• 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\Vdup1

General Information
Symbol	Dmel\Vdup1	Species	D. melanogaster
Name	Vitamin D3 up-regulated protein 1	Annotation symbol	CG7047
Feature type	protein_coding_gene	FlyBase ID	FBgn0035103
Gene Model Status	Current	Stock availability	2 publicly available
Also Known As	dvdup1, vdup1
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	61B2-61B2	Sequence location	3L:176,306..178,963 [-]
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 Vitamin D3 up-regulated protein 1 is referred to in FlyBase by the symbol Dmel\Vdup1 (CG7047, FBgn0035103). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: negative regulation of gene expression. 2 alleles are reported. No phenotypic data is available. It has 5 annotated transcripts and 5 annotated polypeptides. Protein features are: Arrestin C-terminal-like domain; Arrestin, C-terminal; Arrestin-like, N-terminal; Immunoglobulin E-set. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 06-24 hour embryonic stages, at stages throughout the pupal period. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult crop, adult salivary gland, larval trachea, larval carcass. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval central nervous system, larval/adult hindgut, larval salivary gland, adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1641167_s_at completely aligns to an exonic region common to each of the 4 FlyBase-annotated transcript isoforms of Vdup1. Gene sequence location is 3L:176306..178963.
User Contributed Data
	Beta version, feedback welcome
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
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 61B2-61B2   Limits computationally determined from genome sequence between P{PZ}trh10512 and P{EP}EP3104EP3104
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Vdup1 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 5.46 Low-frequency RNA-Seq exon junction(s) not annotated. Annotated transcripts do not represent all supported alternative splices within 5' UTR. DGC clone RE30730 appears problematic: unspliced intron
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Vdup1-RA FBtr0072536  NM_206221   1676   342 Vdup1-RB FBtr0072534  NM_138160   1392   342 Vdup1-RC FBtr0072535  NM_167798   1462   342 Vdup1-RD FBtr0301890  NM_001169832   2020   342 Vdup1-RE FBtr0334069  NM_001274255   1384   342
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Vdup1-PA   FBpp0072435   38.7   342   9.06     NP_995943   AAS64920 Vdup1-PB   FBpp0072433   38.7   342   9.06     NP_612004   AAF47338 Vdup1-PC   FBpp0072434   38.7   342   9.06     NP_728479   AAF47339 Vdup1-PD   FBpp0291104   38.7   342   9.06     NP_001163303   ACZ94575 Vdup1-PE   FBpp0306194   38.7   342   9.06     NP_001261184   AGB93879
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Arrestin-like, N-terminal (IPR011021) Arrestin C-terminal-like domain (IPR011022) Immunoglobulin E-set (IPR014756) Arrestin, C-terminal (IPR014752)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA202079   AA697756   AE014296 AAF47338   AE014296 AAF47339   AE014296 AAS64920   AE014296 ACZ94575   AE014296 AGB93879   AI293733   AI404100   AY071279 AAL48901   AY071606 AAL49228   BI166871   BI215172   BI234951   BI372624   BI482780   CO190552   CO269774   CO271639   CO271666   CO279463   CO283397   CO299561   CO299584   CO302852   CO315630   CO325863   CO325871   EC083655   EC197355   EC197632   EC199745   EC200511   EC204629   EC207016   EC210833   EC216333   EC218029   EC220459   EC222643   EC223041   EC238364   EC245576   EC254118   EC258952   EC258971   GH943387   GH943880   GH944456   GH945957   GH946153   GH947397   GH947580   GH952689   GH954237   GH954794   GH955889   GH958900   GH963816   GH965035   GH968209   GH981358   GH981989   GH982647   GH984493   GH984853
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q0E8K8 Q8SYE1 Q8SYW4
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 4 -- 6   anlage in statu nascendi   (Fisher et al., 2012) foregut anlage in statu nascendi   (Fisher et al., 2012) embryonic stage 7 -- 8   foregut anlage   (Fisher et al., 2012) embryonic stage 9 -- 10   foregut primordium   (Fisher et al., 2012) inclusive hindgut primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   clypeo-labral primordium   (Fisher et al., 2012) dorsal epidermis primordium   (Fisher et al., 2012) foregut primordium   (Fisher et al., 2012) hindgut proper primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   atrium   (Fisher et al., 2012) dorsal head epidermis   (Fisher et al., 2012) embryonic dorsal epidermis   (Fisher et al., 2012) embryonic