E   (determined by in situ hybridisation)   (Kispert et al., 1994)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\byn for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Alternative translation stop created by use of multiphasic reading frames within coding region. Gene model reviewed during 5.45
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) byn-RB FBtr0332070  NM_079307   2618   697 byn-RC FBtr0332071  NM_001274801   2650   599
Additional Transcript Data & Comments
Reported size (kB)	2.6 (longest cDNA) (Kispert et al., 1994)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein byn-PB   FBpp0304380   72.1   697   7.17     NP_524031   AAF49989 byn-PC   FBpp0304381   62.2   599   8.31     NP_001261730   AGB94423
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Transcription factor, T-box (IPR001699) Transcription factor, Brachyury (IPR002070) p53-like transcription factor, DNA-binding (IPR008967) Transcription factor, T-box, conserved site (IPR018186)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014296 AAF49989   AE014296 AGB94423   EC054301   EC055828   EC060554   S74163 AAB32396
UniProtKB/Swiss-Prot	P55965
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic/larval hindgut   (Kispert et al., 1994) anal pad   (Kispert et al., 1994) embryonic stage 4 -- 5   embryo | 0-10% egg length   (Goldstein et al., 1999) Comment:NOT posterior pole embryonic stage 4 -- 6   hindgut anlage in statu nascendi   (Fisher et al., 2012) embryonic stage 5   organism | 0-10% egg length   (Wu and Lengyel, 1998) organism | posterior   (Wu and Lengyel, 1998) embryonic stage 5 -- 10   proctodeum   (Kispert et al., 1994) embryonic stage 7 -- 8   hindgut anlage   (Fisher et al., 2012) embryonic cycle 14   organism | 0-20% egg length   (Kispert et al., 1994) embryonic stage 9 -- 10   inclusive hindgut primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   hindgut proper primordium   (Fisher et al., 2012) embryonic stage 13   small intestine primordium   (Iwaki et al., 2001) large intestine primordium   (Iwaki et al., 2001) embryonic stage 13 -- 16   embryonic hindgut   (Fisher et al., 2012)
Additional Descriptive Data
	Transcription of byn commences at the beginning of embryonic cycle 14 in the posterior terminal region from 0-20% egg length. During cellularization, transcripts recede from the pole and become confined to a ring of cells of which the ventral cells form the posterior part of the ventral furrow, while the dorsal and lateral cells form the primordia of the proctodeum and anal pads. The dorsal and lateral cells are internalized by the amnioproctodeal invagination during gastrulation. The proctodeum continues to express byn during germ band extension. Expression is maintained in the hindgut and anal pads until the end of embryogenesis. (Kispert et al., 1994)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage   anal pad   (Kispert et al., 1994) embryonic/larval hindgut   (Kispert et al., 1994) embryonic stage 5 -- 10   proctodeum   (Kispert et al., 1994) longitudinal visceral muscle primordium | precursor   (Kusch and Reuter, 1999) visceral mesoderm | restricted   (Kusch and Reuter, 1999) embryonic stage 11 -- 13   longitudinal visceral muscle primordium   (Kusch and Reuter, 1999) embryonic stage 15   embryonic hindgut   (Kusch et al., 2002)
Additional Descriptive Data
	byn protein is first detected in the blastoderm in a ring of cells mostly comprising the proctodeal primordium and in the primordia of the anal pads and the hindgut. During germ band extension, the protein is confined to the proctodeum. In the fully retracted germ band, it is found in the hindgut and anal pads. (Kispert et al., 1994)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (Kispert et al., 1994)
Expression Deduced from Reporters
Reporter: P{GawB}bynGal4 Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic Malpighian tubule | restricted   (Denholm et al., 2003) embryonic stage 7 -- 17   embryonic hindgut   (Johansen et al., 2003, Iwaki and Lengyel, 2002) Reporter: P{PZ}bynapro Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic hindgut   • nucleus (Johansen et al., 2003) embryonic stage 11 -- 17   embryonic hindgut   (Iwaki et al., 2001) larval stage   wing disc | restricted   (Copf et al., 2003) adult stage   hindgut   (Moreno and Morata, 1999)
