• 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\cal1

General Information
Symbol	Dmel\cal1	Species	D. melanogaster
Name	chromosome alignment defect 1	Annotation symbol	CG5148
Feature type	protein_coding_gene	FlyBase ID	FBgn0038478
Gene Model Status	Current	Stock availability	7 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	89E12-89E12	Sequence location	3R:12,914,002..12,917,660 [+]
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 chromosome alignment defect 1 is referred to in FlyBase by the symbol Dmel\cal1 (CG5148, FBgn0038478). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding, bridging. There is experimental evidence that it is involved in the biological process: mitotic cell cycle; protein localization to kinetochore; mitotic spindle organization; protein localization to chromosome, centromeric region. 16 alleles are reported. The phenotypes of these alleles are annotated with: trichogen cell; mesothoracic tergum; presumptive embryonic/larval central nervous system. It has one annotated transcript and one annotated polypeptide. Protein features are: Ubiquitin interacting motif. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of 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 ovary. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, adult testis. Comments on Affy2 ProbeSet: ProbeSet 1629762_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of cal1. Gene sequence location is 3R:12914002..12917660.
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 89E12-89E12   Limits computationally determined from genome sequence between P{EP}CG5208EP562&P{EP}DadEP3196 and P{PZ}l(3)0788207882
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\cal1 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 5.48
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) cal1-RA FBtr0083400  NM_142340   3602   979
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 cal1-PA   FBpp0082841   109.5   979   8.17     NP_650597   AAF55389
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Ubiquitin interacting motif (IPR003903)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA940759   AA942262   AA949256   AE014297 AAF55389   AI515858   AI531491   AI541792   AI541793   AW944251   AY069785 AAL39930   BF495023   BI173851   BI242748   BI366505   BI641344   CO153658   CO155892   CO262717   CO264338   CO270515   CO279608   CO284419   CO284633   CO286219   CO288051   CO290177   CO291229   CO301089   CO304471   CO308609   CO313889   CZ468797   CZ468820   EC058631   EC058859   EC062504   EC070959   EC088167   EC197008   EC219389   EC221102   EC221273   EC230450   EC231102   EC237258   EC238241   EC260891   EC265729   ES690832   EV577051   EV578559   EV595631   EV599494   GH750666   GH752152   GH772575   GH773563   GH775607   GH778015   GH782836   GH789327   GH789784   GH808132   GH810290   GH811864   GH819492   GH821493   GH822584   GH822855   GH822935   GH823569   GH825208   GH825251   GH825734   GH827290   GH828280   GH828630   GH830375   GH841033   GH842665   GH846897   GH847266   GH858724   GH864786   GH867592   GH868418   GH874931   GH876506   GH879127   GH879533   GH879870   GH880807   GH885674   GH896846   GH896986   GH897188   GH898529   GH903358   GH908122   GH909023   GH909128   GH911455   GH918128   GH924199   GH926145   GH926491   GH931535   GH932204   GH937318   GH942383
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VEN2 Q8T9G0
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy Stage Tissue/Position (including subcellular localization) Reference day 5 of adulthood & male -- day 7 of adulthood & male   spermatozoon   (Wasbrough et al., 2010)
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
chromosome, centromeric region inferred from direct assay (Schittenhelm et al., 2010) colocalizes_with kinetochore inferred from direct assay (Goshima et al., 2007) nucleolus inferred from direct assay (Schittenhelm et al., 2010)