epipharynx   (Fisher et al., 2012) embryonic esophagus   (Fisher et al., 2012) embryonic foregut   (Fisher et al., 2012) embryonic head epidermis   (Fisher et al., 2012) embryonic hindgut   (Fisher et al., 2012) embryonic hypopharynx   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) embryonic/larval salivary gland   (Fisher et al., 2012)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4   organism | ubiquitous   • nucleus & cytoplasm (Mandalaywala et al., 2008) pole cell   (Mandalaywala et al., 2008) embryonic stage 9 -- 10   ventral neurectoderm | restricted   (Mandalaywala et al., 2008) embryonic stage 10 -- 11   organism | segmentally repeated   (Mandalaywala et al., 2008) embryonic stage 12 -- 16   glial cell | subset   (Mandalaywala et al., 2008) embryonic stage 13   denticle field primordium | restricted   (Mandalaywala et al., 2008) embryonic stage 13 -- 16   embryonic/larval central nervous system | restricted   (Mandalaywala et al., 2008) embryonic stage 14 -- 16   neuron | subset   (Mandalaywala et al., 2008) embryonic stage 16   embryonic/larval peripheral nervous system | restricted   (Mandalaywala et al., 2008) third instar larval stage   embryonic/larval optic lobe | restricted   (Mandalaywala et al., 2008) larval outer optic anlage | restricted   (Mandalaywala et al., 2008) lamina neuropil | restricted   (Mandalaywala et al., 2008) embryonic/larval optic stalk | restricted   (Mandalaywala et al., 2008) medulla | restricted   (Mandalaywala et al., 2008) medulla neuropil | restricted   (Mandalaywala et al., 2008) cortex of medulla | restricted   (Mandalaywala et al., 2008) glial cell | subset   (Mandalaywala et al., 2008) subperineurial glial cell | subset   (Mandalaywala et al., 2008) marginal glial cell | subset   (Mandalaywala et al., 2008) epithelial glial cell | subset   (Mandalaywala et al., 2008) distal medulla glial cell | subset   (Mandalaywala et al., 2008) neuron | subset of cortex of medulla   (Mandalaywala et al., 2008) unfertilized egg stage   unfertilized egg | ubiquitous   (Mandalaywala et al., 2008) western blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 10   organism   • nucleus & cytoplasm (Mandalaywala et al., 2008) third instar larval stage   embryonic/larval central nervous system   • nucleus & cytoplasm (Mandalaywala et al., 2008)
Additional Descriptive Data
	Subcellular localization of Vdup1 in stage 4 embryos vacillates between the cytoplasm and nucleus. (Mandalaywala et al., 2008)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
cytoplasm inferred from direct assay (Mandalaywala et al., 2008) nucleus inferred from direct assay (Mandalaywala et al., 2008)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult crop, adult salivary gland, larval trachea, larval carcass. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval central nervous system, larval/adult hindgut, larval salivary gland, adult carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea    1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea  (1005.225) Larval Carcass  (620.825) Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop  (814.3) Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland  (599.9) Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea  1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea    1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea    1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea  (1005.225) Larval Carcass  620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop  (814.3) Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland  599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea  1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    132.35 Larval Midgut    22.2 Larval Hindgut    451.6 Larval Malpighian Tubules    6.5 Larval Fat Body    13.5 Larval Salivary Gland    272.3 Larval Trachea    1005.225 Larval Carcass    620.825 Adult Head    190.7 Adult Eye    319.325 Adult Brain    8.8 Adult Thoracic-Abdominal Ganglion    17.9 Adult Crop    814.3 Adult Midgut    28.3 Adult Hindgut    427.7 Adult Malpighian Tubules    11.2 Adult Fat Body    18.6 Adult Salivary Gland    599.9 Adult Heart    18.975 Adult VirginFemale Spermatheca    49.3 Adult InseminatedFemale Spermatheca    62.1 Adult Ovary    6.9 Adult Testis    9.8 Adult Male Accessory Gland    22 Adult Carcass    227.9 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    190.7   NA  Eye    319.325   NA  Brain    8.8   132.35  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    no informative data   NA  Crop    814.3   22.2  Midgut    28.3   451.6  Hindgut    427.7   6.5  Malpighian Tubules    no informative data   no