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 hindgut. Expression at moderate levels in the following post-embryonic organs or tissues: larval hindgut. [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    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut  (548.3) Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut  548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    4.2 Larval Midgut    6 Larval Hindgut    351 Larval Malpighian Tubules    9.8 Larval Fat Body    21 Larval Salivary Gland    6.4 Larval Trachea    3.7 Larval Carcass    13.725 Adult Head    4.3 Adult Eye    2.075 Adult Brain    4.5 Adult Thoracic-Abdominal Ganglion    4.1 Adult Crop    6.3 Adult Midgut    7.9 Adult Hindgut    548.3 Adult Malpighian Tubules    11.4 Adult Fat Body    7 Adult Salivary Gland    7 Adult Heart    3.1 Adult VirginFemale Spermatheca    11.1 Adult InseminatedFemale Spermatheca    7.5 Adult Ovary    3.5 Adult Testis    6.2 Adult Male Accessory Gland    14.2 Adult Carcass    8.3 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    4.3   NA  Eye    2.075   NA  Brain    4.5   4.2  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    4.1   NA  Crop    6.3   6  Midgut    7.9   351  Hindgut    548.3   9.8  Malpighian Tubules    no informative data   no informative data  Fat Body    7   6.4  Salivary Gland    7   NA  Heart    3.1   3.7  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    7.5   NA  Ovary    3.5   NA  Testis    6.2   NA  Male Accessory Gland    no informative data   no informative data  Carcass    8.3 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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    2 central nervous system, larvae L3    0 central nervous system, pupae P8    0 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    0 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    2 digestive system, 1-day adult    4 digestive system, 4-day adult    5 digestive system, 20-day adult    4 fat body, larvae L3 wandering    0 fat body, white prepupae    0 fat body, pupae P8    0 carcass, larvae L3 wandering    1 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 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 00-06 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    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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  26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    1 embryo 02-04hr  26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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    26 embryo 04-06hr    16 embryo 06-08hr    11 embryo 08-10hr    9 embryo 10-12hr    7 embryo 12-14hr    5 embryo 14-16hr    6 embryo 16-18hr    6 embryo 18-20hr    6 embryo 20-22hr    7 embryo 22-24hr    6 larva L1    9 larva L2    4 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    3 larva L3 puffstage 7-9    3 white prepupae new    2 white prepupae 12hr    0 white prepupae 24hr    2 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    2 adult male 01day    2 adult male 05day    4 adult male 30day    5 adult female 01day    2 adult female 05day    1 adult female 30day    2 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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    0 cold shock, 4-day adult    1 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    0 Cadmium 50 mM 48 hrs, 4-day adult    1 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    2 Copper 15 mM 48 hrs, 4-day adult    0 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    1 Caffeine 1.5 mg/ml 4 hrs, larvae L3    1 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    0 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    1 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_09 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • PCSP6002 