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 ovary. Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, adult testis. [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    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary  (601.1) Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary  601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    324.225 Larval Midgut    48 Larval Hindgut    80.5 Larval Malpighian Tubules    53.1 Larval Fat Body    50.4 Larval Salivary Gland    68 Larval Trachea    61.175 Larval Carcass    65.475 Adult Head    48.7 Adult Eye    38.85 Adult Brain    160 Adult Thoracic-Abdominal Ganglion    142.5 Adult Crop    73.4 Adult Midgut    36.7 Adult Hindgut    50 Adult Malpighian Tubules    31.6 Adult Fat Body    49.8 Adult Salivary Gland    95.7 Adult Heart    33.45 Adult VirginFemale Spermatheca    59.5 Adult InseminatedFemale Spermatheca    64.7 Adult Ovary    601.1 Adult Testis    118.8 Adult Male Accessory Gland    62.8 Adult Carcass    43.4 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    48.7   NA  Eye    38.85   NA  Brain    160   324.225  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    142.5   NA  Crop    73.4   48  Midgut    36.7   80.5  Hindgut    50   53.1  Malpighian Tubules    31.6   50.4  Fat Body    49.8   68  Salivary Gland    95.7   NA  Heart    33.45   61.175  Trachea    NA   NA  VirginFemale Spermatheca    59.5   NA  InseminatedFemale Spermatheca    64.7   NA  Ovary    601.1   NA  Testis    118.8   NA  Male Accessory Gland    62.8   65.475  Carcass    43.4 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    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female  (94) ovary, mated 4-day female  (84) testis, mated 4-day male    12 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 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    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female  (94) ovary, mated 4-day female  (84) testis, mated 4-day male    12 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 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    21 central nervous system, larvae L3    24 central nervous system, pupae P8    16 head, virgin 1-day female    4 head, virgin 4-day female    5 head, virgin 20-day female    4 head, mated 1-day female    5 head, mated 4-day female    4 head, mated 20-day female    3 head, mated 1-day male    7 head, mated 4-day male    8 head, mated 20-day male    10 salivary gland, larvae L3 wandering    1 salivary gland, white prepupae    3 digestive system, larvae L3 wandering    3 digestive system, 1-day adult    3 digestive system, 4-day adult    5 digestive system, 20-day adult    3 fat body, larvae L3 wandering    1 fat body, white prepupae    6 fat body, pupae P8    11 carcass, larvae L3 wandering    9 carcass, 1-day adult    3 carcass, 4-day adult    6 carcass, 20-day adult    4 ovary, virgin 4-day female    94 ovary, mated 4-day female    84 testis, mated 4-day male    12 accessory gland, mated 4-day male    4 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 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    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (78) embryo 02-04hr  (32) embryo 04-06hr  (28) embryo 06-08hr  (27) embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day  (49) adult female 30day  (48) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 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    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (78) embryo 02-04hr  32 embryo 04-06hr  28 embryo 06-08hr  27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day  (49) adult female 30day  (48) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 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    78 embryo 02-04hr    32 embryo 04-06hr    28 embryo 06-08hr    27 embryo 08-10hr    25 embryo 10-12hr    15 embryo 12-14hr    14 embryo 14-16hr    12 embryo 16-18hr    10 embryo 18-20hr    6 embryo 20-22hr    10 embryo 22-24hr    9 larva L1    4 larva L2    3 larva L3 12hr old    2 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    8 larva L3 puffstage 7-9    10 white prepupae new    10 white prepupae 12hr    12 white prepupae 24hr    15 pupae 2d postWPP    11 pupae 3d postWPP    7 pupae 4d postWPP    5 adult male 01day    8 adult male 05day    11 adult male 30day    11 adult female 01day    23 adult female 05day    