informative data  Fat Body    no informative data   272.3  Salivary Gland    599.9   NA  Heart    18.975   1005.225  Trachea    NA   NA  VirginFemale Spermatheca    49.3   NA  InseminatedFemale Spermatheca    62.1   NA  Ovary    6.9   NA  Testis    9.8   NA  Male Accessory Gland    no informative data   620.825  Carcass    227.9 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    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8  (40) carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 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    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8  (40) carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 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    20 central nervous system, larvae L3    4 central nervous system, pupae P8    5 head, virgin 1-day female    8 head, virgin 4-day female    4 head, virgin 20-day female    6 head, mated 1-day female    4 head, mated 4-day female    4 head, mated 20-day female    5 head, mated 1-day male    9 head, mated 4-day male    6 head, mated 20-day male    8 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    1 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    2 digestive system, 4-day adult    2 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    40 carcass, larvae L3 wandering    18 carcass, 1-day adult    7 carcass, 4-day adult    6 carcass, 20-day adult    5 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 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 high expression to a trough of very low expression. Peak expression observed within 06-24 hour embryonic stages, at stages throughout the pupal period. [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    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr    121 embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP    107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr  (50) embryo 12-14hr  (44) embryo 14-16hr  (72) embryo 16-18hr  (121) embryo 18-20hr  (88) embryo 20-22hr    21 embryo 22-24hr  (27) larva L1    14 larva L2    22 larva L3 12hr old  (38) larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9  (34) white prepupae new  (32) white prepupae 12hr  (52) white prepupae 24hr  (53) pupae 2d postWPP  (50) pupae 3d postWPP  (107) pupae 4d postWPP  (67) adult male 01day  (28) adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 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    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr  (121) embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP  107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 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    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr    121 embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP    107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr    121 embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP    107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    0 embryo 02-04hr    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr  (50) embryo 12-14hr  (44) embryo 14-16hr  (72) embryo 16-18hr  (121) embryo 18-20hr  (88) embryo 20-22hr    21 embryo 22-24hr  27 larva L1    14 larva L2    22 larva L3 12hr old  (38) larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9  (34) white prepupae new  32 white prepupae 12hr  (52) white prepupae 24hr  (53) pupae 2d postWPP  (50) pupae 3d postWPP  (107) pupae 4d postWPP  (67) adult male 01day  28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 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    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr  121 embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP  107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 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    2 embryo 04-06hr    4 embryo 06-08hr    12 embryo 08-10hr    20 embryo 10-12hr    50 embryo 12-14hr    44 embryo 14-16hr    72 embryo 16-18hr    121 embryo 18-20hr    88 embryo 20-22hr    21 embryo 22-24hr    27 larva L1    14 larva L2    22 larva L3 12hr old    38 larva L3 puffstage 1-2    24 larva L3 puffstage 3-6    25 larva L3 puffstage 7-9    34 white prepupae new    32 white prepupae 12hr    52 white prepupae 24hr    53 pupae 2d postWPP    50 pupae 3d postWPP    107 pupae 4d postWPP    67 adult male 01day    28 adult male 05day    14 adult male 30day    15 adult female 01day    20 adult female 05day    4 adult female 30day    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    2 cold shock, 4-day adult    2 heat shock, 4-day adult    5 Cadmium 50 mM 6 hrs, larvae L3    11 Cadmium 50 mM 12 hrs, larvae L3    10 Cadmium 50 mM 48 hrs, 4-day adult    7 Cadmium 100 mM 48 hrs, 4-day adult    1 Copper 0.5 mM 12 hrs, larvae L3    4 Copper 15 mM 48 hrs, 4-day adult    2 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    2 Ethanol 2.5% 3 hrs, larvae L3    3 Ethanol 5% 3 hrs, larvae L3    9 Ethanol 10% 3 hrs, larvae L3    7 Caffeine 1.5 mg/ml 4 hrs, larvae L3    7 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    4 Rotenone 2 μg 12 hrs, larvae L3    7 Rotenone 8 μg 12 hrs, larvae L3    7 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_29 mE1_20_mRNA_expression_cluster_15