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0011723 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7260-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal (with byn1) byn5 lethal (with byn3) byn4 byn5 byn6 lethal (with byn4) byn3 byn5 byn6 lethal (with byn5) byn1 byn3 byn4 byn6 lethal (with byn6) byn3 byn4 byn5 lethal (with Df(3L)vin4) byn1 lethal | partially (with byn1) byn2 byn3 byn4 byn6 lethal | partially (with byn2) byn1 byn3 byn4 byn5 byn6 lethal | partially (with byn3) byn1 byn2 lethal | partially (with byn4) byn1 byn2 lethal | partially (with byn5) byn2 lethal | partially (with byn6) byn1 byn2 lethal | recessive byn2 byn5 bynapro viable, with Scer\GAL4pnr-MD237 bynGD1393 Sterility Allele female sterile (with byn1) byn2 byn3 byn4 byn6 female sterile (with byn2) byn1 byn3 byn4 byn5 byn6 female sterile (with byn3) byn1 byn2 female sterile (with byn4) byn1 byn2 female sterile (with byn5) byn2 female sterile (with byn6) byn1 byn2 Other Phenotypes Allele body color defective, with Scer\GAL4pnr-MD237 bynGD1393 short lived (with byn1) byn2 byn3 byn4 byn6 short lived (with byn2) byn1 byn3 byn4 byn5 byn6 short lived (with byn3) byn1 byn2 short lived (with byn4) byn1 byn2 short lived (with byn5) byn2 short lived (with byn6) byn1 byn2 Phenotype manifest in Allele A1-7 dorsal acute muscle 1 byn5 adult Malpighian tubule Type II cell byn5 circular visceral muscle fiber byn5 egg chamber (with byn1) byn2 byn3 byn4 byn6 egg chamber (with byn2) byn1 byn3 byn4 byn5 byn6 egg chamber (with byn3) byn1 byn2 egg chamber (with byn4) byn1 byn2 egg chamber (with byn5) byn2 egg chamber (with byn6) byn1 byn2 embryonic/larval dorsal vessel byn5 embryonic/larval hindgut | embryonic stage byn5 embryonic anal pad byn1 byn2 byn3 byn4 byn5 byn6 germline cell byn5 head mesoderm | ectopic, with Scer\GAL4twi.PGa bynScer\UAS.cKa hindgut proper primordium byn1 byn2 byn3 byn4 byn5 byn6 longitudinal visceral muscle fiber byn5 longitudinal visceral muscle primordium byn4 byn5 Malpighian tubule byn3 byn5 mesoderm, with Scer\GAL4twi.PGa bynScer\UAS.cKa mesothoracic tergum, with Scer\GAL4pnr-MD237 bynGD1393 midgut constriction byn5 midgut constriction 1 byn5 midgut constriction 2 byn5 midgut constriction 3 byn5 pericardial cell byn5 proctodeum bynapro
Classical Alleles ( 9 )
For All Classical Alleles Show
Allele of byn Class Mutagen Stocks Known lesion byn5 amorphic allele - genetic evidence ethyl methanesulfonate 1 -- bynapro amorphic allele - genetic evidence P-element activity 0 -- byn1 ethyl methanesulfonate 0 -- byn2 ethyl methanesulfonate 0 -- byn3 ethyl methanesulfonate 0 -- byn4 ethyl methanesulfonate 0 -- byn6 ethyl methanesulfonate 0 -- bynGal4 gene conversion P-element activity 0 Yes bynunspecified 0 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of byn Class Mutagen Stocks Known lesion bynGD1393 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes bynKK108984 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes byn+t20 in vitro construct - genomic fragment 0 Yes bynAct5C.PK in vitro construct - regulatory fusion 0 Yes bynScer\UAS.cKa in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)Exel6115 (Ryder, 2004.4.26) Df(3L)vin3 (Kispert et al., 1994, Murakami et al., 1995) Df(3L)vin4 (Broihier et al., 1998, Kispert et al., 1994) Df(3L)vin5 (Kispert et al., 1994) Df(3L)vin6 (Broihier et al., 1998, Kispert et al., 1994) Df(3L)vin7 (Kispert et al., 1994)
Not disrupted in	Df(3L)vin2 (Kispert et al., 1994, Murakami et al., 1995) Df(3L)vin66 (Kispert et al., 1994)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD1393} NA P{KK108984} NA P{UAS-byn.K} NA GAL4 construct P{byn-GAL4.n2} No characterization construct P{Trg20} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{PZ}bynapro No insertion of enhancer trap binary system P{GAL4}bynGal4 No P{GawB}bynGal4 No
Gene Ontology: Function, Process & Cellular Component ( 14 unique terms )
Terms Based on Experimental Evidence ( 7 terms )
Molecular Function
CV term Evidence References
protein homodimerization activity inferred from physical interaction with byn (Kusch et al., 2002) sequence-specific DNA binding RNA polymerase II transcription factor activity inferred from direct assay (Kusch et al., 2002)