49 adult female 30day    48 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Cell Line Expression Data (modENCODE_mRNA-Seq_cell.A) (modENCODE_mRNA-Seq_cell.B)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [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 Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS  (31) ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS  31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    15 Schneider line 2 Sg4    9 embryonic 1182-4H    11 embryonic GM2    10 embryonic Kc167    11 embryonic S1    13 embryonic S3    11 leg disc CME L1    11 wing disc CME-W2    9 wing disc ML-DmD8    11 wing disc ML-DmD9    11 wing disc ML-DmD16-c3    13 wing disc ML-DmD21    7 wing disc ML-DmD32    11 haltere disc ML-DmD17-c3    12 eye-antennal disc ML-DmD11    7 antennal disc ML-DmD20-c5    8 mixed discs ML-DmD4-c1    11 CNS ML-DmBG1-c1    16 CNS ML-DmBG2-c2    10 tumorous blood cells mbn2    9 ovary fGS/OSS    31 ovary OSC    11 ovary OSS    12 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [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    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult  (68) Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult  (34) Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3  (58) Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (50) Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult  (43) Paraquat 10 mM 48 hrs, 4-day adult  (36) Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 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    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult  (68) Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult  (34) Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3  (58) Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (50) Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult  (43) Paraquat 10 mM 48 hrs, 4-day adult  (36) Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 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    19 cold shock, 4-day adult    14 heat shock, 4-day adult    25 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    4 Cadmium 50 mM 48 hrs, 4-day adult    22 Cadmium 100 mM 48 hrs, 4-day adult    68 Copper 0.5 mM 12 hrs, larvae L3    6 Copper 15 mM 48 hrs, 4-day adult    34 Zinc 5 mM 12 hrs, larvae L3    3 Zinc 4.5 mM 48 hrs, 4-day adult    13 Ethanol 2.5% 3 hrs, larvae L3    58 Ethanol 5% 3 hrs, larvae L3    3 Ethanol 10% 3 hrs, larvae L3    4 Caffeine 1.5 mg/ml 4 hrs, larvae L3    3 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    50 Caffeine 25 mg/ml 48 hrs, 4-day adult    18 Paraquat 5 mM 48 hrs, 4-day adult    43 Paraquat 10 mM 48 hrs, 4-day adult    36 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    2 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_13 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0038478 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5148-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage | recessive cal1c03646 lethal | recessive cal1MB04866 viable, with Scer\GAL4pnr-MD237 cal1GD11553 Other Phenotypes Allele mitotic cell cycle defective | embryonic cycle 16, with Scer\GAL4prd.RG1 cal1Scer\UAS.T:Avic\GFP-EGFP neuroanatomy defective | embryonic stage | recessive cal1c03646 visible, with Scer\GAL4pnr-MD237 cal1GD11553 Phenotype manifest in Allele mesothoracic tergum, with Scer\GAL4pnr-MD237 cal1GD11553 presumptive embryonic/larval central nervous system cal1c03646 trichogen cell, with Scer\GAL4pnr-MD237 cal1GD11553
Classical Alleles ( 4 )
For All Classical Alleles Show
Allele of cal1 Class Mutagen Stocks Known lesion cal1c03646 piggyBac transposase 2 Yes cal1c03789 piggyBac transposase 1 -- cal1MB04866 1 Yes cal1unspecified 0 --