External Data & Images
Linkouts	BDGP expression data • RE65532 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0035103 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7047-RB FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Vdup1 Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable, with Scer\GAL4pnr-MD237 Vdup1GD4976 Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Vdup1 Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Vdup1 Class Mutagen Stocks Known lesion Vdup1GD4976 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Vdup1Scer\UAS.cMa in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)Exel6083 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{UAS-Vdup1.M} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{SUPor-P}KG05089 NA
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
Terms Based on Experimental Evidence ( 3 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
negative regulation of gene expression inferred from direct assay (Mandalaywala et al., 2008)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Mandalaywala et al., 2008) nucleus inferred from direct assay (Mandalaywala et al., 2008)
Terms Based on Predictions or Assertions ( 1 term )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
signal transduction inferred from electronic annotation with InterPro:IPR014752 (FlyBase Curators et al., 2004-)
Cellular Component ( 0 terms)
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 Vdup1 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 63587 DroID - A comprehensive database of gene and protein interactions. • FBgn0035103 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 38023
Orthologs
OrthoDB Orthologs (30) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6W3T72 Dipteran inclusive ortholog search EOG6F4SKS Insect inclusive ortholog search EOG6M0CXR Arthropod inclusive ortholog search EOG6MPG65 Metazoa inclusive ortholog search EOG6CZQ94
Orthologs in Drosophila Species (EOG6W3T72)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Vdup1     Drosophila simulans   Dsim\GD13537 Y   Drosophila sechellia   Dsec\GM14300 Y   Drosophila erecta   Dere\GG14685 Y   Drosophila yakuba   Dyak\GE21046 Y   Drosophila ananassae   Dana\GF24927 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA20057 Y   Drosophila persimilis   Dper\GL16087 Y   Drosophila willistoni   Dwil\GK12676 Y   Drosophila virilis   Dvir\GJ16089 Y   Drosophila mojavensis   Dmoj\GI12789 Y   Drosophila grimshawi   Dgri\GH15733 Y
Orthologs in non-Drosophila Dipterans (EOG6F4SKS)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL007164   Anopheles gambiae Malaria mosquito  Agam\AGAP002691   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ002892
Orthologs in non-Dipteran Insects (EOG6M0CXR)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\ArrL2   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG008167   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH17931   Atta cephalotes Leafcutter ant  Acep\ACEP12756   Camponotus floridanus Florida carpenter ant  Cflo\CFLO17723   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL13003   Linepithema humile Argentine ant  Lhum\LH20616   Pogonomyrmex barbatus Red harvester ant  Pbar\PB21800   Acyrthosiphon pisum Pea aphid  Apim\ACYPI005464   Bombyx mori Silkmoth  Bmor\BGIBMGA013509   Pediculus humanus Human body louse  Phum\PHUM142010   Tribolium castaneum Red flour beetle  Tcas\TC010863
Orthologs in non-Insect Arthropods (EOG6MPG65)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\NUP107   Ixodes scapularis Deer tick  Isca\ISCW024005
Orthologs in non-Arthropod Metazoa (EOG6CZQ94)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_027045gn
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD13537 Drosophila sechellia Dsec\GM14300 Drosophila erecta Dere\GG14685 Drosophila yakuba Dyak\GE21046 Drosophila ananassae Dana\GF24927 Drosophila pseudoobscura pseudoobscura Dpse\GA20057 Drosophila persimilis Dper\GL16087 Drosophila willistoni Dwil\GK12676 Drosophila virilis Dvir\GJ16089 Drosophila mojavensis Dmoj\GI12789 Drosophila grimshawi Dgri\GH15733