Biological Process
CV term Evidence References
hindgut morphogenesis inferred from expression pattern AND inferred from mutant phenotype (Kispert et al., 1994) Malpighian tubule morphogenesis inferred from mutant phenotype (Singer et al., 1996) midgut development inferred from mutant phenotype (Singer et al., 1996) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Kusch et al., 2002)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Kispert et al., 1994)
Terms Based on Predictions or Assertions ( 9 terms )
Molecular Function
CV term Evidence References
DNA binding inferred from sequence or structural similarity with mouse T (Kispert et al., 1994) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:P20293 (FlyBase, 1992-)
Biological Process
CV term Evidence References
cell fate determination traceable author statement (Murakami et al., 1999) embryonic development via the syncytial blastoderm non-traceable author statement (Reuter et al., 1994) hindgut morphogenesis non-traceable author statement (Swiss-Prot Project Members, 1997.2.1) traceable author statement (Murakami et al., 1999) mesoderm migration involved in gastrulation traceable author statement (Howard, 1998) pole cell migration traceable author statement (Howard, 1998) regulation of transcription, DNA-dependent inferred from sequence or structural similarity with UniProtKB:P20293 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:P20293 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1997.2.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions byn allele Gene References byn5 fkh (Kusch and Reuter, 1999) tor (Li and Li, 2003) bynScer\UAS.cKa fkh (Kusch and Reuter, 1999)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 64710 DroID - A comprehensive database of gene and protein interactions. • FBgn0011723 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39349
Orthologs
OrthoDB Orthologs (239) - 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 EOG6QVCX8, EOG68GWNK, EOG6WM5FR, EOG62NJM6 Dipteran inclusive ortholog search EOG6W0XN0 Insect inclusive ortholog search EOG60CGBR, EOG602VMZ Arthropod inclusive ortholog search EOG605QFW Metazoa inclusive ortholog search EOG6677CK
Orthologs in Drosophila Species (EOG6QVCX8, EOG68GWNK, EOG6WM5FR, EOG62NJM6)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Ccp84Ab     Drosophila melanogaster fruit fly  Dmel\CG13059     Drosophila melanogaster fruit fly  Dmel\CG42784     Drosophila melanogaster fruit fly  Dmel\CG5181     Drosophila melanogaster fruit fly  Dmel\sba     Drosophila melanogaster fruit fly  Dmel\Pif2     Drosophila melanogaster fruit fly  Dmel\Strn-Mlck     Drosophila melanogaster fruit fly  Dmel\byn     Drosophila melanogaster fruit fly  Dmel\CG43332     Drosophila melanogaster fruit fly  Dmel\CHES-1-like     Drosophila melanogaster fruit fly  Dmel\srp     Drosophila simulans   Dsim\GD25582   Y Drosophila sechellia   Dsec\GM20106   Y Drosophila erecta   Dere\GG22317   Y Drosophila yakuba   Dyak\GE14114   Y Drosophila ananassae   Dana\GF13334   Y Drosophila pseudoobscura pseudoobscura   Dpse\GA30265   Y Drosophila persimilis   Dper\GL20658   Y Drosophila persimilis   Dper\GL20657   Y Drosophila willistoni   Dwil\GK22103   Y Drosophila virilis   Dvir\GJ20095   Y Drosophila virilis   Dvir\GJ16020   Y Drosophila virilis   Dvir\GJ18382   Y Drosophila mojavensis   Dmoj\GI20421   Y Drosophila grimshawi   Dgri\GH19834   Y
Orthologs in non-Drosophila Dipterans (EOG6W0XN0)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL008057 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ012863 Y