Alleles Carried on Transgenic Constructs ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Allele of cal1 Class Mutagen Stocks Known lesion cal1GD11553 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes cal1HMS02281 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cal1C.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1M.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1MtnA.C.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1MtnA.N.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1N-C.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1N.Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1NIG.5148R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes cal1Scer\UAS.cSa in vitro construct - regulatory fusion 0 Yes cal1Scer\UAS.T:Avic\GFP-EGFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cal1T:Avic\GFP-EGFP in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)Exel6176 (Ryder, 2004.4.26, Schittenhelm et al., 2010)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{NIG.5148R} NA P{TRiP.HMS02281} NA P{UAS-cal1.C.EGFP} NA P{UAS-cal1.EGFP} NA P{UAS-cal1.M.EGFP} NA P{UAS-cal1.N.EGFP} NA P{UAS-cal1.N-C.EGFP} NA P{UAS-cal1.S} NA characterization construct P{gcal1-EGFP} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{PB}cal1c03646 NA PBac{PB}cal1c03789 NA insertion of enhancer trap binary system Mi{ET1}cal1MB04866 No
Gene Ontology: Function, Process & Cellular Component ( 8 unique terms )
Terms Based on Experimental Evidence ( 8 terms )
Molecular Function
CV term Evidence References
protein binding, bridging inferred from physical interaction with cid, Cenp-C (Schittenhelm et al., 2010)
Biological Process
CV term Evidence References
mitotic cell cycle inferred from mutant phenotype (Schittenhelm et al., 2010) mitotic spindle organization inferred from mutant phenotype (Goshima et al., 2007) protein localization to chromosome, centromeric region inferred from mutant phenotype (Schittenhelm et al., 2010) protein localization to kinetochore inferred from mutant phenotype (Schittenhelm et al., 2010)
Cellular Component
CV term Evidence References
chromosome, centromeric region inferred from direct assay (Schittenhelm et al., 2010) colocalizes_with kinetochore inferred from direct assay (Goshima et al., 2007) nucleolus inferred from direct assay (Schittenhelm et al., 2010)
Terms Based on Predictions or Assertions ( 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 cal1 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 67105 DroID - A comprehensive database of gene and protein interactions. • FBgn0038478 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42065
Orthologs
OrthoDB Orthologs (12) - 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 EOG6VX2R6 Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG6VX2R6)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\cal1     Drosophila simulans   Dsim\GD19138 Y   Drosophila sechellia   Dsec\GM15207 Y   Drosophila erecta   Dere\GG22006 Y   Drosophila yakuba   Dyak\GE24611 Y   Drosophila ananassae   Dana\GF17127 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA18691 Y   Drosophila persimilis   Dper\GL27269 Y   Drosophila willistoni   Dwil\GK13917 Y   Drosophila virilis   Dvir\GJ22914 Y   Drosophila mojavensis   Dmoj\GI10559 Y   Drosophila grimshawi   Dgri\GH21560 Y
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD19138 Drosophila sechellia Dsec\GM15207 Drosophila erecta Dere\GG22006 Drosophila yakuba Dyak\GE24611 Drosophila ananassae Dana\GF17127 Drosophila pseudoobscura pseudoobscura Dpse\GA18691 Drosophila persimilis Dper\GL27269 Drosophila willistoni Dwil\GK13917 Drosophila virilis Dvir\GJ22914 Drosophila mojavensis Dmoj\GI10559 Drosophila grimshawi Dgri\GH21560
Stocks & Reagents
Stocks Listed in FlyBase ( 7 )
Bloomington	11309 w1118; PBac{PB}cal1c03646/TM6B, Tb1 24832 w1118; Mi{ET1}cal1MB04866/TM6C, Sb1 41716 y1 sc* v1; P{TRiP.HMS02281}attP2/TM3, Sb1
Harvard	- PBac{PB}cal1c03646 - PBac{PB}cal1c03789
VDRC	v45248 w1118; P{GD11553}v45248 v45249 w1118; P{GD11553}v45249/TM3
Genomic Clones ( 2 )
	BACR01E04 BACR02L16 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 102 )
	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	SD02553
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT03834 LD22975 LD26370 LD28080 LD41547 RE16971 RE40165 RE52057 SD06965 SD06966 SD24574