Stocks & Reagents
Stocks Listed in FlyBase ( 2 )
VDRC	v15204 w1118 P{GD4976}v15204 v15203 w1118; P{GD4976}v15203
Genomic Clones ( 2 )
	BACR11J11 BACR45O17 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 59 )
	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	RE30730 RE65532
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH23694 HL03111 LD04011 LP06936 RE07111 RE21510 RE59632
Other clones	20772 43357 47870 47898 50258 56229 61703 158662 176981 192822 214287.20 214309.24 214571.23 CK01.41C.E9 CK01.61C.H5 CK01.129B.H12 CK01.169D.F3 CK01.169D.H8 EK048531 EK095862 EK104122 EK104164 EK134358 EK163041 EK175814 EK175853 EK185032 EK262050 EP02815 EP02827 RP004019683 RP004088929 RP004108793 RP004117465 RP004140853 RP004198529 RP004207864 RP004208361 RP004218498 RP004221983 RP004224505 RP004226585 RP004232306 RP004240428 RP004245703 RP004251294 RP004458322 RP004497298 RP004510182 RP004548301
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0035103 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 38023
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Vdup1 CG7047 (Mandalaywala et al., 2008)
Source for database merge of
Additional comments
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_138160 NM_167798 NM_206221 NM_001169832 NM_001274255 RefSeq (Proteins) • NP_612004 NP_728479 NP_995943 NP_001163303 NP_001261184 DDBJ / EMBL / GenBank • AAF47338 AAF47339 AAL48901 AAL49228 AAS64920 ACZ94575 AGB93879 AY071279 AY071606 BI234951 BI482780 Entrez Gene - A searchable database of RefSeq genes. • 38023 UniProtKB/TrEMBL • Q0E8K8 Q8SYE1 Q8SYW4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Arrestin-like, N-terminal (IPR011021) Arrestin C-terminal-like domain (IPR011022) Immunoglobulin E-set (IPR014756) Arrestin, C-terminal (IPR014752) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • RE65532
Linkouts
	BioGRID - A database of protein and genetic interactions • 63587 DroID - A comprehensive database of gene and protein interactions. • FBgn0035103 DRSC - Results from RNAi screens. • FBgn0035103 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0035103 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG7047-RB FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0035103 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 38023 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 38023 modMine - Data generated by the modENCODE project. • FBgn0035103
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG7047 (Mandalaywala et al., 2008, Lebo et al., 2009) dvdup1 (Levendusky et al., 2009, Mandalaywala et al., 2008, Chang et al., 2010) vdup1 (Levendusky et al., 2009) VDUP1 (Mandalaywala et al., 2008) Vdup1
Name Synonym	CG7047   vitamin D3 up-regulated protein 1 (Chang et al., 2010) vitamin-D3 upregulated protein 1 (Levendusky et al., 2009) vitamin D3 up-regulated protein 1 (Mandalaywala et al., 2008) Vitamin D3 up-regulated protein 1
Secondary FlyBase IDs
References ( 15 )
Research paper	Chang et al., 2010, Brain Res. 1324: 1--13 Hedgehog-dependent down-regulation of the tumor suppressor, vitamin D3 up-regulated protein 1 (VDUP1), precedes lamina development in Drosophila. [FBrf0210439] Lebo et al., 2009, BMC Genomics 10: 80 Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis. [FBrf0207472] Levendusky et al., 2009, J. Comp. Neurol. 517(5): 581--600 Expression and regulation of vitamin D3 upregulated protein 1 (VDUP1) is conserved in mammalian and insect brain. [FBrf0208919] Mandalaywala et al., 2008, Dev. Biol. 315(2): 489--504 The tumor suppressor, vitamin D3 up-regulated protein 1 (VDUP1), functions downstream of REPO during Drosophila gliogenesis. [FBrf0204114]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 33. Fuzzy Cluster Members. [FBrf0213980] The modENCODE Consortium, 2010, Science 330(6012): DataS14: Gene co-expression clusters. [FBrf0213979] Mummery-Widmer et al., 2009, Nature 458(7241): Supplementary Table 2 - Genome-wide bristle screen results. [FBrf0214518] Giot et al., 2003, Science 302(5651): Tables S1 to S7. [FBrf0166452]
Personal communication to FlyBase	Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215] Ryder, 2004.4.26, Exelixis CG deletion data. Exelixis CG deletion data. [FBrf0184335] Gene Disruption Project members, 2001-, (Computer file) (Computer file) [FBrf0132177] BDGP Project Members, 2000-, Berkeley Drosophila Genome Project. (Computer file) Berkeley Drosophila Genome Project. (Computer file) [FBrf0125078]
FlyBase analysis	FlyBase, 1992-, FlyBase curation. FlyBase curation. [FBrf0105495]
Website	Fisher et al., 2012, BDGP insitu homepage BDGP insitu homepage [FBrf0219073]