Orthologs in non-Dipteran Insects (EOG60CGBR, EOG602VMZ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB47946 Y Apis mellifera Western honey bee  Amel\GB47948 Y Apis mellifera Western honey bee  Amel\GB47947 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG016102 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG016115 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG016114 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG016113 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG015617 Y Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH27154 Y Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH15218 Y Atta cephalotes Leafcutter ant  Acep\ACEP15048 Y Atta cephalotes Leafcutter ant  Acep\ACEP26046 Y Camponotus floridanus Florida carpenter ant  Cflo\CFLO14725 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL25964 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL24167 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL28060 Y Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL20757 Y Linepithema humile Argentine ant  Lhum\LH14217 Y Linepithema humile Argentine ant  Lhum\LH25501 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB26557 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB15729 Y Solenopsis invicta Red fire ant  Sinv\SINV12027 Y Solenopsis invicta Red fire ant  Sinv\SINV12023 Y Solenopsis invicta Red fire ant  Sinv\SINV12020 Y Acyrthosiphon pisum Pea aphid  Apim\ACYPI069103 Y Acyrthosiphon pisum Pea aphid  Apim\ACYPI007076 Y Bombyx mori Silkmoth  Bmor\BGIBMGA002035 Y Bombyx mori Silkmoth  Bmor\BGIBMGA002036 Y Pediculus humanus Human body louse  Phum\PHUM541150 Y Tribolium castaneum Red flour beetle  Tcas\TC002962 Y
Orthologs in non-Insect Arthropods (EOG605QFW)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\Thtpa Y Daphnia pulex Water flea  Dpux\JGI_V11_53743 Y Daphnia pulex Water flea  Dpux\JGI_V11_305289 Y
Orthologs in non-Arthropod Metazoa (EOG6677CK)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\ssq-4 Y Caenorhabditis elegans Nematode  Cele\him-4 Y Caenorhabditis elegans Nematode  Cele\Y48C3A.12 Y Caenorhabditis elegans Nematode  Cele\ZC178.2 Y Caenorhabditis elegans Nematode  Cele\F11E6.3 Y Caenorhabditis elegans Nematode  Cele\ZK617.1 Y Caenorhabditis elegans Nematode  Cele\F41E6.11 Y Caenorhabditis elegans Nematode  Cele\ttn-1 Y Caenorhabditis elegans Nematode  Cele\npp-4 Y Caenorhabditis elegans Nematode  Cele\cut-2 Y Caenorhabditis elegans Nematode  Cele\ssq-3 Y Caenorhabditis elegans Nematode  Cele\ssq-2 Y Caenorhabditis elegans Nematode  Cele\W07G1.5 Y Caenorhabditis elegans Nematode  Cele\col-135 Y Caenorhabditis elegans Nematode  Cele\ssq-1 Y Caenorhabditis elegans Nematode  Cele\dur-1 Y Caenorhabditis elegans Nematode  Cele\C10G11.7 Y Caenorhabditis elegans Nematode  Cele\B0205.10 Y Caenorhabditis elegans Nematode  Cele\C02B10.5 Y Caenorhabditis elegans Nematode  Cele\ZC373.4 Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_023876gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_017487gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_000057gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_000442gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_008085gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_009818gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_010006gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_015813gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_013917gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_011693gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_008653gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_003460gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_023875gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_005613gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_001282gn Y Danio rerio Zebrafish  Drer\ENSDARG00000044673 Y Danio rerio Zebrafish  Drer\im:7148400 Y Danio rerio Zebrafish  Drer\ENSDARG00000034801 Y Danio rerio Zebrafish  Drer\ttnb Y Danio rerio Zebrafish  Drer\mylk4 Y Danio rerio Zebrafish  Drer\hmcn2 Y Danio rerio Zebrafish  Drer\mylk2 Y Danio rerio Zebrafish  Drer\hmcn1 Y Danio rerio Zebrafish  Drer\dscama Y Danio rerio Zebrafish  Drer\ENSDARG00000091260 Y Danio rerio Zebrafish  Drer\BX548021.2 Y Danio rerio Zebrafish  Drer\dscamb Y Danio rerio Zebrafish  Drer\ENSDARG00000004753 Y Danio rerio Zebrafish  Drer\dscaml1 Y Danio rerio Zebrafish  Drer\ttna Y Danio rerio Zebrafish  Drer\mylk3 Y Danio rerio Zebrafish  