Other clones	21221 30210 54606 107840 156097 522666 525681 CK01.80A.F9 CK01.85B.G9 CK01.94A.F8 CK01.99D.E10 CK01.102B.H4 CK01.109D.H8 Dmel_dig_015212_0641_2490 Dmel_dig_017564_0682_3533 Dmel_neb_013632_0931_1621 Dmel_neb_014215_0618_2751 EK062121 EK067625 EK073256 EK076751 EK086162 EK099164 EK135459 EK138622 EK166017 EK166442 EK180042 EK234236 EK244745 EK258838 EN02529 EN06931 RP003065099 RP003068798 RP003075525 RP003088417 RP003091782 RP003111793 RP003116726 RP003121340 RP003135872 RP003136815 RP003149585 RP003149905 RP003166937 RP003178898 RP003184135 RP003215429 RP003224452 RP003236130 RP003237195 RP003241792 RP003250951 RP003252929 RP003257106 RP003263143 RP003270098 RP003291543 RP003295165 RP003300896 RP003313177 RP003316365 RP003320890 RP003324753 RP003335267 RP003336531 RP003347976 RP003348758 RP003349553 RP003385605 RP003387061 RP003390740 RP003404643 RP003404971 RP003410162 RP003429388 RP003462953 RP003467641 RP003472824 RP003479386 RP003499777 RP003542108 RP003556651 RP003568562 RP003630359 RP003636978 RP003663139 RP003676100 RP003677030
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0038478 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42065
Antibody Information
Other Information
Discoverer
Etymology
	Named "chromosome alignment defect 1" after the observed cellular phenotype following treatment of S2 cells with cal1 dsRNA. (Goshima et al., 2007)
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: cal1 CG5148 (Goshima et al., 2007)
Source for database merge of
Additional comments
Other Comments
	RNAi screen using dsRNA made from templates generated with primers directed against this gene results in chromosome misalignment on the metaphase spindle and a spindle that is aberrantly long when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA. (Goshima et al., 2007)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_142340 RefSeq (Proteins) • NP_650597 DDBJ / EMBL / GenBank • AAF55389 AAL39930 AI531491 AW944251 AY069785 CZ468797 CZ468820 Entrez Gene - A searchable database of RefSeq genes. • 42065 UniProtKB/TrEMBL • Q8T9G0 Q9VEN2
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Ubiquitin interacting motif (IPR003903)
Linkouts
	BioGRID - A database of protein and genetic interactions • 67105 DroID - A comprehensive database of gene and protein interactions. • FBgn0038478 DRSC - Results from RNAi screens. • FBgn0038478 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0038478 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5148-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0038478 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 42065 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 42065 modMine - Data generated by the modENCODE project. • FBgn0038478
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	cal1 (Schittenhelm et al., 2010, Venkei et al., 2011, Wasbrough et al., 2010) Cal1 (Goshima et al., 2007, Wright et al., 2010) CAL1 (Erhardt et al., 2008, Phansalkar et al., 2012) CG5148 (Goshima et al., 2007, Goshima et al., 2007, Erhardt et al., 2008, Wright et al., 2010, Japanese National Institute of Genetics, 2012.5.21, Ni et al., 2010.12.1) CLD2 (Erhardt et al., 2008)
Name Synonym	CG5148   chromosome alignment defect 1 (Goshima et al., 2007, ) Chromosome alignment defect 1 (Phansalkar et al., 2012)
Secondary FlyBase IDs
References ( 23 )
Generate a list of	All references relating to this gene ( 23 )
List References by type	Research paper  ( 8 ) Supplementary material  ( 6 ) Personal communication to FlyBase  ( 8 ) Stock list  ( 1 )
Recent research papers ( 4 )
	Dunleavy et al., 2012, PLoS Biol. 10(12): e1001460 The Cell Cycle Timing of Centromeric Chromatin Assembly in Drosophila Meiosis Is Distinct from Mitosis Yet Requires CAL1 and CENP-C. [FBrf0220464] Phansalkar et al., 2012, Chromosome Res. 20(5): 493--504 Evolutionary insights into the role of the essential centromere protein CAL1 in Drosophila. [FBrf0219033] Raychaudhuri et al., 2012, PLoS Biol. 10(12): e1001434 Transgenerational propagation and quantitative maintenance of paternal centromeres depends on cid/cenp-a presence in Drosophila sperm. [FBrf0220497] Venkei et al., 2011, Genetics 187(1): 131--140 Drosophila mis12 complex acts as a single functional unit essential for anaphase chromosome movement and a robust spindle assembly checkpoint. [FBrf0212773] Show all research papers ...