Drer\ENSDARG00000029048 Y Danio rerio Zebrafish  Drer\ENSDARG00000039311 Y Xenopus tropicalis Western clawed frog  Xtro\tn3 Y Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000015021 Y Xenopus tropicalis Western clawed frog  Xtro\mylk3 Y Xenopus tropicalis Western clawed frog  Xtro\mylk4 Y Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000033779 Y Xenopus tropicalis Western clawed frog  Xtro\dscaml1 Y Xenopus tropicalis Western clawed frog  Xtro\mylk Y Xenopus tropicalis Western clawed frog  Xtro\dscam Y Xenopus tropicalis Western clawed frog  Xtro\hmcn1 Y Xenopus tropicalis Western clawed frog  Xtro\hmcn2 Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000024448 Y Gallus gallus Domestic chicken  Ggal\LOC427896 Y Gallus gallus Domestic chicken  Ggal\NOVA1 Y Gallus gallus Domestic chicken  Ggal\HMCN1 Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000011775 Y Gallus gallus Domestic chicken  Ggal\DSCAM Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000024060 Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000011759 Y Gallus gallus Domestic chicken  Ggal\770789 Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000007204 Y Gallus gallus Domestic chicken  Ggal\MYLK2 Y Gallus gallus Domestic chicken  Ggal\MYLK3 Y Gallus gallus Domestic chicken  Ggal\MYLK Y Gallus gallus Domestic chicken  Ggal\DSCAML1 Y Gallus gallus Domestic chicken  Ggal\MYLK4 Y Gallus gallus Domestic chicken  Ggal\LOC428278 Y Gallus gallus Domestic chicken  Ggal\ENSGALG00000011771 Y Mus musculus House mouse  Mmus\Lce1j Y Mus musculus House mouse  Mmus\Krtap6-1 Y Mus musculus House mouse  Mmus\Krtap6-1 Y Mus musculus House mouse  Mmus\Krtap16-7 Y Mus musculus House mouse  Mmus\Syn2 Y Mus musculus House mouse  Mmus\Lce1l Y Mus musculus House mouse  Mmus\Gm14185 Y Mus musculus House mouse  Mmus\Gm14193 Y Mus musculus House mouse  Mmus\Gm14193 Y Mus musculus House mouse  Mmus\Gm10217 Y Mus musculus House mouse  Mmus\Dscaml1 Y Mus musculus House mouse  Mmus\Gm10229 Y Mus musculus House mouse  Mmus\Dscam Y Mus musculus House mouse  Mmus\Hist1h1d Y Mus musculus House mouse  Mmus\Krtap16-8 Y Mus musculus House mouse  Mmus\Mylk Y Mus musculus House mouse  Mmus\Lce1c Y Mus musculus House mouse  Mmus\ENSMUSG00000051747 Y Mus musculus House mouse  Mmus\Barhl2 Y Mus musculus House mouse  Mmus\Gm14177 Y Mus musculus House mouse  Mmus\Hmcn1 Y Mus musculus House mouse  Mmus\Marcks Y Mus musculus House mouse  Mmus\Gm14190 Y Mus musculus House mouse  Mmus\Hist1h1c Y Mus musculus House mouse  Mmus\Foxd3 Y Mus musculus House mouse  Mmus\Gm10563 Y Mus musculus House mouse  Mmus\Gm17606 Y Mus musculus House mouse  Mmus\Gm14191 Y Mus musculus House mouse  Mmus\Tmem158 Y Mus musculus House mouse  Mmus\Gm14181 Y Mus musculus House mouse  Mmus\Krtap16.10L Y Mus musculus House mouse  Mmus\Mylk4 Y Mus musculus House mouse  Mmus\Gm6871 Y Mus musculus House mouse  Mmus\Gm11595 Y Mus musculus House mouse  Mmus\Mylk2 Y Mus musculus House mouse  Mmus\Krtap6-1 Y Mus musculus House mouse  Mmus\Lce1e Y Mus musculus House mouse  Mmus\Gm11564 Y Mus musculus House mouse  Mmus\Gm10974 Y Mus musculus House mouse  Mmus\Krtap4-9 Y Mus musculus House mouse  Mmus\Hmcn2 Y Mus musculus House mouse  Mmus\Gm14196 Y Mus musculus House mouse  Mmus\Phgr1 Y Mus musculus House mouse  Mmus\Mylk3 Y Mus musculus House mouse  Mmus\Gm14192 Y Mus musculus House mouse  Mmus\Lce1f Y Mus musculus House mouse  Mmus\Gm14193 Y Mus musculus House mouse  Mmus\Krtap4-8 Y Mus musculus House mouse  Mmus\Gm11034 Y Mus musculus House mouse  Mmus\Gm14178 Y Mus musculus House mouse  Mmus\Gm8223 Y Mus musculus House mouse  Mmus\Sox3 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000030872 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000043220 Y Rattus norvegicus Norway rat  Rnor\Dscaml1 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000039623 Y Rattus norvegicus Norway rat  Rnor\Hmcn1 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000022637 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000030293 Y Rattus norvegicus Norway rat  Rnor\Mylk3 Y Rattus norvegicus Norway rat  Rnor\Mylk2 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000038781 Y Rattus norvegicus Norway rat  Rnor\RGD1565323 Y Rattus norvegicus Norway rat  Rnor\Dscam Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000030744 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000033548 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000038410 Y Rattus norvegicus Norway rat  Rnor\Mylk Y Rattus norvegicus Norway rat  Rnor\LOC684744 Y Rattus norvegicus Norway rat  Rnor\ENSRNOG00000008820 Y Homo sapiens Human  Hsap\KRTAP6-1 Y Homo sapiens Human  Hsap\ENSG00000249992 Y Homo sapiens Human  Hsap\ENSG00000257153 Y Homo sapiens Human  Hsap\ELN Y Homo sapiens Human  Hsap\PHGR1 Y Homo sapiens Human  Hsap\KRTAP5-5 Y Homo sapiens Human  Hsap\DSCAM Y Homo sapiens Human  Hsap\HMCN1 Y Homo sapiens Human  Hsap\MYLK3 Y Homo sapiens Human  Hsap\ENSG00000065534 Y Homo sapiens Human  Hsap\KRTAP5-8 Y Homo sapiens Human  Hsap\ENSG00000262483 Y Homo sapiens Human  Hsap\NKX1-1 Y Homo sapiens Human  Hsap\ENSG00000262498 Y Homo sapiens Human  Hsap\ENSG00000258264 Y Homo sapiens Human  Hsap\HMCN2 Y Homo sapiens Human  Hsap\KRTAP5-1 Y Homo sapiens Human  Hsap\ENSG00000257917 Y Homo sapiens Human  Hsap\ENSG00000263306 Y Homo sapiens Human  Hsap\CT47B1 Y Homo sapiens Human  Hsap\DSCAML1 Y Homo sapiens Human  Hsap\FOXD3 Y Homo sapiens Human  Hsap\KRTAP5-4 Y Homo sapiens Human  Hsap\BAG3 Y Homo sapiens Human  Hsap\ENSG00000262626 Y Homo sapiens Human  Hsap\MARCKS Y Homo sapiens Human  Hsap\MYLK2 Y Homo sapiens Human  Hsap\TTN Y Homo sapiens Human  Hsap\MYLK4 Y
Human Orthologs (29)
Gene OMIM HGNC Hsap\KRTAP6-1     Hsap\ENSG00000249992     Hsap\ENSG00000257153     Hsap\ELN     Hsap\PHGR1     Hsap\KRTAP5-5     Hsap\DSCAM     Hsap\HMCN1     Hsap\MYLK3     Hsap\ENSG00000065534     Hsap\KRTAP5-8     Hsap\ENSG00000262483     Hsap\NKX1-1     Hsap\ENSG00000262498     Hsap\ENSG00000258264     Hsap\HMCN2     Hsap\KRTAP5-1     Hsap\ENSG00000257917     Hsap\ENSG00000263306     Hsap\CT47B1     Hsap\DSCAML1     Hsap\FOXD3     Hsap\KRTAP5-4     Hsap\BAG3     Hsap\ENSG00000262626     Hsap\MARCKS     Hsap\MYLK2     Hsap\TTN     Hsap\MYLK4
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD14339 Drosophila sechellia Dsec\GM25308 Drosophila erecta Dere\GG15542 Drosophila yakuba Dyak\GE21864 Drosophila ananassae Dana\GF25302 Drosophila pseudoobscura pseudoobscura Dpse\GA20217 Drosophila persimilis Dper\GL25108 Drosophila willistoni Dwil\GK25266 Drosophila virilis Dvir\GJ13700 Drosophila mojavensis Dmoj\GI11508 Drosophila grimshawi Dgri\GH14805
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	26186 byn5 e*/TM6B, Tb1 ca1
VDRC	v101534 P{KK108984}VIE-260B v43909 w1118; P{GD1393}v43909
Genomic Clones ( 1 )
	BACR15K18 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
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	11982 EC054301 EC055828
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0011723 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39349
Antibody Information
Other Information
Discoverer
Etymology
	The mutant phenotype and the similarity of the encoded gene product to the vertebrate Brachyury protein caused the gene named to be changed from "Trg" to "brachyenteron" ("byn"), or "short gut". (Singer et al., 1996)
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: byn CG7260 (Zhang, 1999.11)
Source for database merge of
Additional comments
Other Comments
	byn injected into Xenopus embryos exhibits a strong endoderm-inducing activity. (Marcellini et al., 2003) byn, supported by fkh, mediates the early specification of the caudal visceral mesoderm along with zfh1. The functions of byn in the mesoderm of Drosophila are comparable to the roles of the vertebrate Brachyury genes during gastrulation. (Kusch and Reuter, 1999) Like zfh1, byn is required for the migration of the caudal visceral mesoderm, but unlike zfh1, it is not required for gonadal mesoderm development. (Broihier et al., 1998) cad acts in hindgut development through fog, fkh and wg, but does not play a role in activating tll, hkb, byn and bowl which are also required for proper hindgut development. cad, fkh, byn and wg constitute a conserved constellation of genes that plays a required role in gastrulation and gut development. (Wu and Lengyel, 1998) Phenotypic analysis demonstrates byn is required to regulate specific gene activity in the primordia of the anal pads and hindgut. In the absence of byn activity, programmed cell death occurs in the primordia resulting in reduced and abnormal anal pads and hindgut. byn is also required for the formation of midgut restrictions and elongation of the Malpighian tubules. tll is necessary and sufficient to activate byn. (Singer et al., 1996) byn plays a key role in the development of tissues derived from the proctodeum. (Murakami et al., 1995) byn is involved in the specification of the hindgut and anal pads and is a target for regulation by tll and hkb. (Kispert et al., 1994) byn is required for specification of the hindgut and anal pads. (Reuter et al., 1994) Product is detected by an antibody against the mouse T gene. (Reuter, 1994)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079307 NM_001274801 RefSeq (Proteins) • NP_524031 NP_001261730 DDBJ / EMBL / GenBank • AAB32396 AAF49989 AGB94423 S74163 Entrez Gene - A searchable database of RefSeq genes. • 39349 UniProtKB/Swiss-Prot • P55965
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Transcription factor, T-box (IPR001699) Transcription factor, Brachyury (IPR002070) p53-like transcription factor, DNA-binding (IPR008967) Transcription factor, T-box, conserved site (IPR018186) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • PCSP6002
Linkouts
	BioGRID - A database of protein and genetic interactions • 64710 DroID - A comprehensive database of gene and protein interactions. • FBgn0011723 DRSC - Results from RNAi screens. • FBgn0011723 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0011723 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7260-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0011723 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39349 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /gene/trg.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39349 modMine - Data generated by the modENCODE project. • FBgn0011723 REDfly - A database of transcriptional regulatory elements. • FBgn0011723
Synonyms & Secondary IDs ( 19 )
Reported As
Symbol Synonym	apro   Byn (Kusch et al., 2000) byn (Moran and Jimenez, 2006, Fox et al., 2010, Takashima et al., 2008, Hamaguchi et al., 2012, Ismat et al., 2010, Fox and Spradling, 2009, Uddin et al., 2011) byn/apro (Takashima and Murakami, 2001) CG7260 (Keleman et al., 2009.8.5) Dm-BYN (Prpic et al., 2003) dm-Trg (Papaioannou and Silver, 1998) D-TRA (Reuter, 1994) DTrg (Walldorf et al., 1997) D-Trg   Tra   Trg (Kispert, 1995.3.14, Porsch et al., 1998, Diaz et al., 1996, Marcellini et al., 2003) trg (Hughes, 1999)
Name Synonym	aproctous   Brachyenteron (Kusch et al., 2000, Cho et al., 2005) brachyenteron (Kusch et al., 1997, Moran and Jimenez, 2006, Wolfstetter et al., 2009, Fox and Spradling, 2009, Uddin et al., 2011) brachyury (Marcellini, 2006) T related antigen (Reuter, 1994) T-related gene
Secondary FlyBase IDs
	FBgn0014890
References ( 72 )
Generate a list of	All references relating to this gene ( 72 )
List References by type	Research paper  ( 37 ) Supplementary material  ( 4 ) Review  ( 12 ) Personal communication to FlyBase  ( 3 ) Abstract  ( 8 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Curated genome annotation  ( 3 ) Protein sequence record  ( 1 ) Website  ( 1 ) Letter  ( 1 )
Recent research papers ( 2 )
	Hamaguchi et al., 2012, Mech. Dev. 129(9-12): 236--243 Dorsoventral patterning of the Drosophila hindgut is determined by interaction of genes under the control of two independent gene regulatory systems, the dorsal and terminal systems. [FBrf0219771] Uddin et al., 2011, Int. J. Dev. Biol. 55(10-11-12): 945--952 The drumstick gene acts cell-non-autonomously and triggers specification of the small intestine in the Drosophila hindgut. [FBrf0217187] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...